Contacts of the helix formed by residues 90 - 99 (chain B) in PDB entry 2W77
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 90 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B GLN* 4.7 8.7 + - - +
45B GLU* 3.8 33.7 + - - +
89B LEU* 1.3 74.6 - - - +
91B PRO* 1.3 81.4 - - - +
92B ASN* 3.3 20.7 - - - +
93B GLN* 3.4 18.9 + - + +
94B ALA* 3.0 20.6 + - - +
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Residues in contact with PRO 91 (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 GLN 3.9 21.3 - - - +
46B VAL* 4.4 11.7 - - + -
48B PHE* 4.3 15.3 - - + -
62B PHE* 3.6 13.3 - - + -
66B ALA* 5.2 7.2 - - + -
68B ILE* 6.0 4.5 - - + -
89B LEU 3.5 1.5 - - - +
90B GLU* 1.3 92.8 - - - +
92B ASN* 1.3 66.0 + - - +
94B ALA* 3.0 14.6 + - - +
95B ILE* 3.1 12.3 + - - +
108B PHE* 5.2 2.7 - - + -
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Residues in contact with ASN 92 (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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90B GLU* 3.3 21.7 - - - +
91B PRO* 1.3 78.5 - - - +
93B GLN* 1.3 76.8 + - - +
95B ILE* 3.8 3.7 - - - +
96B THR* 3.2 22.2 + - - +
108B PHE* 3.5 37.8 - - + -
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Residues in contact with GLN 93 (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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89B LEU* 3.7 26.6 - - + +
90B GLU* 3.4 29.2 + - + +
91B PRO 3.1 0.8 - - - -
92B ASN* 1.3 81.5 + - - +
94B ALA* 1.3 66.2 + - - +
96B THR* 3.2 14.7 + - + +
97B GLU* 3.0 25.7 + - + +
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Residues in contact with ALA 94 (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 PHE* 3.5 25.6 - - + -
62B PHE* 3.5 18.4 - - + -
85B ILE* 3.6 10.8 - - + +
89B LEU* 3.8 19.7 - - + -
90B GLU 3.0 7.0 + - - +
91B PRO 3.0 8.6 + - - +
93B GLN* 1.3 75.7 - - - +
95B ILE* 1.3 65.0 + - - +
97B GLU* 3.1 1.6 + - - -
98B LEU* 2.9 25.8 + - - +
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Residues in contact with ILE 95 (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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59B LEU* 3.7 29.6 - - + -
62B PHE* 3.5 33.8 - - + -
91B PRO 3.1 10.5 + - - +
92B ASN 3.8 12.6 - - - +
94B ALA* 1.3 78.2 - - - +
96B THR* 1.3 66.9 + - - +
98B LEU* 3.5 11.2 + - + -
99B LEU* 3.2 32.5 + - + +
106B VAL* 4.2 12.3 - - + -
108B PHE* 3.9 22.0 - - + -
113B ILE* 3.8 18.2 - - + -
115B ILE* 4.0 14.6 - - + -
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Residues in contact with THR 96 (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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92B ASN 3.2 18.5 + - - +
93B GLN* 3.2 18.4 - - + +
94B ALA 3.1 0.2 - - - -
95B ILE* 1.3 84.5 - - - +
97B GLU* 1.3 61.9 + - + +
99B LEU* 3.8 10.4 + - - +
100B ARG* 3.8 12.0 + - - +
106B VAL* 4.5 14.7 - - - +
108B PHE* 5.9 1.9 - - - -
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Residues in contact with GLU 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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83B SER* 2.8 26.2 + - - +
84B ALA 4.5 8.3 - - - +
85B ILE* 3.8 17.0 - - + -
89B LEU* 5.7 2.5 - - + -
93B GLN* 3.0 17.4 + - + +
94B ALA* 3.1 0.6 + - - -
96B THR* 1.3 79.4 - - + +
98B LEU* 1.3 60.8 + - - +
99B LEU 3.0 1.8 - - - -
100B ARG* 2.8 42.2 + - - +
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Residues in contact with LEU 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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50B ILE* 4.1 24.5 - - + -
55B LEU* 4.0 14.1 - - + -
58B ALA* 4.4 10.8 - - + +
59B LEU* 4.1 4.7 - - + -
62B PHE* 4.2 11.7 - - + -
82B SER* 3.4 16.7 - - - -
83B SER 2.9 35.3 + - - +
85B ILE* 3.6 27.3 - - + +
94B ALA 2.9 16.3 + - - +
95B ILE* 3.9 13.0 - - + +
97B GLU* 1.3 77.8 - - - +
99B LEU* 1.3 78.9 + - + +
100B ARG 3.3 0.9 - - - -
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Residues in contact with LEU 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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55B LEU* 3.6 37.5 - - + -
59B LEU* 4.1 9.0 - - + -
95B ILE* 3.2 16.7 + - + +
96B THR* 4.0 7.2 - - - +
97B GLU 3.0 0.8 - - - -
98B LEU* 1.3 85.7 - - + +
100B ARG* 1.3 65.5 + - - +
101B GLY 3.1 0.7 + - - -
102B THR* 2.9 34.0 + - - +
103B GLY 4.3 1.2 + - - -
104B ALA* 3.9 23.1 + - + +
106B VAL* 3.5 32.3 - - + -
115B ILE* 3.7 22.9 - - + -
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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