Contacts of the helix formed by residues 125 - 148 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B THR* 2.7 21.1 + - - -
124B ILE* 1.3 86.7 - - - +
126B SER* 1.3 66.8 + - - -
127B SER 3.2 2.0 - - - -
128B GLU* 3.6 5.0 + - - +
129B ALA* 3.2 8.8 + - - +
275B HIS* 4.0 4.9 - - - -
285B GLY* 3.7 11.9 - - - -
467B PO4 3.7 14.1 - - - -
318C SER 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLY* 1.3 69.2 - - - -
127B SER* 1.3 55.7 + - - +
129B ALA* 3.1 7.0 + - - +
130B CYS* 2.5 51.0 + - - -
163B GLN* 5.7 0.9 - - - -
165B CYS* 5.4 2.2 - - - -
243B ASP* 4.7 1.5 + - - -
245B ALA* 3.6 16.6 - - - +
271B SER* 5.0 0.7 - - - -
272B ALA* 3.5 8.0 + - - -
273B SER* 2.7 36.6 + - - -
285B GLY* 4.3 1.6 - - - -
467B PO4 3.0 19.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLY 3.2 0.2 - - - -
126B SER* 1.3 78.1 - - - +
128B GLU* 1.3 64.1 + - - +
130B CYS* 3.1 2.8 + - - +
131B MET* 3.0 30.8 + - - +
165B CYS* 3.9 21.5 - - - +
168B LYS* 4.1 6.1 + - - -
467B PO4 2.8 20.8 + - - -
315C ILE 2.6 26.8 + - - -
316C ASN 3.9 2.2 - - - -
317C PHE* 3.8 19.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ASN 5.3 0.4 - - - -
123B THR* 3.3 24.2 - - + -
124B ILE* 3.2 20.8 + - - +
125B GLY 3.6 4.7 + - - +
126B SER 3.4 0.4 - - - -
127B SER* 1.3 77.2 - - - +
129B ALA* 1.3 58.6 + - - +
131B MET* 3.0 13.1 + - - +
132B LEU* 2.8 38.5 + - + +
314B ALA* 3.7 6.3 - - - +
315B ILE* 2.7 34.3 + - + +
316B ASN* 2.8 35.3 + - - +
319B ARG* 4.6 2.6 + - - -
315C ILE* 4.5 5.5 + - + -
316C ASN* 3.8 15.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B THR* 3.6 16.7 - - - +
125B GLY 3.2 12.9 + - - +
126B SER* 3.1 10.5 + - - +
128B GLU* 1.3 79.1 - - - +
130B CYS* 1.3 58.0 + - - +
132B LEU* 3.4 2.0 + - - +
133B GLY* 3.0 24.9 + - - -
241B HIS* 4.4 1.9 - - - -
271B SER* 3.8 9.6 - - - -
286B TRP 3.6 23.8 - - - +
287B VAL* 3.8 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B SER* 2.5 29.9 + - - +
127B SER 3.5 2.5 - - - +
129B ALA* 1.3 70.0 - - - +
131B MET* 1.3 60.9 + - - +
133B GLY 3.3 0.3 + - - -
134B GLY* 2.8 30.0 + - - -
165B CYS* 3.0 40.8 - - + +
166B TRP* 3.5 37.7 - - + -
169B PHE* 5.4 1.1 - - - -
241B HIS* 4.8 0.4 - - - -
243B ASP* 3.8 9.6 - - - -
271B SER* 4.0 14.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B SER* 3.0 21.8 + - - +
128B GLU* 3.0 9.6 + - - +
130B CYS* 1.3 77.6 - - - +
132B LEU* 1.3 57.5 + - - +
134B GLY* 3.3 0.3 + - - -
135B MET* 2.9 33.9 + - - +
165B CYS* 4.6 4.7 - - + +
168B LYS* 4.4 20.9 - - + -
169B PHE* 4.3 22.5 - - - -
172B TYR* 4.7 2.7 - - + -
173B TRP* 3.6 26.2 - - + -
315B ILE* 3.4 29.8 - - + -
315C ILE* 3.1 40.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B THR* 3.6 21.1 - - + -
123B THR* 3.7 18.8 - - + -
128B GLU* 2.8 23.7 + - + +
129B ALA 3.9 3.4 - - - +
130B CYS 3.2 0.2 - - - -
131B MET* 1.3 69.6 - - - +
133B GLY* 1.3 62.6 + - - +
135B MET* 3.4 9.7 + - + -
136B ALA* 2.9 25.8 + - - +
287B VAL* 3.8 4.7 - - + -
289B TRP* 4.0 8.1 - - + -
313B PHE* 3.3 65.9 - - + +
314B ALA* 4.2 0.9 - - - -
315B ILE* 3.9 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ALA 3.0 15.2 + - - -
130B CYS 3.7 2.0 - - - -
132B LEU* 1.3 74.7 - - - +
134B GLY* 1.3 55.7 + - - +
136B ALA* 3.3 3.5 + - - +
137B MET* 2.9 36.5 + - - +
140B ARG* 5.3 0.3 + - - -
166B TRP* 5.0 0.4 - - - -
241B HIS* 4.0 21.5 - - - -
269B SER* 4.4 5.3 + - - -
287B VAL* 4.7 1.1 - - - -
289B TRP* 4.2 11.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B CYS 2.8 17.2 + - - -
133B GLY* 1.3 72.9 - - - +
135B MET* 1.3 58.4 + - - +
137B MET* 3.0 19.2 + - - +
138B LYS 2.9 24.1 + - - -
166B TRP* 4.2 3.9 - - - -
169B PHE* 3.4 32.2 - - - -
203B ILE* 4.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B MET 2.9 19.2 + - - +
132B LEU* 3.7 15.7 - - + +
134B GLY* 1.3 73.5 - - - +
136B ALA* 1.3 59.1 + - - +
138B LYS* 3.1 6.1 + - - -
139B TRP* 2.9 41.2 + - + +
169B PHE* 3.6 2.1 - - - -
173B TRP* 3.5 48.2 - - + +
299B LEU* 3.7 7.6 - - + -
313B PHE* 3.9 26.5 - - + -
315B ILE* 4.1 8.3 - - + -
172C TYR* 3.5 41.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU 2.9 14.7 + - - +
133B GLY 3.6 3.4 - - - +
135B MET* 1.3 74.5 - - - +
137B MET* 1.3 64.4 + - - +
140B ARG* 3.0 36.3 + - - +
289B TRP* 3.4 33.2 - - + +
295B LEU* 4.2 0.9 - - + -
296B PRO* 4.0 16.8 - - + +
299B LEU* 3.7 12.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLY 2.9 11.4 + - - +
134B GLY* 3.3 26.2 - - - +
136B ALA* 1.3 76.9 - - - +
138B LYS* 1.3 64.2 + - - +
140B ARG* 3.1 25.7 + - - +
141B TRP* 3.0 24.3 + - - +
157B LEU* 3.6 25.4 - - + -
166B TRP* 4.1 5.8 - - + -
203B ILE* 3.8 18.4 - - + +
204B GLY* 3.7 28.3 - - - -
206B VAL* 3.7 15.3 - - + -
239B ASP 6.0 0.4 - - - -
240B MET 4.8 0.7 - - - -
241B HIS* 3.8 30.7 - - + +
269B SER* 5.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B GLY 2.9 15.5 + - - +
135B MET* 3.6 6.5 - - - +
137B MET* 1.3 76.2 - - - +
139B TRP* 1.3 73.2 + - + +
141B TRP* 3.5 7.4 + - + -
142B ARG* 2.8 57.3 + - + +
152B THR 5.9 0.4 - - - -
155B PRO* 4.7 13.4 - - + +
169B PHE* 4.7 2.2 - - + -
173B TRP* 2.9 42.3 + - + +
174B ASP* 4.8 4.8 + - - +
175B VAL* 4.4 13.0 - - + -
203B ILE* 3.9 22.0 - - + +
174C ASP* 3.6 15.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B MET* 2.9 41.0 + - + +
138B LYS* 1.3 94.7 - - + +
140B ARG* 1.3 60.1 + - - +
142B ARG* 3.2 39.1 - - - +
143B LYS* 2.9 40.8 + - + +
173B TRP* 4.9 0.7 - + - -
296B PRO* 3.7 18.4 - - + -
298B GLU* 4.0 32.3 - - + +
299B LEU* 3.5 30.9 - - + +
171C ARG* 3.4 32.0 - - + +
172C TYR* 3.7 20.0 - - - -
174C ASP* 3.9 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ALA* 3.0 34.4 + - - +
137B MET* 3.6 28.8 - - - +
139B TRP* 1.3 75.4 - - - +
141B TRP* 1.3 62.8 + - - +
143B LYS* 4.0 5.5 - - - +
144B ARG* 3.0 26.8 + - - +
203B ILE 5.2 1.6 + - - -
239B ASP* 4.2 17.7 + - - +
240B MET 4.9 1.6 + - - -
268B LYS* 3.5 40.7 - - - +
269B SER* 5.1 3.4 + - - -
289B TRP* 4.2 4.4 - - - +
293B GLU 4.0 6.7 - - - +
294B ALA* 2.7 46.6 + - - +
296B PRO* 3.8 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B MET 3.0 15.9 + - - +
138B LYS* 3.7 9.0 - - + +
140B ARG* 1.3 76.4 - - - +
142B ARG* 1.3 85.6 + - + +
144B ARG* 3.2 22.2 + - - +
145B MET* 2.8 55.4 + - + +
152B THR* 3.5 39.0 - - - -
155B PRO* 3.4 25.8 - - + -
200B GLU 2.8 25.3 + - - -
201B ASN* 3.6 35.7 - - - +
202B THR 3.9 15.5 - - - -
203B ILE* 3.7 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LYS* 2.8 41.1 + - + +
139B TRP* 3.2 45.4 - - - +
141B TRP* 1.3 99.1 - - + +
143B LYS* 1.3 59.4 + - + +
145B MET* 3.3 1.4 + - - +
146B GLU* 2.9 55.6 + - - +
152B THR* 3.9 23.0 + - - +
174C ASP* 2.8 40.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B TRP* 2.9 25.7 + - + +
140B ARG* 4.0 4.9 - - - +
142B ARG* 1.3 74.1 - - + +
144B ARG* 1.3 61.2 + - - +
146B GLU* 3.7 14.4 - - - +
147B ALA* 2.9 31.9 + - - +
296B PRO* 3.8 22.2 - - - +
297B GLN 5.0 1.0 - - - +
298B GLU* 3.0 42.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ARG 3.0 20.0 + - - +
141B TRP* 3.6 25.2 - - - +
143B LYS* 1.3 76.7 - - - +
145B MET* 1.3 84.0 + - - +
147B ALA* 3.3 8.3 + - - +
148B ALA* 3.2 22.8 + - - +
200B GLU* 4.2 5.9 + - - +
202B THR 5.3 2.4 + - - -
236B ILE* 5.0 7.9 - - - +
237B ASP* 2.9 42.0 + - - +
238B ILE* 4.9 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B TRP* 2.8 37.7 + - + +
144B ARG* 1.3 89.6 - - - +
146B GLU* 1.3 64.6 + - - +
147B ALA 3.2 1.1 - - - -
148B ALA* 3.0 12.3 + - - +
149B GLY 3.0 0.2 + - - -
150B LYS* 3.0 55.2 + - + +
151B PRO* 3.5 20.4 - - + +
152B THR* 3.8 16.2 - - + -
200B GLU* 3.8 34.8 - - + +
201B ASN* 4.0 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ARG* 2.9 40.9 + - - +
143B LYS* 3.7 15.7 - - - +
145B MET* 1.3 76.4 - - - +
147B ALA* 1.3 62.7 + - - +
149B GLY* 3.0 13.8 + - - +
150B LYS 4.7 4.5 - - - +
152B THR* 4.1 13.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LYS 2.9 18.9 + - - +
144B ARG* 3.7 7.0 - - - +
145B MET 3.2 0.4 - - - -
146B GLU* 1.3 76.7 - - - +
148B ALA* 1.3 58.5 + - - +
149B GLY 3.4 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ARG* 3.2 13.0 + - - +
145B MET* 3.0 12.1 + - - +
147B ALA* 1.3 79.9 - - - +
149B GLY* 1.3 59.2 + - - +
150B LYS* 3.4 32.1 - - + +
----------------------------------------------------------
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