Contacts of the helix formed by residues 163 - 174 (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 GLN 163 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B SER* 5.7 0.8 - - - -
127B SER* 5.6 0.3 - - - -
161B PRO 4.1 0.2 + - - -
162B VAL* 1.3 86.0 - - - +
164B ILE* 1.3 89.7 + - - +
165B CYS* 3.0 34.1 + - - +
166B TRP* 3.1 12.3 + - - +
167B HIS* 3.9 0.5 - - - -
208B THR* 5.0 5.6 + - + +
212B THR* 3.5 24.7 + - + +
213B TYR* 3.9 5.2 - - - -
243B ASP* 4.3 17.2 + - - +
245B ALA* 5.9 6.7 - - + -
276B LYS* 5.9 3.5 - - - +
465B HIS* 3.3 24.7 + - - +
466B THR* 4.9 0.8 - - - -
467B PO4 4.2 14.4 + - - -
317C PHE* 4.0 17.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B VAL 4.0 0.2 + - - -
163B GLN* 1.3 93.1 - - - +
165B CYS* 1.3 67.4 + - + +
167B HIS* 2.9 24.4 + - + -
168B LYS* 3.1 20.6 + - + +
213B TYR* 4.2 4.7 + - - -
465B HIS* 3.9 16.0 + - + +
301C PHE* 4.1 36.3 - - + -
302C ASN 5.6 1.1 - - - +
303C VAL* 3.7 28.0 - - + -
317C PHE* 3.9 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B SER* 4.9 2.9 - - - -
127B SER* 3.9 28.9 - - - +
130B CYS* 3.0 43.8 - - + +
131B MET* 4.6 4.5 - - + +
163B GLN* 3.0 19.5 + - - +
164B ILE* 1.3 79.5 - - - +
166B TRP* 1.3 74.0 + - - +
168B LYS* 3.5 10.7 + - - +
169B PHE* 2.8 29.8 + - - +
243B ASP* 4.1 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B CYS* 3.5 44.0 - - + -
134B GLY* 4.2 7.9 - - - -
137B MET* 4.1 24.9 - - + -
157B LEU* 4.6 6.5 - - + -
159B CYS* 5.4 0.7 - - - -
162B VAL* 2.7 44.7 - - + +
163B GLN 3.1 5.2 + - - -
164B ILE 3.1 1.2 - - - -
165B CYS* 1.3 86.0 - - - +
167B HIS* 1.3 66.4 + - - +
169B PHE* 3.7 23.7 - + + +
170B ALA* 3.0 25.5 + - - +
177B LEU* 4.5 11.9 - - + +
206B VAL* 3.8 17.6 - - + +
241B HIS* 3.6 31.2 - + - -
243B ASP* 2.9 27.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B VAL* 3.5 29.2 + - + +
163B GLN 3.9 8.5 - - - -
164B ILE* 2.9 17.1 + - + +
166B TRP* 1.3 79.6 - - - +
168B LYS* 1.3 56.0 + - - +
170B ALA* 3.2 6.4 + - - +
171B ARG* 3.0 29.1 + - - +
177B LEU* 4.0 15.3 - - + +
179B GLU* 3.2 29.6 + - - -
213B TYR* 5.4 1.7 + - - -
301C PHE* 3.8 21.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B SER* 4.1 3.0 + - - +
131B MET* 4.4 8.7 - - + -
164B ILE* 3.1 25.4 + - + +
165B CYS* 3.7 14.1 - - - +
167B HIS* 1.3 73.7 - - - +
169B PHE* 1.3 56.7 + - - +
171B ARG 3.3 0.7 + - - -
172B TYR* 2.7 56.1 + - + -
301C PHE* 3.7 34.7 - - + -
312C THR* 5.0 9.8 + - - -
314C ALA* 2.9 32.6 + - - +
315C ILE 3.9 3.8 + - - -
316C ASN 3.0 22.2 + - - -
317C PHE* 3.8 22.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B CYS 5.6 0.2 - - - -
131B MET* 4.3 17.3 - - - +
134B GLY* 3.4 43.5 - - - -
135B MET* 3.6 4.7 - - - -
138B LYS* 4.7 4.0 - - + -
157B LEU* 4.5 9.4 - - + -
165B CYS 2.8 21.2 + - - +
166B TRP* 3.7 27.1 - + + +
168B LYS* 1.3 71.3 - - - +
170B ALA* 1.3 63.5 + - + +
173B TRP* 2.9 71.1 + + + +
175B VAL* 4.0 30.5 - - + -
203B ILE* 4.2 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU* 6.1 0.2 - - + -
166B TRP 3.0 18.3 + - - +
167B HIS* 3.5 4.9 - - - +
169B PHE* 1.3 82.7 - - + +
171B ARG* 1.3 58.8 + - - +
174B ASP* 2.9 25.1 + - - -
175B VAL* 3.0 33.6 + - + +
177B LEU* 3.9 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B HIS 3.0 15.3 + - - +
168B LYS 3.8 2.5 - - - +
170B ALA* 1.3 79.7 - - - +
172B TYR* 1.3 71.1 + - + +
173B TRP 3.4 0.3 + - - -
174B ASP* 3.6 6.9 + - - +
139C TRP* 3.2 30.6 - - + +
297C GLN 4.6 1.2 + - - -
298C GLU* 2.6 55.5 + - - +
299C LEU* 5.1 0.7 - - + -
300C VAL 4.7 5.0 + - - -
301C PHE* 3.3 39.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B MET* 4.7 5.4 - - + -
168B LYS* 2.7 40.5 + - + +
171B ARG* 1.3 74.6 - - + +
173B TRP* 1.3 79.3 + + + +
174B ASP* 3.6 1.6 - - - +
135C MET* 3.4 31.0 - - + -
139C TRP* 3.8 11.7 - - - -
173C TRP* 2.8 26.9 + - - +
299C LEU* 2.8 42.2 + - + -
301C PHE* 3.6 25.1 - + - -
312C THR 4.6 0.3 + - - -
313C PHE* 3.1 26.9 - + - -
314C ALA 3.9 23.2 + - - -
315C ILE* 4.8 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B MET* 3.6 28.3 - - + -
135B MET* 3.5 38.7 - - + +
138B LYS* 2.9 39.7 + - + +
139B TRP* 4.9 0.9 - + - -
169B PHE* 2.9 54.6 + + + +
172B TYR* 1.3 98.6 - + + +
174B ASP* 1.3 69.7 - - - +
175B VAL* 3.4 6.2 + - + +
315B ILE* 4.0 18.6 - - + -
172C TYR 2.9 28.5 + - - -
173C TRP* 3.3 38.8 - + - -
315C ILE* 5.2 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LYS* 4.8 3.0 + - - +
153B ASP 5.4 0.9 - - - +
155B PRO* 3.8 16.1 - - - +
170B ALA 2.9 7.7 + - - -
171B ARG 3.6 8.9 + - - +
172B TYR 4.8 0.9 - - - +
173B TRP* 1.3 81.6 - - - +
175B VAL* 1.3 62.0 + - - +
176B GLU 4.3 0.3 + - - -
138C LYS* 3.8 12.1 + - - -
139C TRP* 4.1 6.0 - - - -
142C ARG* 2.8 44.1 + - - -
----------------------------------------------------------
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