Contacts of the helix formed by residues 165 - 184 (chain B) in PDB entry 4WYV
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 SER 165 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ASP* 2.9 9.7 + - - -
164B TYR* 1.3 79.4 - - - +
166B ARG* 1.3 71.7 + - - +
167B PRO 3.3 2.2 - - - -
168B LEU* 3.0 27.2 + - - +
169B HIS* 3.2 26.1 + - - -
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Residues in contact with ARG 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ILE* 4.8 18.6 - - - +
107B TYR* 4.3 20.9 - - - +
108B LEU* 4.5 25.7 + - - +
111B GLU* 4.4 17.9 + - - +
154B LEU* 4.3 14.8 - - - +
158B SER* 3.4 22.9 - - - +
163B ASP* 2.9 21.7 + - - +
165B SER* 1.3 80.0 + - - +
167B PRO* 1.4 69.7 - - + +
169B HIS* 2.9 13.6 + - + +
170B ILE* 2.9 41.3 + - + +
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Residues in contact with PRO 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B SER* 3.6 38.4 - - - +
158B SER* 3.7 2.9 - - - +
159B VAL* 3.9 17.9 - - + -
163B ASP 3.6 14.1 - - - +
164B TYR 4.0 0.7 - - - -
165B SER 3.4 5.8 - - - +
166B ARG* 1.4 93.5 - - + +
168B LEU* 1.3 54.7 + - - +
170B ILE* 3.8 4.2 - - + +
171B SER* 2.9 31.9 + - - -
205B VAL* 4.3 2.6 - - - +
208B VAL* 3.8 12.8 - - + -
209B VAL* 3.6 6.9 - - + +
212B LEU* 4.0 12.8 - - + -
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Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A THR* 5.6 2.7 - - + -
164B TYR 3.4 23.8 - - - +
165B SER* 3.0 18.8 + - - +
167B PRO* 1.3 75.5 - - - +
169B HIS* 1.3 68.1 + - + +
171B SER* 3.6 3.5 + - - -
172B THR* 3.2 25.3 + - - -
209B VAL* 4.1 29.1 - - + +
212B LEU* 5.2 7.2 - - + -
213B SER* 5.6 2.0 - - - +
217B PHE 4.9 15.9 - - - +
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Residues in contact with HIS 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B TYR* 3.8 10.8 - - - +
111B GLU* 3.4 34.7 + - - +
165B SER* 3.2 35.9 + - - -
166B ARG* 2.9 9.8 + - + +
168B LEU* 1.3 79.5 - - + +
170B ILE* 1.3 59.4 + - - +
172B THR* 3.2 7.5 + - - -
173B PHE* 2.8 29.6 + - - +
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Residues in contact with ILE 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B TYR* 3.5 23.3 - - + +
151B LEU* 3.5 47.3 - - + +
154B LEU* 4.1 16.4 - - + -
155B SER* 3.8 18.8 - - - +
166B ARG* 2.9 34.6 + - + +
167B PRO* 3.8 7.9 - - + +
169B HIS* 1.3 75.3 - - - +
171B SER* 1.3 56.1 + - - +
173B PHE* 3.3 2.9 + - - +
174B ILE* 2.9 38.0 + - + +
205B VAL* 4.0 12.8 - - + -
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Residues in contact with SER 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B PRO 2.9 18.4 + - - -
168B LEU 3.7 5.6 - - - -
170B ILE* 1.3 74.0 - - - +
172B THR* 1.3 57.6 - - - +
174B ILE* 3.5 0.7 + - - +
175B ASN* 2.9 46.2 + - - -
205B VAL* 3.2 25.8 - - - +
206B GLU* 3.9 15.1 - - - +
209B VAL* 3.8 13.6 - - - +
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Residues in contact with THR 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLN* 5.4 15.2 - - + +
168B LEU 3.2 11.8 + - - -
169B HIS* 3.2 10.8 + - - -
171B SER* 1.3 73.8 - - - +
173B PHE* 1.3 68.7 + - - +
175B ASN* 3.3 5.4 + - - +
176B GLU* 3.0 42.8 + - + +
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Residues in contact with PHE 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B TYR* 3.6 24.7 - + + +
111B GLU 4.3 6.7 - - - +
112B THR* 3.9 4.3 - - - -
113B LEU* 3.7 44.9 - - + -
147B LEU* 4.0 13.7 - - + -
151B LEU* 3.4 34.5 - - + -
169B HIS 2.8 20.1 + - - +
170B ILE* 3.6 5.2 - - - +
172B THR* 1.3 73.1 - - - +
174B ILE* 1.3 59.2 + - + +
176B GLU* 2.9 33.0 + - - +
177B LEU* 3.0 38.6 + - + +
3F VAL* 4.3 9.4 - - + -
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Residues in contact with ILE 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ALA* 3.5 34.1 - - + +
151B LEU* 4.3 2.9 - - + -
152B SER 4.2 1.1 - - - +
170B ILE* 2.9 32.8 + - + +
171B SER* 4.1 4.5 - - - +
173B PHE* 1.3 79.8 - - + +
175B ASN* 1.3 58.6 + - - +
177B LEU* 3.2 12.9 + - + +
178B ASP* 2.9 26.9 + - - +
198B LEU* 4.3 11.1 - - + +
201B ASP* 4.4 5.2 - - + +
202B VAL* 3.6 35.0 - - + +
205B VAL* 4.1 22.0 - - + -
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Residues in contact with ASN 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLN* 3.4 29.5 + - - +
153A ARG* 3.1 26.3 + - - -
171B SER* 2.9 31.0 + - - +
172B THR* 3.8 4.3 - - - +
174B ILE* 1.3 81.2 - - - +
176B GLU* 1.3 55.5 + - - +
178B ASP* 3.5 8.6 + - - +
179B SER* 3.0 30.7 + - - -
202B VAL* 3.9 9.8 + - - +
205B VAL* 5.8 0.6 - - - +
206B GLU* 3.4 26.8 + - - +
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Residues in contact with GLU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B THR* 3.0 35.7 + - + +
173B PHE* 2.9 17.9 + - - +
175B ASN* 1.3 77.4 - - - +
177B LEU* 1.3 49.0 + - - +
179B SER* 3.3 9.5 + - - -
180B GLY 2.8 28.8 + - - -
3F VAL* 3.3 41.6 + - + +
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Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LEU* 4.0 20.9 - - + -
144B VAL* 3.9 28.0 - - + +
147B LEU* 5.4 0.4 - - + -
148B ALA* 4.2 27.6 - - + +
173B PHE* 3.0 45.9 + - + +
174B ILE* 3.2 14.6 + - + +
176B GLU* 1.3 71.4 - - - +
178B ASP* 1.3 61.6 + - - +
180B GLY* 3.0 3.4 + - - +
181B PHE* 2.8 44.7 + - + -
198B LEU* 4.5 4.3 - - + -
3F VAL* 4.5 6.7 - - + -
7F PHE* 4.3 7.3 - - + -
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Residues in contact with ASP 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLN* 4.8 3.1 - - - +
153A ARG* 4.7 13.9 + - - -
174B ILE 2.9 16.6 + - - +
175B ASN* 3.7 7.3 - - - +
177B LEU* 1.3 76.2 - - - +
179B SER* 1.3 61.8 + - - +
181B PHE* 3.3 2.2 + - - +
182B ARG* 3.1 44.7 + - - +
195B TYR* 3.4 23.9 + - - -
198B LEU* 3.9 13.7 - - + +
199B LYS* 5.5 4.2 + - - +
202B VAL* 4.0 24.4 - - + +
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Residues in contact with SER 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A THR* 3.8 28.9 + - - +
43A GLN* 6.0 1.4 - - - +
175B ASN 3.0 16.2 + - - -
176B GLU* 3.3 12.3 + - - -
178B ASP* 1.3 76.3 - - - +
180B GLY* 1.3 64.9 + - - +
182B ARG* 3.5 12.0 + - - +
183B LEU* 3.5 10.9 + - - +
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Residues in contact with GLY 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B GLU 2.8 17.5 + - - -
177B LEU 3.0 5.3 + - - -
179B SER* 1.3 73.5 - - - +
181B PHE* 1.3 62.8 + - - +
183B LEU* 3.2 23.1 + - - +
184B LEU* 3.7 2.4 + - - +
3F VAL* 5.1 2.2 - - - -
4F SER* 5.8 2.2 - - - -
7F PHE* 3.5 38.0 - - - +
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Residues in contact with PHE 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU* 4.0 33.2 - - + -
144B VAL* 4.6 10.3 - - + -
145B LEU* 3.6 42.8 - - + -
177B LEU* 2.8 30.6 + - + -
178B ASP 3.3 3.1 + - - +
180B GLY* 1.3 67.9 - - - +
182B ARG* 1.3 57.5 + - - +
184B LEU* 2.7 51.8 + - + +
186B LEU* 4.3 15.1 - - + +
191B LEU* 5.2 0.9 - - + -
195B TYR* 3.3 33.3 - + + -
198B LEU* 3.7 15.9 - - + -
7F PHE* 3.9 18.1 - + - -
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Residues in contact with ARG 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG* 2.9 42.4 + - + +
39A LEU* 3.6 26.9 - - + +
40A THR* 3.4 29.8 - - + -
43A GLN* 3.1 33.3 + - - +
97A ARG* 4.7 11.1 - - - +
153A ARG* 5.7 1.6 - - - +
178B ASP* 3.1 35.8 + - - +
179B SER* 3.7 3.6 - - - +
180B GLY 3.4 0.2 - - - -
181B PHE* 1.3 74.7 - - - +
183B LEU* 1.3 58.4 + - - +
184B LEU 3.4 1.0 + - - +
195B TYR* 3.5 25.4 + - - +
199B LYS* 5.8 6.9 - - - +
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Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN* 5.8 0.2 + - - -
36A ARG* 4.3 9.0 + - - -
40A THR* 4.6 5.3 - - + +
179B SER 3.5 7.3 + - - +
180B GLY* 3.2 14.9 + - - +
181B PHE 3.1 0.6 - - - -
182B ARG* 1.3 78.7 - - - +
184B LEU* 1.3 59.4 + - + +
185B ASN* 3.8 1.0 + - - +
4F SER* 4.6 2.5 - - - +
7F PHE* 4.2 7.0 - - + +
8F VAL* 3.3 43.1 - - + +
11F GLN* 3.1 64.9 + - + +
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Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG* 3.9 6.6 + - - -
141B LEU* 3.6 30.3 - - + -
180B GLY 4.0 7.0 - - - +
181B PHE* 2.7 40.8 + - + +
182B ARG* 3.4 6.4 - - - +
183B LEU* 1.3 73.9 - - + +
185B ASN* 1.3 59.7 + - - +
186B LEU* 3.5 17.4 + - + +
7F PHE* 3.9 24.2 - - + +
10F LEU* 4.0 3.8 - - + -
11F GLN* 3.5 41.3 - - + +
14F LEU* 3.7 15.0 - - + -
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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) + - + + + + + -
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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