Contacts of the strand formed by residues 72 - 79 (chain B) in PDB entry 1J7H
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 72 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU* 6.6 0.2 - - + -
58B VAL* 5.8 2.5 - - + -
62B ILE* 4.6 15.5 - - + -
68B THR 3.7 2.9 + - - +
69B ALA* 2.8 48.8 + - + +
70B ALA 3.2 3.8 - - - +
71B ASP* 1.3 75.7 - - - +
73B VAL* 1.3 57.9 + - - +
74B LYS 3.1 7.4 - - - +
75B THR* 3.0 31.2 - - + +
95B PHE* 6.0 0.4 - - + -
96B PHE* 4.1 13.0 - - + -
103B ASN* 4.1 6.2 + - - -
105B PRO* 3.0 31.7 - - + +
125B ALA* 3.8 9.4 - - + -
126B ILE 3.0 20.9 - - - +
127B ALA* 3.8 8.9 - - + +
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Residues in contact with VAL 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 4.5 3.8 - - + -
71B ASP 3.0 0.9 + - - +
72B ILE* 1.3 73.8 - - - +
74B LYS* 1.3 74.0 + - + +
103B ASN* 5.2 0.7 - - - +
105B PRO* 3.1 5.6 - - - +
106B ALA 2.8 17.7 + - - -
126B ILE* 2.8 38.3 + - + +
128B VAL* 3.0 48.0 - - + +
4C GLN* 3.2 38.9 - - + +
22C VAL* 3.3 13.2 - - - +
24C LEU* 4.4 0.4 - - + -
29C LEU* 5.8 4.0 - - + -
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Residues in contact with LYS 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE* 3.1 2.8 - - - +
73B VAL* 1.3 88.2 - - + +
75B THR* 1.3 79.0 + - - +
76B THR* 3.8 13.7 + - - -
105B PRO* 4.0 0.2 - - - -
106B ALA* 3.2 30.3 - - + +
107B ARG 4.8 2.0 - - - -
108B SER* 4.3 20.5 + - - -
125B ALA* 3.0 1.7 - - - +
126B ILE* 2.7 40.2 + - + +
22C VAL* 5.1 3.4 - - + -
29C LEU* 5.0 20.9 - - + -
30C THR 5.0 10.5 - - - +
31C SER* 5.5 0.4 - - - +
124C GLU* 5.6 5.4 - - - -
126C ILE* 5.7 7.7 - - - +
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Residues in contact with THR 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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72B ILE* 3.0 20.4 - - + +
74B LYS* 1.3 79.5 + - - +
76B THR* 1.3 68.4 + - - +
77B VAL* 4.0 19.1 - - + -
92B TYR* 3.1 31.2 + - + +
96B PHE* 5.6 0.2 - - + -
105B PRO* 3.7 4.8 - - - +
106B ALA 2.6 19.1 + - - +
107B ARG* 3.2 6.8 - - - +
108B SER* 2.9 22.9 + - - -
123B ILE* 4.8 6.1 - - + -
125B ALA* 3.2 16.6 - - + +
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Residues in contact with THR 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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74B LYS* 3.8 13.7 + - - +
75B THR* 1.3 74.7 - - - +
77B VAL* 1.3 68.9 + - - +
78B PHE* 3.5 26.5 - - + -
108B SER* 2.7 44.0 + - - +
123B ILE* 4.2 0.2 - - - +
124B GLU* 2.8 54.6 + - + +
78C PHE* 6.2 0.4 - - + -
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Residues in contact with VAL 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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75B THR* 4.0 11.2 - - + -
76B THR* 1.3 85.5 - - - +
78B PHE* 1.3 70.8 + - - +
79B VAL* 3.8 9.2 + - + +
85B PHE* 5.2 2.7 - - + -
88B VAL* 5.9 7.0 - - + -
92B TYR* 5.2 4.3 - - + -
107B ARG* 3.5 23.3 - - - +
108B SER 3.5 3.0 + - - -
109B CYS* 2.9 43.0 - - - +
110B VAL 3.3 1.4 + - - -
121B LEU* 4.9 6.3 - - + -
122B GLU 2.7 23.8 - - - +
123B ILE* 4.1 18.6 - - + -
124B GLU* 4.3 0.4 - - - -
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Residues in contact with PHE 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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76A THR* 6.3 0.2 - - + -
78A PHE* 6.2 2.7 - + - -
108A SER* 4.1 10.8 - - - -
110A VAL* 3.2 38.6 - - + -
76B THR* 3.5 22.9 - - + -
77B VAL* 1.3 77.2 - - - +
79B VAL* 1.3 62.5 + - - +
108B SER 4.6 0.9 - - - -
110B VAL* 3.5 15.7 - - + -
112B VAL* 3.6 24.5 - - + -
115B LEU* 3.5 14.8 - - + -
121B LEU* 3.1 10.0 - - - +
122B GLU* 3.0 36.7 + - + +
124B GLU* 2.7 37.7 - - + -
78C PHE* 6.2 2.7 - + - -
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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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77B VAL* 4.4 10.3 - - + +
78B PHE* 1.3 78.6 - - - +
80B LYS* 1.3 60.7 + - - +
81B ASP 4.0 8.5 - - - +
82B LEU* 3.8 25.4 - - + +
85B PHE* 3.6 33.9 - - + +
88B VAL* 5.8 5.2 - - + -
109B CYS 5.5 0.4 - - - -
110B VAL* 2.9 18.3 + - - +
111B GLU* 3.1 20.7 - - + +
112B VAL* 3.1 26.8 + - - +
115B LEU* 4.7 0.4 - - - -
120B GLY 4.2 4.0 - - - +
121B LEU* 5.2 4.9 - - + -
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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