Contacts of the strand formed by residues 79 - 86 (chain A) in PDB entry 3GBG
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 ILE 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ARG* 3.5 1.9 - - - -
14A MET* 2.6 51.1 + - + +
35A ILE* 3.6 28.7 - - + -
36A ASP* 3.7 5.2 - - - +
37A SER* 3.5 28.3 - - - +
38A GLY* 4.6 0.2 - - - -
39A ILE 3.7 13.2 - - - +
40A ALA* 5.1 1.3 - - + -
73A SER* 3.7 18.4 - - - +
75A SER* 3.5 30.1 - - - +
77A GLU* 3.8 7.2 - - + +
78A ASN* 1.3 79.7 - - - +
80A ASN* 1.3 68.2 + - - +
81A VAL* 4.5 3.8 - - + -
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Residues in contact with ASN 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A VAL* 3.8 22.9 - - + +
12A TYR 3.4 2.5 - - - +
13A ARG* 3.9 24.1 + - - +
35A ILE* 3.5 1.7 - - - -
36A ASP* 2.8 63.2 + - + +
78A ASN* 6.0 0.7 - - - -
79A ILE* 1.3 77.3 - - - +
81A VAL* 1.3 62.2 + - - +
82A SER* 3.8 2.6 + - - +
273A VAL* 5.5 2.8 - - - +
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Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ASN 3.8 0.5 - - - +
11A VAL* 3.3 3.5 - - - -
12A TYR* 2.8 46.4 + - + +
14A MET* 4.3 28.5 - - + -
33A PHE* 4.1 12.3 - - + -
34A TRP 3.5 11.2 - - - +
35A ILE* 4.2 16.2 - - + -
71A LEU* 4.4 6.7 - - + -
79A ILE* 4.5 0.4 - - + -
80A ASN* 1.3 74.7 - - - +
82A SER* 1.3 65.8 + - - +
83A VAL* 3.9 2.1 + - + -
5975A PAM 3.9 42.4 - - + -
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Residues in contact with SER 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ASN 3.5 4.7 - - - -
11A VAL* 4.3 8.7 - - - +
32A MET 3.9 0.2 - - - +
33A PHE* 3.0 27.7 - - - +
34A TRP* 3.0 40.0 + - - -
36A ASP* 5.3 5.0 - - - +
80A ASN* 3.8 3.5 + - - +
81A VAL* 1.3 73.4 - - - +
83A VAL* 1.3 61.0 + - - +
84A ILE 4.2 0.2 - - - -
131A VAL* 3.5 31.8 - - - +
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Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A GLN 3.6 1.6 - - - +
9A THR* 3.2 5.2 - - - -
10A ASN* 2.7 42.0 + - + +
12A TYR* 3.7 31.4 - - + -
31A LYS* 4.7 10.1 - - + -
32A MET 3.5 7.9 - - - +
33A PHE* 3.9 12.1 - - + -
81A VAL* 4.3 2.7 - - + -
82A SER* 1.3 78.4 - - - +
84A ILE* 1.3 70.0 + - - +
85A THR* 4.6 6.6 + - - +
131A VAL* 5.0 0.4 - - - +
230A LYS* 5.5 0.4 - - - +
5975A PAM 4.0 44.6 - - + +
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Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PHE* 4.1 26.2 - - + -
8A GLN 3.5 2.5 - - - -
9A THR* 3.7 19.3 - - + -
31A LYS* 3.2 6.2 - - - +
32A MET* 2.8 53.8 + - + +
34A TRP* 3.4 37.9 - - + -
83A VAL* 1.3 75.2 - - - +
85A THR* 1.3 66.4 + - - +
86A ILE* 4.0 6.0 + - + +
127A LEU* 3.7 4.0 - - + +
130A VAL* 3.7 26.9 - - + -
131A VAL* 4.3 2.9 - - + +
148A PHE* 5.3 1.1 - - + -
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Residues in contact with THR 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A SER 3.9 0.2 - - - +
7A PHE* 3.5 4.5 - - - -
8A GLN* 2.6 66.6 + - + +
29A ASP* 4.1 18.4 - - + +
30A TYR 3.7 9.2 - - - +
31A LYS* 2.7 36.5 + - + +
83A VAL* 4.6 3.6 + - - +
84A ILE* 1.3 76.1 - - - +
86A ILE* 1.3 64.2 + - - +
87A SER 4.0 0.2 + - - -
230A LYS* 3.9 1.4 + - - -
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Residues in contact with ILE 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A SER 3.5 7.6 - - - +
7A PHE* 4.2 10.3 - - + -
29A ASP* 3.6 22.2 - - - +
30A TYR* 3.0 22.4 + - + +
32A MET* 3.6 28.9 - - + -
84A ILE* 4.3 9.9 - - + +
85A THR* 1.3 77.5 - - - +
87A SER* 1.3 70.9 + - - +
88A ASP* 5.2 0.2 - - - +
90A PHE* 3.6 22.7 - - + -
91A ILE* 3.5 28.9 - - + +
94A LEU* 5.2 0.4 - - + -
148A PHE* 4.4 9.9 - - + -
152A PHE* 3.7 19.7 - - + -
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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