Contacts of the strand formed by residues 32 - 40 (chain E) 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 LYS 32 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23E LEU* 2.8 45.3 + - + +
24E GLU* 3.9 8.1 - - - +
26E LEU* 3.7 22.4 - - + -
27E GLY 2.8 22.4 + - - +
28E ASN* 4.9 0.6 + - - +
29E VAL* 3.6 22.2 - - + -
31E ARG* 1.3 75.9 - - - +
33E ILE* 1.3 61.3 + - - +
75E GLY 3.5 6.3 - - - +
76E GLN* 4.2 1.3 - - + +
86E VAL* 4.5 5.6 - - - +
106E VAL* 4.9 0.4 - - - +
168E GLY 3.2 8.0 + - - +
169E HIS* 3.4 42.2 + - + -
170E ALA* 2.8 25.3 + - - +
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Residues in contact with ILE 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E LEU* 3.9 4.5 - - - -
26E LEU* 4.4 0.8 - - - +
32E LYS* 1.3 75.8 - - - +
34E ALA* 1.3 71.3 + - - +
35E VAL* 4.0 17.0 - - + -
74E ASN* 3.2 8.1 - - - +
75E GLY* 2.9 43.0 + - - +
86E VAL* 4.4 4.3 - - + -
104E PHE* 3.8 41.7 - - + -
106E VAL* 4.0 9.9 - - + -
164E MET* 3.8 28.3 - - + -
170E ALA* 3.4 17.7 - - + +
172E LEU* 4.2 6.7 - - + -
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Residues in contact with ALA 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E LEU* 3.6 27.5 - - + +
22E VAL* 3.5 26.5 - - + -
23E LEU* 3.7 13.6 - - + +
33E ILE* 1.3 72.5 - - - +
35E VAL* 1.3 62.4 + - - +
73E TYR 3.7 4.3 - - - -
170E ALA 2.9 11.6 + - - +
171E ILE* 3.7 4.3 - - + +
172E LEU 3.0 25.6 + - - +
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Residues in contact with VAL 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E LEU* 3.8 7.5 - - - +
22E VAL* 5.7 0.2 - - - +
33E ILE* 4.0 31.2 - - + +
34E ALA* 1.3 78.2 - - - +
36E GLY* 1.3 61.6 + - - +
37E ILE* 4.1 24.5 - - + -
71E LEU* 5.6 0.9 - - + -
72E LEU* 3.6 3.1 - - - +
73E TYR* 2.8 52.0 + - + +
90E ILE* 4.4 13.7 - - + -
102E VAL* 5.4 0.9 - - + -
104E PHE* 4.9 10.8 - - + -
172E LEU* 3.5 26.0 - - + +
174E ILE* 5.3 0.2 - - + -
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Residues in contact with GLY 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E LEU* 3.6 14.7 - - - +
19E LEU* 3.7 13.9 - - - +
35E VAL* 1.3 76.2 - - - +
37E ILE* 1.3 65.1 + - - +
71E LEU 3.2 10.1 - - - -
72E LEU* 4.5 0.4 - - - -
172E LEU 3.0 11.8 + - - +
173E GLU* 3.6 1.7 - - - -
174E ILE* 3.0 25.8 + - - +
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Residues in contact with ILE 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E LEU* 3.7 4.9 - - - +
35E VAL* 4.1 18.8 - - + -
36E GLY* 1.3 80.6 - - - +
38E ASP* 1.3 62.8 + - - +
39E ASN 3.7 0.5 + - - -
45E TRP* 3.4 33.3 - - + -
65E VAL* 5.1 0.2 - - - +
69E LYS 4.1 0.2 - - - +
70E ALA* 3.1 2.8 - - - -
71E LEU* 3.0 54.3 + - + +
90E ILE* 4.9 11.4 - - + -
92E TYR* 5.5 1.8 - - + -
100E LEU* 4.8 3.8 - - + -
102E VAL* 4.0 28.7 - - + -
174E ILE* 3.3 22.2 - - + +
176E VAL* 4.6 2.9 - - + -
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Residues in contact with ASP 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E GLY* 3.3 28.5 - - - +
14E LEU* 3.7 6.5 - - + +
37E ILE* 1.3 73.4 - - - +
39E ASN* 1.3 65.4 + - - +
40E GLU* 2.7 38.8 + - - +
45E TRP* 3.8 6.2 - - - -
69E LYS 3.9 0.7 - - - +
70E ALA* 3.9 6.1 - - - -
174E ILE 2.9 8.1 + - - +
175E HIS* 3.1 41.6 + - + +
176E VAL 3.1 22.2 + - - -
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Residues in contact with ASN 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E ILE 3.7 0.6 + - - -
38E ASP* 1.3 72.1 + - - +
40E GLU* 1.3 56.4 + - - +
41E SER* 2.6 27.4 + - - -
42E GLY 4.3 0.2 + - - -
43E LYS 3.0 18.6 + - - +
45E TRP* 3.0 28.2 - - + +
65E VAL* 3.0 35.6 + - + -
66E ALA 3.2 11.2 + - - +
67E HIS* 3.5 1.3 - - - -
68E GLY* 2.6 35.7 + - - -
69E LYS 2.8 21.9 + - - +
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Residues in contact with GLU 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E GLY* 4.1 3.3 - - - -
12E ALA 5.2 0.2 + - - -
38E ASP* 2.7 36.0 - - - +
39E ASN* 1.3 73.7 - - - +
41E SER* 1.3 62.2 + - - +
42E GLY 3.2 3.9 + - - -
67E HIS* 3.4 29.0 + - + -
68E GLY* 3.3 20.7 - - - +
176E VAL 2.8 17.9 + - - +
177E THR* 3.8 19.7 - - + -
178E LYS* 3.3 18.4 + - - -
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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