Contacts of the strand formed by residues 73 - 80 (chain B) in PDB entry 4GID
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 GLN 73 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B THR* 3.1 4.1 - - - -
68B VAL* 2.9 47.4 + - + +
71B PRO* 4.0 7.0 + - + +
72B PRO* 1.3 74.3 - - - +
74B THR* 1.3 64.7 + - - +
75B LEU* 3.7 4.0 + - + +
99B TYR 3.9 4.3 - - - +
100B TYR* 3.5 16.3 - - - -
101B GLN* 2.8 57.9 + - - +
104B LEU* 4.1 17.7 + - - +
105B SER* 4.3 8.1 - - - +
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Residues in contact with THR 74 (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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65B GLU* 3.5 40.0 - - + +
66B MET 3.4 5.8 - - - +
67B THR* 4.0 11.5 - - + +
72B PRO* 4.0 3.6 + - - +
73B GLN* 1.3 72.7 - - - +
75B LEU* 1.3 74.3 + - - +
98B ARG* 3.6 35.8 + - - +
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Residues in contact with LEU 75 (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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65B GLU* 3.7 2.4 - - - +
66B MET* 2.8 36.8 + - + +
68B VAL* 3.7 32.5 - - + -
73B GLN* 4.2 5.4 - - + +
74B THR* 1.3 82.9 - - - +
76B ASN* 1.3 64.2 + - - +
77B ILE* 3.7 15.8 + - + +
88B VAL* 4.3 17.0 - - + -
89B GLY 5.4 0.4 - - - +
98B ARG* 4.0 11.4 - - + +
99B TYR* 3.9 27.6 - - - +
100B TYR* 4.2 17.9 - - + +
164B GLU* 3.5 22.2 - - + +
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Residues in contact with ASN 76 (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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55B ARG* 3.6 10.6 + - - +
63B TYR* 3.5 25.6 - - + -
64B VAL 3.7 1.1 - - - -
65B GLU* 4.0 20.8 + - - +
75B LEU* 1.3 74.3 + - - +
77B ILE* 1.3 60.9 - - - +
98B ARG* 3.1 21.6 + - - +
162B ASN* 3.0 44.0 + - - +
163B TRP* 3.5 3.9 - - - -
164B GLU* 2.8 39.7 + - - +
165B GLY 3.2 5.4 + - - -
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Residues in contact with ILE 77 (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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63B TYR* 3.1 5.5 - - - +
64B VAL* 2.8 41.3 + - + +
66B MET* 3.6 39.7 - - + -
68B VAL* 6.0 0.7 - - + -
75B LEU* 3.9 15.0 - - + +
76B ASN* 1.3 81.5 - - - +
78B LEU* 1.3 61.6 + - - +
79B VAL 3.5 0.7 + - - -
86B PHE* 4.0 5.2 - - + -
88B VAL* 3.9 20.0 - - + -
165B GLY* 3.7 16.6 - - - +
166B ILE 3.4 8.1 - - - +
167B LEU* 3.3 41.1 - - + +
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Residues in contact with LEU 78 (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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61B GLY* 3.5 24.5 - - - -
62B TYR 3.5 11.4 - - - +
63B TYR* 3.7 4.7 - - - +
76B ASN 4.2 0.8 + - - -
77B ILE* 1.3 70.9 - - - +
79B VAL* 1.3 65.4 + - - +
80B ASP* 3.6 9.8 + - + -
163B TRP* 3.4 39.9 - - + +
165B GLY 2.9 18.8 + - - +
166B ILE* 3.5 16.9 - - + +
167B LEU* 2.7 32.7 + - - +
277B SER 5.8 0.2 - - - +
278B GLY* 4.5 5.6 - - - -
501B 0GH 3.4 39.5 - - + -
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Residues in contact with VAL 79 (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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54B LEU* 4.5 11.2 - - + -
62B TYR* 3.0 20.0 + - + +
64B VAL* 4.0 17.0 - - + +
77B ILE 4.0 1.8 - - - +
78B LEU* 1.3 76.7 - - - +
80B ASP* 1.3 53.8 + - - +
167B LEU* 4.1 7.2 - - + -
169B LEU* 3.3 26.7 - - + -
200B LEU* 4.0 23.8 - - + -
202B LEU* 5.9 2.0 - - + -
222B MET* 3.7 28.0 - - + -
277B SER* 2.6 35.1 + - - +
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Residues in contact with ASP 80 (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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78B LEU* 3.6 5.3 + - + -
79B VAL* 1.3 74.0 - - - +
81B THR* 1.3 59.4 + - - +
82B GLY* 2.8 12.6 + - - -
83B SER* 2.6 29.5 + - - +
166B ILE* 3.6 23.3 - - + +
167B LEU 3.1 12.0 + - - +
168B GLY* 3.3 3.8 - - - -
169B LEU* 2.9 23.8 + - - -
276B ASP* 2.7 28.2 - - - +
277B SER* 3.2 1.6 - - - -
278B GLY* 3.3 6.5 + - - +
501B 0GH 3.3 24.7 - - - +
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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