Contacts of the strand formed by residues 169 - 178 (chain B) in PDB entry 3ZWG
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 HIS 169 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU* 3.9 20.0 - - + +
28B ASN* 4.4 11.9 - - - -
29B VAL 3.0 25.6 + - - -
30B LYS* 3.8 9.1 + - - -
32B LYS* 3.5 32.6 + - + -
165B ASN* 2.9 21.1 + - - -
167B SER* 3.8 3.7 - - - -
168B GLY* 1.3 82.9 - - - +
170B ALA* 1.3 59.2 + - - +
171B ILE* 4.0 0.5 + - - +
58C ASP* 3.7 16.0 + - - +
79C ARG* 5.4 10.6 + - - -
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Residues in contact with ALA 170 (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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23B LEU* 3.6 4.2 - - - +
32B LYS 2.8 9.4 + - - +
33B ILE* 3.3 20.3 - - + -
34B ALA 2.9 26.0 + - - -
106B VAL* 3.7 22.0 - - + -
115B ASN* 4.2 7.9 - - - +
164B MET* 4.1 11.0 - - + -
165B ASN* 3.2 10.1 - - - +
167B SER 4.3 1.8 - - - +
169B HIS* 1.3 73.7 - - - +
171B ILE* 1.3 65.6 + - - +
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Residues in contact with ILE 171 (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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16B PHE* 4.7 4.7 - - + +
19B LEU* 3.7 33.2 - - + +
20B LYS* 4.1 35.2 - - + +
23B LEU* 4.2 15.3 - - + -
34B ALA* 3.7 4.0 - - + -
163B PHE* 3.5 2.3 - - - +
164B MET* 3.4 25.0 - - - +
165B ASN* 2.8 17.5 + - + +
169B HIS 5.1 1.6 - - - +
170B ALA* 1.3 77.6 - - - +
172B LEU* 1.3 63.3 + - - +
173B GLU 4.6 0.9 - - - +
58C ASP* 3.8 22.4 - - + +
60C VAL* 3.8 22.9 - - + -
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Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 3.9 3.4 - - - +
33B ILE* 4.3 11.9 - - + -
34B ALA 3.0 13.0 + - - +
35B VAL* 3.5 18.0 - - + -
36B GLY 3.0 25.8 + - - +
102B VAL* 4.4 3.6 - - + -
103B LEU 4.4 2.7 - - - +
104B PHE* 4.2 19.7 - - + -
117B TRP* 3.7 44.6 - - + -
163B PHE 3.3 15.0 - - - +
164B MET* 4.0 8.7 - - + -
170B ALA 4.2 0.2 - - - -
171B ILE* 1.3 72.8 - - - +
173B GLU* 1.3 60.7 + - - +
174B ILE* 3.7 28.5 - - + -
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Residues in contact with GLU 173 (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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14B LEU* 4.2 18.7 - - + +
15B GLY* 4.2 12.1 - - - -
16B PHE 4.1 10.6 + - - -
19B LEU* 3.8 11.1 - - + +
36B GLY 3.7 2.9 - - - -
149B TRP* 3.8 19.4 - - + -
161B ARG 3.9 0.2 - - - +
162B GLY* 3.0 3.6 - - - -
163B PHE* 2.8 39.3 + - + +
171B ILE* 4.2 1.0 - - - +
172B LEU* 1.3 72.3 - - - +
174B ILE* 1.3 62.8 + - - +
175B HIS* 2.9 31.2 + - + +
60C VAL* 3.5 27.1 - - + +
63C HIS* 6.0 0.5 - - - +
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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
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14B LEU* 4.2 1.0 - - - +
35B VAL* 5.2 0.4 - - + -
36B GLY 3.0 10.4 + - - +
37B ILE* 3.3 17.2 - - + -
38B ASP* 2.9 23.9 + - - +
102B VAL* 3.6 34.1 - - + -
117B TRP* 4.1 10.5 - - + -
119B VAL* 3.8 25.1 - - + -
160B SER* 4.8 2.9 - - - -
161B ARG 3.2 9.0 - - - +
162B GLY* 4.3 0.4 - - - -
172B LEU* 3.7 28.7 - - + -
173B GLU* 1.3 80.8 - - - +
175B HIS* 1.3 76.5 + - - +
176B VAL* 4.4 12.6 - - + -
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Residues in contact with HIS 175 (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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11B GLY 5.0 1.1 - - - -
14B LEU* 4.4 15.0 - - + +
38B ASP* 3.1 37.3 + - + +
40B GLU* 5.7 0.4 - - - +
149B TRP* 4.5 2.0 - + - -
159B LYS 3.8 0.5 - - - +
160B SER* 3.7 1.6 - - - -
161B ARG* 2.6 78.9 + - - +
173B GLU* 2.9 36.6 + - + +
174B ILE* 1.3 80.0 - - - +
176B VAL* 1.3 63.0 + - - +
177B THR* 3.8 14.0 + - + +
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Residues in contact with VAL 176 (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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37B ILE* 4.6 1.3 - - + -
38B ASP 3.1 7.2 + - - +
40B GLU* 2.8 31.4 + - - +
41B SER* 3.3 14.1 + - - -
45B TRP* 3.7 38.4 - - + -
100B LEU* 4.1 18.6 - - + -
102B VAL* 6.2 0.2 - - + -
119B VAL* 4.6 2.0 - - + -
154B LEU* 4.3 18.4 - - + -
158B LEU* 4.3 11.2 - - + -
159B LYS 3.5 8.1 - - - +
160B SER* 4.6 4.5 - - - -
174B ILE* 4.1 15.5 - - + -
175B HIS* 1.3 74.4 - - - +
177B THR* 1.3 60.9 + - - +
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Residues in contact with THR 177 (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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40B GLU* 3.7 24.7 - - + -
41B SER* 4.4 3.8 - - - -
158B LEU* 3.5 4.5 - - - +
159B LYS* 3.0 48.8 + - - +
161B ARG* 5.9 3.8 - - + +
175B HIS* 4.1 18.8 + - + +
176B VAL* 1.3 79.7 - - - +
178B LYS* 1.3 72.7 + - - +
179B ALA 3.3 0.2 + - - -
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Residues in contact with LYS 178 (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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40B GLU 3.3 24.4 + - - -
41B SER* 3.6 15.9 - - - +
42B GLY* 4.3 10.3 - - - -
67B HIS* 3.6 25.9 + - - -
157B GLY 3.8 6.7 - - - +
158B LEU* 4.5 3.8 - - + -
159B LYS* 3.8 5.5 + - - -
177B THR* 1.3 81.7 + - - +
179B ALA* 1.3 64.6 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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