Contacts of the strand formed by residues 96 - 103 (chain B) in PDB entry 3HIG
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 GLU 96 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B MET* 3.7 10.4 - - - +
75B LEU* 3.1 52.0 + - + +
77B PRO* 6.1 0.9 - - - +
94B VAL* 3.8 12.9 + - + +
95B ARG* 1.3 77.6 - - - +
97B ALA* 1.3 65.3 + - - +
115B ALA* 4.0 12.4 - - - +
116B VAL 3.4 10.1 - - - +
117B GLY* 4.7 0.2 - - - -
119B LEU* 4.0 8.3 - - - +
124B TYR* 2.6 40.8 + - + +
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Residues in contact with ALA 97 (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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36B LEU* 4.0 7.2 - - + -
44B VAL* 3.7 34.3 - - + -
72B ILE* 4.0 13.2 - - + -
73B GLU 3.4 10.5 - - - +
75B LEU* 4.0 4.3 - - - -
96B GLU* 1.3 74.5 - - - +
98B ARG* 1.3 60.3 + - - +
99B ALA 4.0 0.2 - - - -
114B PHE 3.4 0.3 - - - +
115B ALA* 3.3 7.1 - - - +
116B VAL* 2.7 42.7 + - + +
119B LEU* 4.1 1.8 - - + +
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Residues in contact with ARG 98 (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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71B LEU* 3.7 8.9 - - - +
72B ILE* 3.2 7.8 - - - +
73B GLU* 2.7 76.3 + - + +
74B MET 5.0 0.2 - - - +
75B LEU* 3.8 25.0 - - + +
97B ALA* 1.3 72.0 - - - +
99B ALA* 1.3 61.7 + - - +
100B VAL* 3.6 12.6 - - + +
113B GLU* 2.7 44.7 + - - +
114B PHE 3.4 6.5 - - - +
128B LEU* 4.8 7.0 - - + -
329B ARG* 3.6 13.3 - - - +
331B SER* 3.5 18.6 + - - -
636B SER* 6.0 1.4 - - - -
637B ILE* 4.0 22.0 - - - +
638B TYR* 4.5 1.8 - - - -
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Residues in contact with ALA 99 (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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44B VAL* 4.8 2.5 - - + -
48B LEU* 3.9 28.7 - - + -
69B VAL* 4.6 4.9 - - + -
71B LEU 3.4 6.3 - - - +
72B ILE* 4.6 4.9 - - + -
97B ALA 4.0 0.2 - - - -
98B ARG* 1.3 75.6 - - - +
100B VAL* 1.3 62.8 + - - +
101B ILE* 3.9 5.3 + - + -
113B GLU* 3.4 2.8 - - - +
114B PHE* 2.8 38.6 + - + +
116B VAL* 3.9 17.5 - - + -
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Residues in contact with VAL 100 (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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69B VAL* 3.6 2.9 - - - -
70B PHE* 2.8 28.8 + - + +
71B LEU* 2.9 36.0 + - + +
98B ARG* 3.6 29.6 - - - +
99B ALA* 1.3 73.0 - - - +
101B ILE* 1.3 59.7 + - - +
102B PHE* 4.2 13.0 - - + -
111B VAL* 3.4 30.1 - - + -
112B THR 3.9 2.7 - - - -
113B GLU* 3.6 15.3 - - + +
637B ILE* 4.4 7.6 - - + -
638B TYR* 3.6 8.3 - - - +
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Residues in contact with ILE 101 (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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48B LEU* 4.6 7.6 - - + -
54B LEU* 4.3 12.8 - - + -
56B LEU* 4.2 8.7 - - + -
68B THR 3.4 15.0 - - - +
69B VAL* 4.4 21.8 - - + -
99B ALA* 4.7 3.6 - - + +
100B VAL* 1.3 77.0 - - - +
102B PHE* 1.3 74.4 + - - +
103B PHE* 3.6 30.8 + - + -
111B VAL* 3.4 3.6 - - - +
112B THR 3.0 35.0 + - - +
114B PHE* 3.8 13.5 - - + -
125B MET* 3.8 28.3 - - + -
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Residues in contact with PHE 102 (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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66B LYS 3.5 1.0 - - - +
67B ASN* 3.1 5.5 - - - -
68B THR* 2.9 46.2 + - + +
70B PHE* 3.4 56.1 - + + -
100B VAL* 4.2 3.8 - - + -
101B ILE* 1.3 75.0 - - - +
103B PHE* 1.3 60.4 + - - +
104B GLY 3.5 1.3 + - - -
110B ASN 4.0 4.3 - - - -
111B VAL* 3.7 28.5 - - + -
138B TRP* 3.9 12.3 - + + -
141B ARG* 3.8 39.3 - - + -
142B PRO* 3.9 17.3 - - + -
144B SER* 5.4 5.4 - - - -
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Residues in contact with PHE 103 (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* 4.1 22.9 - - + -
67B ASN* 3.2 33.7 - - + -
101B ILE* 3.6 27.8 + - + -
102B PHE* 1.3 67.9 - - - +
104B GLY* 1.3 59.0 + - - +
105B ASP 3.5 0.4 - - - -
106B GLN* 3.4 22.2 - - - +
109B PRO* 3.1 8.3 - - - +
110B ASN* 2.8 50.2 + - - +
112B THR* 4.0 9.4 - - - -
114B PHE* 3.9 24.9 - + - -
138B TRP* 3.8 1.1 - - - -
1F NAG 3.7 23.8 - - - -
2F NAG 3.7 21.3 - - + -
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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