Contacts of the strand formed by residues 77 - 84 (chain B) in PDB entry 4O6M
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 PHE 77 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B VAL* 3.1 2.9 - - - -
74B SER* 2.8 36.5 + - - +
75B ASP* 3.0 27.9 + - + -
76B GLY* 1.3 78.4 - - - +
78B THR* 1.3 63.8 + - - +
79B VAL* 3.3 1.7 + - - +
117B LYS* 3.7 36.6 - - + -
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Residues in contact with THR 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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55B GLU* 5.4 6.2 - - - +
71B ILE* 3.7 28.1 - - + +
72B LEU 3.5 4.0 - - - -
73B VAL* 4.1 6.4 - - - +
76B GLY 3.8 3.3 + - - -
77B PHE* 1.3 71.3 - - - +
79B VAL* 1.3 62.5 + - - +
80B GLY 4.0 12.1 - - - +
81B TYR* 4.0 28.0 - - + +
117B LYS* 4.4 14.6 - - - -
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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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53B ILE* 3.9 23.0 - - + +
54B LEU 4.6 3.3 + - - -
55B GLU* 4.7 6.8 + - - +
57B VAL* 3.9 32.9 - - + +
59B ILE* 5.5 2.0 - - + -
72B LEU* 2.6 19.8 + - + +
73B VAL 3.7 4.3 - - - -
74B SER* 3.5 41.1 - - - +
77B PHE 3.8 1.6 - - - +
78B THR* 1.3 75.0 - - - +
80B GLY* 1.3 56.5 + - - +
113B ILE* 4.0 22.9 - - + -
115B ALA* 4.4 3.4 - - + -
117B LYS* 5.5 7.9 - - + -
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Residues in contact with GLY 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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51B LEU* 4.9 3.1 - - - -
52B ILE 3.1 13.7 - - - -
53B ILE* 4.4 7.2 - - - -
54B LEU 5.4 0.2 - - - -
71B ILE* 3.9 6.4 - - - +
72B LEU* 2.9 33.8 + - - +
78B THR* 3.7 2.8 - - - +
79B VAL* 1.3 81.7 - - - +
81B TYR* 1.3 70.2 + - - -
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Residues in contact with TYR 81 (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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50B TYR 3.7 1.0 - - - +
51B LEU* 3.4 6.0 - - - +
52B ILE* 2.7 58.4 + - + +
54B LEU* 3.6 31.5 - - + +
70B LYS 4.3 2.2 - - - -
71B ILE* 4.5 17.7 - - + +
78B THR* 4.0 25.0 - - + +
80B GLY* 1.3 77.0 - - - -
82B PHE* 1.3 60.2 + - - +
83B PHE* 3.5 39.8 + + + -
99B ILE* 4.3 14.9 - - + +
103B LEU* 4.2 19.2 - - + +
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Residues in contact with PHE 82 (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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2B ARG* 3.2 30.7 - - - -
34B PHE* 4.1 7.6 - + - -
49B ASP* 3.8 28.0 - - + -
50B TYR 3.3 13.9 - - - -
51B LEU* 4.4 10.1 - - + -
66B LEU* 3.4 37.7 - - + -
68B GLY 3.1 36.3 - - - -
69B ARG* 3.7 4.4 - - - +
70B LYS* 3.0 44.3 + - + +
72B LEU* 4.7 10.0 - - + +
80B GLY 4.2 0.8 + - - -
81B TYR* 1.3 71.1 - - - +
83B PHE* 1.3 68.7 + - - +
108B LEU* 5.0 0.2 - - - +
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Residues in contact with PHE 83 (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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49B ASP* 4.1 2.9 - - - +
50B TYR* 2.8 36.1 + - + +
52B ILE* 4.1 13.7 - - + -
69B ARG* 5.4 1.6 - - - +
81B TYR* 3.5 36.1 - + + -
82B PHE* 1.3 87.2 - - - +
84B GLY* 1.3 65.6 + - - +
87B PHE* 3.6 37.9 - + + -
99B ILE* 4.1 20.2 - - + -
102B TYR* 3.2 37.5 - + + -
103B LEU* 4.1 9.0 - - + -
108B LEU* 3.4 27.4 - - + -
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Residues in contact with GLY 84 (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 GLU 4.0 3.8 - - - -
49B ASP* 4.9 3.1 - - - -
50B TYR* 3.5 5.2 - - - -
69B ARG* 5.3 4.4 - - - +
83B PHE* 1.3 78.1 - - - +
85B GLY* 1.3 66.2 + - - -
86B ASP* 3.1 11.7 - - - -
87B PHE* 3.1 18.7 + - - +
102B TYR* 3.2 10.7 + - - -
418B SO4 4.0 21.5 + - - -
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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