Contacts of the helix formed by residues 125 - 149 (chain F) in PDB entry 3FZ7
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 125 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A SER 5.1 0.2 - - - -
123F THR* 2.7 23.1 + - - -
124F ILE* 1.3 80.8 - - - +
126F SER* 1.3 65.1 + - - -
127F SER 3.2 2.9 + - - -
128F GLU* 3.5 4.3 + - - +
129F ALA* 3.2 11.4 + - - +
275F HIS* 3.8 11.7 - - - -
284F CYS 4.1 0.2 - - - -
285F GLY* 3.8 12.8 - - - -
467F PO4 3.8 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 126 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125F GLY* 1.3 69.7 - - - -
127F SER* 1.3 56.8 + - - +
129F ALA* 4.2 5.2 - - - -
130F CYS* 2.7 49.2 + - - -
165F CYS* 4.9 2.5 - - - -
243F ASP* 4.7 0.7 + - - -
245F ALA* 3.4 19.5 - - - +
271F SER* 4.7 0.9 + - - -
272F ALA* 3.3 20.1 + - - -
273F SER* 2.6 25.3 + - - -
285F GLY* 4.6 0.6 - - - -
467F PO4 3.1 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 127 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ILE 2.8 24.2 + - - -
316A ASN* 4.1 1.1 - - - -
317A PHE* 4.0 19.1 - - - +
125F GLY* 5.6 0.2 - - - -
126F SER* 1.3 81.5 - - - +
128F GLU* 1.3 63.4 + - - +
130F CYS* 3.6 1.7 - - - +
131F MET* 2.9 28.7 + - - +
165F CYS* 3.5 27.5 - - - +
168F LYS* 4.4 4.9 + - - +
467F PO4 3.0 19.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 128 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ILE* 4.4 4.1 + - + -
316A ASN* 3.9 13.3 + - - +
122F ASN 5.4 0.4 - - - -
123F THR* 3.3 20.4 - - + -
124F ILE* 3.0 25.1 + - - +
125F GLY 3.5 4.7 + - - +
126F SER 3.5 0.2 - - - -
127F SER* 1.3 76.2 - - - +
129F ALA* 1.3 64.1 + - - +
131F MET* 3.0 11.3 + - - +
132F LEU* 2.9 32.0 + - + +
314F ALA* 3.7 8.7 - - - +
315F ILE* 2.9 39.8 + - + +
316F ASN* 3.0 30.8 + - - +
319F ARG* 4.7 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F THR* 3.7 16.7 - - + +
125F GLY 3.2 16.5 + - - +
126F SER* 3.7 6.5 - - - +
128F GLU* 1.3 77.8 - - - +
130F CYS* 1.3 57.2 + - - +
132F LEU* 3.3 3.4 + - - +
133F GLY* 2.9 25.1 + - - -
271F SER* 3.7 11.0 - - - -
272F ALA 4.9 0.2 - - - +
286F TRP 3.6 24.2 - - - +
287F VAL* 3.7 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 130 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F SER* 2.7 31.5 + - - +
127F SER 3.6 3.1 - - - +
129F ALA* 1.3 69.4 - - - +
131F MET* 1.3 54.4 + - + +
133F GLY* 3.0 1.9 + - - -
134F GLY* 2.6 35.0 + - - -
165F CYS* 3.3 35.0 - - + +
166F TRP* 3.4 41.0 - - + -
169F PHE* 5.6 0.4 - - + -
241F HIS* 4.7 1.1 - - - -
243F ASP* 3.9 8.5 - - - -
271F SER* 3.7 16.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 131 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ILE* 3.5 46.9 - - + +
127F SER* 2.9 19.5 - - - +
128F GLU* 3.0 8.7 + - - +
130F CYS* 1.3 76.3 - - - +
132F LEU* 1.3 53.4 + - - +
135F MET* 2.7 40.7 + - + +
165F CYS 4.4 8.3 - - - +
168F LYS* 5.0 6.7 - - + -
169F PHE* 4.1 21.9 - - - -
172F TYR* 4.8 8.1 - - + -
173F TRP* 3.7 28.9 - - + -
315F ILE* 3.6 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121F THR* 3.6 21.1 - - + -
123F THR* 3.8 19.1 - - + -
128F GLU* 2.9 23.1 + - + +
129F ALA 3.7 4.3 - - - +
131F MET* 1.3 76.4 - - - +
133F GLY* 1.3 63.5 + - - +
135F MET* 4.0 11.2 - - + -
136F ALA* 3.0 27.4 + - - +
287F VAL* 4.0 2.2 - - + -
289F TRP* 4.0 8.3 - - + -
313F PHE* 3.4 63.5 - - + +
314F ALA* 4.3 2.0 - - + -
315F ILE* 4.1 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 133 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129F ALA 2.9 15.4 + - - -
130F CYS 3.4 3.1 - - - -
132F LEU* 1.3 76.6 - - - +
134F GLY* 1.3 56.9 + - - +
136F ALA* 3.6 2.3 + - - +
137F MET* 2.9 35.9 + - - +
140F ARG* 5.2 0.2 + - - -
166F TRP* 4.9 0.4 - - - -
241F HIS* 3.9 22.7 - - - -
269F SER* 4.3 7.4 + - - -
287F VAL* 4.6 0.4 - - - -
289F TRP* 4.3 9.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 134 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F CYS 2.6 19.9 + - - -
133F GLY* 1.3 71.4 - - - +
135F MET* 1.3 58.7 + - - +
137F MET* 3.1 19.4 + - - +
138F LYS* 2.8 24.1 + - - +
166F TRP* 4.1 4.2 - - - -
169F PHE* 3.4 31.3 - - - -
203F ILE* 4.0 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 135 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A TYR* 3.6 42.2 - - + +
131F MET 2.7 21.6 + - - +
132F LEU* 3.9 29.4 - - + +
134F GLY* 1.3 71.1 - - - +
136F ALA* 1.3 54.1 + - - +
138F LYS* 2.8 26.8 + - - +
139F TRP* 2.8 21.3 + - + -
169F PHE* 3.5 2.2 - - - -
173F TRP* 3.4 53.2 - - + +
299F LEU* 3.9 10.1 - - + -
313F PHE* 4.0 12.1 - - + -
315F ILE* 4.1 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 136 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F LEU 3.0 18.9 + - - +
133F GLY 3.7 2.7 - - - +
135F MET* 1.3 76.4 - - - +
137F MET* 1.3 55.8 + - - +
139F TRP* 3.3 1.4 + - - +
140F ARG* 2.9 39.3 + - - +
289F TRP* 3.4 26.5 - - - +
295F LEU* 4.0 17.3 - - + -
296F PRO* 3.8 5.1 - - + +
299F LEU* 3.5 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 137 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F GLY 2.9 11.9 + - - +
134F GLY* 3.1 24.4 + - - +
136F ALA* 1.3 75.7 - - - +
138F LYS* 1.3 63.3 + - - +
140F ARG* 3.4 29.2 + - - +
141F TRP* 3.1 24.8 + - - +
157F LEU* 3.7 22.9 - - + -
166F TRP* 4.1 5.4 - - + -
203F ILE* 3.8 17.3 - - + +
204F GLY* 3.5 30.7 - - - -
206F VAL* 3.7 15.5 - - + -
239F ASP* 5.5 0.7 - - + -
240F MET 4.7 0.9 - - - -
241F HIS* 3.8 29.4 - - + +
269F SER* 5.3 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 138 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A TYR 5.8 0.4 + - - -
174A ASP* 4.1 13.3 + - - -
134F GLY 2.8 12.2 + - - +
135F MET* 2.8 10.8 + - - +
137F MET* 1.3 76.8 - - - +
139F TRP* 1.3 67.8 + - + +
141F TRP* 3.2 14.3 + - + +
142F ARG* 2.8 56.7 + - + +
152F THR 6.0 0.9 - - - -
155F PRO* 4.5 14.3 - - + +
169F PHE* 4.8 0.4 - - + -
173F TRP* 2.7 40.4 + - + +
174F ASP* 4.7 5.3 + - - +
175F VAL* 4.0 16.4 - - + +
203F ILE* 4.0 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 139 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ARG* 3.4 33.2 - - + +
172A TYR* 3.8 17.7 - - - -
174A ASP* 3.7 5.6 - - - -
135F MET* 2.8 33.0 + - + +
138F LYS* 1.3 92.2 - - + +
140F ARG* 1.3 60.2 + - - +
142F ARG* 3.1 39.1 - - + +
143F LYS* 2.8 38.7 + - + +
173F TRP* 5.0 1.1 - + - -
296F PRO* 3.6 19.5 - - + -
298F GLU* 3.6 39.3 - - + +
299F LEU* 3.6 27.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 140 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F ALA* 2.9 29.9 + - - +
137F MET* 3.4 34.6 + - - +
138F LYS 3.3 0.2 - - - -
139F TRP* 1.3 75.9 - - - +
141F TRP* 1.3 63.9 + - - +
143F LYS* 3.9 6.3 - - - +
144F ARG* 3.1 24.4 + - - +
203F ILE 5.0 1.0 + - - -
239F ASP* 4.0 19.8 + - - +
240F MET 4.8 1.4 + - - -
268F LYS* 3.5 38.4 - - - +
269F SER* 4.7 4.2 + - - -
289F TRP* 4.2 5.9 - - - +
293F GLU 4.1 6.7 - - - +
294F ALA* 2.8 44.8 + - - +
296F PRO* 3.8 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 141 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F MET 3.1 17.6 + - - +
138F LYS* 3.5 9.4 - - + +
140F ARG* 1.3 75.5 - - - +
142F ARG* 1.3 88.8 + - + +
144F ARG* 3.2 20.8 + - + +
145F MET* 3.0 44.6 + - + +
152F THR* 3.7 36.8 - - + -
155F PRO* 3.6 26.5 - - + -
200F GLU 2.9 21.8 + - - -
201F ASN* 3.7 34.8 - - - +
202F THR 3.6 17.9 - - - -
203F ILE* 3.6 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 142 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ASP* 2.9 41.5 + - - -
138F LYS* 2.8 36.5 + - + +
139F TRP* 3.1 47.2 - - + +
141F TRP* 1.3 88.5 - - + +
143F LYS* 1.3 57.2 + - + +
145F MET* 3.2 1.7 + - - -
146F GLU* 2.9 55.3 + - - +
152F THR* 3.6 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 143 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139F TRP* 2.8 28.7 + - + +
140F ARG* 3.9 5.8 - - - +
142F ARG* 1.3 74.0 - - + +
144F ARG* 1.3 57.6 + - - +
146F GLU* 3.8 13.9 - - - +
147F ALA* 2.9 29.8 + - - +
296F PRO* 4.2 20.9 - - + +
297F GLN 4.7 1.6 - - - +
298F GLU* 3.2 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 144 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140F ARG 3.1 18.2 + - - +
141F TRP* 3.6 19.5 - - - +
142F ARG 3.2 0.2 - - - -
143F LYS* 1.3 77.2 - - - +
145F MET* 1.3 66.3 + - + +
147F ALA* 3.4 8.9 + - + +
148F ALA* 3.2 22.3 + - + +
202F THR 5.9 0.8 + - - -
236F ILE* 5.8 1.8 - - - +
237F ASP* 2.8 58.3 + - - +
239F ASP* 4.4 13.9 + - - -
268F LYS* 5.8 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 145 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141F TRP* 3.0 35.1 + - + +
144F ARG* 1.3 78.2 - - + +
146F GLU* 1.3 55.0 + - - +
148F ALA* 2.9 6.9 + - - +
149F GLY 2.7 30.7 + - - -
150F LYS* 2.9 42.4 + - + +
151F PRO* 3.4 20.2 - - + +
152F THR* 3.7 16.6 - - + -
200F GLU* 3.4 34.5 - - + +
201F ASN* 4.0 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 146 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142F ARG* 2.9 44.7 + - - +
143F LYS* 3.8 15.7 - - - +
145F MET* 1.3 71.5 - - - +
147F ALA* 1.3 63.0 + - - +
148F ALA 2.9 5.3 + - - -
149F GLY* 2.9 14.4 + - - +
150F LYS 4.8 2.7 - - - +
152F THR* 4.2 11.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 147 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143F LYS 2.9 19.3 + - - +
144F ARG* 3.5 8.7 - - + +
146F GLU* 1.3 75.8 - - - +
148F ALA* 1.3 58.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144F ARG* 3.2 15.1 + - + +
145F MET* 2.9 8.1 + - - +
147F ALA* 1.3 79.9 - - + +
149F GLY* 1.3 59.1 + - - +
150F LYS* 3.3 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 149 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145F MET 2.7 9.2 + - - -
146F GLU* 2.9 12.6 + - - -
147F ALA 3.5 0.6 + - - -
148F ALA* 1.3 75.3 - - - +
150F LYS* 1.3 58.9 + - - -
151F PRO* 4.3 1.2 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il