Contacts of the strand formed by residues 169 - 178 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23F LEU* 3.8 20.5 - - + +
28F ASN* 4.4 13.0 - - - -
29F VAL 3.0 21.5 + - - -
30F LYS* 3.7 12.7 + - - -
32F LYS* 3.4 34.5 + - + -
165F ASN* 3.0 20.4 + - - -
167F SER* 3.3 6.1 - - - -
168F GLY* 1.3 83.3 - - - +
170F ALA* 1.3 59.2 + - - +
171F ILE* 5.0 0.5 - - - +
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Residues in contact with ALA 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F LEU* 3.6 3.9 - - - +
32F LYS 2.8 11.2 + - - +
33F ILE* 3.3 19.6 - - + -
34F ALA 2.9 26.0 + - - -
106F VAL* 3.8 22.2 - - + -
115F ASN* 4.2 7.2 - - - +
164F MET* 4.1 10.8 - - + -
165F ASN* 3.2 10.1 - - - +
167F SER 4.3 1.3 - - - +
169F HIS* 1.3 73.7 - - - +
171F ILE* 1.3 67.3 + - - +
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Residues in contact with ILE 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F PHE* 4.7 10.8 - - + +
19F LEU* 3.7 30.3 - - + -
20F LYS* 4.1 35.9 - - + +
23F LEU* 4.2 15.9 - - + -
34F ALA* 3.7 5.8 - - + -
163F PHE* 3.5 7.2 - - + +
164F MET* 3.4 25.2 - - - +
165F ASN* 2.8 20.0 + - + +
169F HIS 5.0 1.1 - - - +
170F ALA* 1.3 78.9 - - - +
172F LEU* 1.3 62.7 + - - +
173F GLU* 4.7 4.3 - - + +
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Residues in contact with LEU 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F LEU* 4.0 3.7 - - - +
33F ILE* 4.2 12.3 - - + +
34F ALA 3.0 12.9 + - - +
35F VAL* 3.5 16.4 - - + -
36F GLY 3.0 25.5 + - - +
102F VAL* 4.3 6.1 - - + -
104F PHE* 4.2 19.7 - - + -
117F TRP* 3.7 39.9 - - + -
163F PHE 3.3 15.5 - - - +
164F MET* 4.0 8.3 - - + -
170F ALA 4.1 0.4 - - - -
171F ILE* 1.3 73.4 - - - +
173F GLU* 1.3 59.3 + - - +
174F ILE* 3.7 33.2 - - + -
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Residues in contact with GLU 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F LEU* 4.1 18.3 - - + +
15F GLY* 4.2 11.7 - - - -
16F PHE* 4.1 17.8 + - - +
19F LEU* 3.8 13.3 - - + +
36F GLY 3.7 3.4 - - - -
149F TRP* 3.9 22.4 - - + -
161F ARG 3.8 0.3 - - - +
162F GLY* 3.0 3.6 - - - -
163F PHE* 2.8 40.2 + - + +
171F ILE* 4.1 4.8 - - + +
172F LEU* 1.3 70.6 - - - +
174F ILE* 1.3 62.7 + - - +
175F HIS* 2.9 30.9 + - + +
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Residues in contact with ILE 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F LEU* 4.1 1.0 - - - +
36F GLY 3.0 11.1 + - - +
37F ILE* 3.3 17.5 - - + -
38F ASP* 2.9 24.1 + - - +
102F VAL* 3.6 34.1 - - + -
117F TRP* 4.0 11.4 - - + -
119F VAL* 3.8 24.9 - - + -
160F SER* 4.7 3.1 - - - -
161F ARG 3.2 9.4 - - - +
162F GLY* 4.2 0.4 - - - -
172F LEU* 3.7 28.7 - - + -
173F GLU* 1.3 80.6 - - - +
175F HIS* 1.3 76.0 + - - +
176F VAL* 4.3 13.2 - - + -
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Residues in contact with HIS 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F GLY 5.0 1.3 - - - -
14F LEU* 4.5 15.0 - - + +
38F ASP* 3.1 38.5 + - + +
40F GLU* 5.7 0.4 - - - +
149F TRP* 4.5 1.8 - + - -
159F LYS 3.8 0.5 - - - +
160F SER* 3.7 1.4 - - - -
161F ARG* 2.6 81.7 + - + +
173F GLU* 2.9 35.9 + - + +
174F ILE* 1.3 79.4 - - - +
176F VAL* 1.3 64.0 + - - +
177F THR* 3.7 13.6 + - + +
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Residues in contact with VAL 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F ILE* 4.6 2.2 - - + -
38F ASP 3.1 7.6 + - - +
40F GLU* 2.8 31.4 + - - +
41F SER* 3.2 14.4 + - - -
45F TRP* 3.6 37.9 - - + -
100F LEU* 4.1 19.5 - - + -
119F VAL* 4.7 2.2 - - + -
154F LEU* 4.2 19.1 - - + -
158F LEU* 4.3 11.0 - - + -
159F LYS 3.6 7.9 - - - +
160F SER* 4.6 4.0 - - - -
174F ILE* 4.3 14.8 - - + -
175F HIS* 1.3 73.9 - - - +
177F THR* 1.3 60.3 + - - +
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Residues in contact with THR 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F GLU* 3.8 22.9 - - + -
41F SER* 4.4 4.9 - - - -
158F LEU* 3.5 5.1 - - - +
159F LYS* 3.0 51.2 + - - +
161F ARG* 5.8 3.8 - - + +
175F HIS* 4.0 18.6 + - + +
176F VAL* 1.3 81.7 - - - +
178F LYS* 1.3 74.4 + - - +
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Residues in contact with LYS 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F GLU 3.4 24.7 + - - -
41F SER* 3.5 15.5 - - - +
42F GLY* 4.2 11.0 - - - -
67F HIS* 3.8 20.0 + - - -
157F GLY 3.7 7.4 - - - +
158F LEU* 4.5 2.9 - - + -
159F LYS* 3.8 5.0 + - - -
177F THR* 1.3 81.9 + - - +
179F ALA* 1.3 65.4 + - - +
44G THR* 5.7 0.6 - - - +
64G LYS* 3.3 29.3 - - - +
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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