Contacts of the strand formed by residues 57 - 66 (chain B) in PDB entry 3GJ0
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 GLY 57 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B HIS* 4.9 0.4 - - - -
54B THR* 2.7 43.0 + - - +
55B ASN 3.5 1.0 - - - -
56B ARG* 1.3 80.0 - - - +
58B PRO* 1.3 77.9 - - - +
59B ILE* 4.1 1.7 - - - +
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Residues in contact with PRO 58 (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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9B VAL* 4.1 13.9 + - - +
51B VAL* 4.6 6.7 - - + -
52B PHE 3.5 7.9 - - - +
53B HIS* 4.1 25.3 - - + +
57B GLY* 1.3 85.8 - - - +
59B ILE* 1.3 64.4 + - - +
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Residues in contact with ILE 59 (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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9B VAL* 3.6 31.6 - - + -
11B PHE* 4.4 7.0 - - + -
51B VAL* 3.3 7.1 - - - +
52B PHE* 2.9 45.7 + - + +
54B THR* 3.7 18.8 - - + +
56B ARG* 6.0 0.9 - - + +
57B GLY 3.7 7.2 + - - +
58B PRO* 1.3 80.2 - - - +
60B LYS* 1.3 60.3 + - - +
61B PHE* 3.9 19.7 - - + -
165B ALA* 3.6 30.7 - - + -
169B ILE* 4.1 14.4 - - + -
176B PHE* 4.4 5.6 - - + -
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Residues in contact with LYS 60 (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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8B GLN* 4.8 15.4 + - - +
9B VAL 3.0 12.8 + - - +
10B GLN* 3.2 20.7 + - + +
11B PHE* 2.8 29.6 + - - -
36B GLU* 5.9 0.6 + - - -
49B PRO* 3.9 13.2 - - + +
50B LEU 3.4 13.7 - - - +
51B VAL* 3.6 22.4 - - + -
59B ILE* 1.3 78.1 - - - +
61B PHE* 1.3 66.3 + - - +
62B ASN* 3.3 28.9 - - - +
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Residues in contact with PHE 61 (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 PHE* 3.5 31.6 - + + +
13B LEU* 3.7 17.7 - - + -
48B HIS 3.2 3.6 - - - +
50B LEU* 2.8 39.5 + - + +
52B PHE* 3.8 20.2 - + - -
59B ILE* 3.9 19.3 - - + -
60B LYS* 1.3 72.3 - - - +
62B ASN* 1.3 60.8 + - - +
63B VAL* 3.3 16.0 + - + +
85B CYS* 3.9 16.8 - - - -
161B PHE* 3.5 43.7 - + + -
164B LEU* 4.1 7.4 - - + -
165B ALA* 3.8 14.8 - - + -
168B LEU* 4.0 5.4 - - + -
176B PHE* 5.2 0.2 - + - -
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Residues in contact with ASN 62 (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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10B GLN* 3.0 31.8 + - - +
11B PHE 2.8 14.1 + - - +
12B LYS* 3.7 4.8 - - + -
13B LEU 3.0 24.2 + - - +
47B VAL* 3.8 17.7 - - + +
48B HIS 3.5 2.9 - - - -
49B PRO* 3.5 17.4 - - - +
60B LYS* 3.3 23.9 - - - +
61B PHE* 1.3 70.0 - - - +
63B VAL* 1.3 61.1 + - - +
64B TRP* 3.4 12.9 - - - +
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Residues in contact with VAL 63 (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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13B LEU* 3.4 15.7 - - + -
15B LEU* 4.0 28.0 - - + -
27B VAL* 3.6 25.4 - - + -
46B GLU 3.4 2.4 - - - +
47B VAL* 3.3 2.9 - - - -
48B HIS* 2.9 37.9 + - - +
50B LEU* 3.9 22.7 - - + -
61B PHE* 3.7 22.7 - - + +
62B ASN* 1.3 72.0 - - - +
64B TRP* 1.3 66.2 + - - +
65B ASP 3.5 0.6 + - - +
87B ILE* 6.3 0.4 - - + -
161B PHE* 4.1 11.4 - - + -
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Residues in contact with TRP 64 (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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12B LYS* 3.4 47.1 - - + +
13B LEU 2.8 13.4 + - - +
14B VAL* 4.3 2.7 - - + -
15B LEU* 3.3 13.7 + - - +
40B VAL* 6.1 0.9 - - + -
43B LEU* 3.7 31.6 - - + -
45B VAL* 3.8 23.1 - - + -
46B GLU 4.0 0.9 - - - -
47B VAL* 3.7 28.9 - - + +
62B ASN* 3.4 19.5 + - - +
63B VAL* 1.3 73.8 - - - +
65B ASP* 1.3 58.5 + - - +
78B GLY 3.7 11.2 - - - -
79B TYR* 2.8 55.0 + + + +
81B ILE* 6.0 0.2 - - + -
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Residues in contact with ASP 65 (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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15B LEU* 4.1 8.8 - - + +
23B LYS* 3.8 21.3 - - - +
24B THR* 2.5 39.4 + - - +
27B VAL* 3.9 24.5 - - + +
45B VAL* 3.3 3.9 - - - +
46B GLU* 2.9 45.9 + - + +
48B HIS* 4.3 8.7 - - + +
63B VAL* 3.5 1.5 + - + +
64B TRP* 1.3 73.2 - - - +
66B THR* 1.3 73.2 + - - +
301B MG 4.3 0.7 - - - -
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Residues in contact with THR 66 (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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15B LEU 4.5 6.3 + - - +
16B VAL* 5.8 0.2 - - - -
23B LYS* 4.3 18.8 + - - -
24B THR* 4.2 0.3 + - - -
44B GLY 4.0 6.5 - - - -
45B VAL* 4.6 1.1 - - - +
46B GLU* 5.1 1.4 - - - +
64B TRP 4.1 0.2 + - - -
65B ASP* 1.3 89.6 + - - +
67B ALA* 1.3 58.7 + - - +
68B GLY* 3.1 21.8 + - - -
75B LEU* 3.8 41.3 - - + -
79B TYR* 4.0 16.1 - - + +
301B MG 3.9 7.4 - - - -
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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