Contacts of the strand formed by residues 71 - 78 (chain B) in PDB entry 6H25
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 LEU 71 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ILE* 6.4 3.1 - - + -
64B ARG* 3.3 38.4 - - + +
65B ALA* 4.9 3.4 - - - -
66B LEU* 5.0 15.0 - - + +
70B ALA* 1.3 74.7 - - - +
72B VAL* 1.3 78.3 + - - +
73B ASN* 4.4 11.0 - - + +
119B SER 2.7 11.7 + - - +
120B GLN* 3.5 16.1 - - + +
121B ILE* 2.9 28.1 + - - +
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Residues in contact with VAL 72 (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* 1.3 85.8 - - - +
73B ASN* 1.3 62.5 + - - +
74B CYS* 3.8 23.1 - - - -
104B ARG* 3.7 29.4 + - + +
107B PHE* 3.7 34.5 - - + +
108B GLU* 4.7 13.6 - - + +
111B ILE* 4.3 6.5 - - + -
113B THR* 4.3 19.5 - - + -
121B ILE* 3.4 18.4 - - + +
123B ILE* 4.4 6.5 - - + -
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Residues in contact with ASN 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ARG* 5.9 2.4 - - - +
71B LEU* 4.2 9.7 - - + +
72B VAL* 1.3 73.2 - - - +
74B CYS* 1.3 71.9 + - - +
75B GLN* 4.5 3.0 + - - +
104B ARG* 4.1 14.0 + - - +
120B GLN* 4.0 25.1 - - + +
121B ILE 2.9 10.5 + - - +
122B ASP* 3.3 7.5 - - + +
123B ILE 2.8 26.7 + - - +
124B TYR* 5.0 12.9 + - - -
94E GLU* 6.1 2.6 - - - +
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Residues in contact with CYS 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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72B VAL* 3.8 21.1 + - - -
73B ASN* 1.3 87.5 + - - +
75B GLN* 1.3 61.0 + - - +
76B TYR 4.3 0.4 - - - -
100B GLY* 3.7 30.1 - - - +
101B LEU* 6.1 0.5 - - - +
103B LEU* 3.8 18.4 - - + -
104B ARG* 3.8 27.0 + - + +
107B PHE* 5.1 0.4 - - - -
123B ILE* 3.4 28.5 - - + +
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Residues in contact with GLN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ASN* 4.3 3.6 - - - +
74B CYS* 1.3 74.9 - - - +
76B TYR* 1.3 70.0 + - - +
77B SER* 4.0 9.6 + - - -
96B SER* 5.9 0.4 - - - +
100B GLY* 4.9 1.1 - - - -
123B ILE 3.3 6.5 + - - +
124B TYR* 3.3 32.4 - - + -
125B VAL* 3.5 24.4 + - - +
87E ALA* 3.5 9.8 - - - +
94E GLU* 2.8 34.4 + - - +
95E GLY* 4.1 7.9 + - - -
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Residues in contact with TYR 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 CYS 4.3 0.2 - - - -
75B GLN* 1.3 78.1 - - - +
77B SER* 1.3 62.9 + - - +
78B SER* 4.2 24.5 - - - -
95B LYS* 5.9 3.6 - - + -
96B SER* 2.8 42.8 + - - +
99B MET* 3.6 37.7 - - + +
100B GLY* 4.0 24.0 - - - +
103B LEU* 5.9 3.8 - - + -
125B VAL* 4.0 12.8 - - + -
127B VAL* 4.1 12.8 - - + +
134B THR* 3.3 23.2 - - + +
138B CYS* 3.5 30.7 - - + -
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Residues in contact with SER 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 GLN* 4.0 12.0 + - - -
76B TYR* 1.3 79.3 - - - +
78B SER* 1.3 63.5 + - - +
89B ARG* 5.6 7.6 - - - -
96B SER* 5.7 0.4 - - - -
125B VAL 3.4 13.4 + - - +
126B GLN* 3.4 38.1 + - - +
127B VAL 3.4 2.9 + - - -
84E ASP* 5.2 8.7 + - - -
86E SER* 5.3 4.1 - - - -
87E ALA* 5.5 5.7 + - - +
88E SER* 5.4 0.3 + - - -
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Residues in contact with SER 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TYR* 4.2 24.3 + - - -
77B SER* 1.3 76.1 - - - +
79B ALA* 1.3 74.4 + - - +
80B THR* 3.8 1.4 + - - +
82B SER* 4.0 13.3 + - - -
89B ARG* 4.3 18.6 - - - +
96B SER* 6.1 0.4 - - - -
126B GLN* 5.4 0.9 - - - -
127B VAL* 4.1 13.2 + - - +
84E ASP* 4.7 6.2 - - - +
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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