Contacts of the strand formed by residues 32 - 40 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G LEU* 2.9 42.1 + - + +
24G GLU* 4.0 8.5 + - - +
26G LEU* 3.7 22.9 - - + -
27G GLY 2.8 23.4 + - - +
28G ASN* 4.9 0.6 + - - +
29G VAL* 3.6 20.6 - - + -
31G ARG* 1.3 77.2 - - - +
33G ILE* 1.3 61.7 + - - +
75G GLY 3.4 6.3 - - - +
76G GLN* 4.2 1.8 - - + +
86G VAL* 4.5 6.1 - - - +
106G VAL* 4.9 0.7 - - - +
168G GLY 3.2 7.4 + - - +
169G HIS* 3.4 42.8 + - + -
170G ALA* 2.8 24.9 + - - +
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Residues in contact with ILE 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G LEU* 3.8 4.5 - - - -
26G LEU* 4.4 0.7 - - - +
32G LYS* 1.3 76.7 - - - +
34G ALA* 1.3 68.9 + - - +
35G VAL* 4.0 15.7 - - + -
74G ASN* 3.3 6.6 - - - +
75G GLY* 2.9 41.0 + - - +
86G VAL* 4.4 4.5 - - + -
104G PHE* 3.8 42.4 - - + -
106G VAL* 3.9 10.3 - - + -
164G MET* 3.7 27.8 - - + -
170G ALA* 3.4 18.8 - - + +
172G LEU* 4.2 7.0 - - + -
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Residues in contact with ALA 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G LEU* 3.6 27.4 - - + +
22G VAL* 3.5 27.4 - - + -
23G LEU* 3.6 14.0 - - + +
33G ILE* 1.3 73.5 - - - +
35G VAL* 1.3 61.8 + - - +
73G TYR 3.6 4.3 - - - -
170G ALA 2.9 11.2 + - - +
171G ILE* 3.7 2.9 - - + -
172G LEU 3.0 25.8 + - - +
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Residues in contact with VAL 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G LEU* 3.8 8.1 - - - +
33G ILE* 4.0 30.3 - - + -
34G ALA* 1.3 78.4 - - - +
36G GLY* 1.3 61.9 + - - +
37G ILE* 4.1 23.1 - - + -
71G LEU* 5.7 0.7 - - + -
72G LEU* 3.6 3.3 - - - +
73G TYR* 2.9 51.7 + - + +
90G ILE* 4.5 13.0 - - + -
102G VAL* 5.4 1.1 - - + -
104G PHE* 4.9 10.8 - - + -
172G LEU* 3.6 26.2 - - + +
174G ILE* 5.3 0.4 - - + -
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Residues in contact with GLY 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G LEU* 3.7 14.0 - - - +
19G LEU* 3.8 12.8 - - - +
35G VAL* 1.3 77.2 - - - +
37G ILE* 1.3 67.0 + - - +
71G LEU 3.2 10.5 - - - -
72G LEU* 4.5 0.4 - - - -
172G LEU 3.0 11.6 + - - +
173G GLU* 3.7 1.6 - - - -
174G ILE* 3.0 25.6 + - - +
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Residues in contact with ILE 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G LEU* 3.7 4.5 - - - +
35G VAL* 4.1 17.3 - - + -
36G GLY* 1.3 82.2 - - - +
38G ASP* 1.3 61.9 + - - +
39G ASN 3.7 0.5 + - - -
45G TRP* 3.4 32.6 - - + -
65G VAL* 5.1 0.2 - - - +
69G LYS 4.1 0.3 - - - +
70G ALA* 3.1 2.6 - - - -
71G LEU* 3.0 55.2 + - + +
90G ILE* 5.0 11.2 - - + -
92G TYR* 5.4 1.6 - - + -
100G LEU* 4.8 3.6 - - + -
102G VAL* 4.1 28.5 - - + -
174G ILE* 3.4 21.8 - - + +
176G VAL* 4.7 2.7 - - + -
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Residues in contact with ASP 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G GLY* 3.2 29.7 - - - +
14G LEU* 3.6 6.0 - - + +
37G ILE* 1.3 71.4 - - - +
39G ASN* 1.3 65.4 + - - +
40G GLU* 2.8 36.4 + - + +
45G TRP* 3.8 5.6 - - - -
69G LYS 3.9 0.7 - - - +
70G ALA* 3.9 5.8 - - - -
174G ILE 2.9 9.7 + - - +
175G HIS* 3.1 41.2 + - + +
176G VAL 3.1 23.0 + - - -
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Residues in contact with ASN 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G ILE 3.7 0.6 + - - -
38G ASP* 1.3 72.2 + - - +
40G GLU* 1.3 56.9 + - - +
41G SER* 2.5 28.1 + - - -
43G LYS 3.0 20.6 + - - +
45G TRP* 3.0 28.4 - - + -
65G VAL* 3.1 33.3 + - + -
66G ALA 3.3 9.4 + - - +
67G HIS* 3.5 1.8 - - - +
68G GLY* 2.6 35.7 + - - -
69G LYS 2.8 21.1 + - - +
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Residues in contact with GLU 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G GLY* 4.1 4.2 - - - -
12G ALA 5.2 0.2 + - - -
38G ASP* 2.8 36.6 - - + +
39G ASN* 1.3 74.5 - - - +
41G SER* 1.3 64.1 + - - +
42G GLY 3.2 3.8 + - - -
67G HIS* 3.3 28.4 + - + -
68G GLY* 3.3 20.3 - - - -
175G HIS* 5.6 0.4 - - - +
176G VAL 2.8 17.5 + - - +
177G THR* 3.7 20.0 - - + -
178G LYS* 3.4 18.0 + - - -
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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
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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