Contacts of the helix formed by residues 92 - 101 (chain B) in PDB entry 2QJ3
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 VAL 92 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B PRO 5.2 0.4 - - - +
8B GLY* 4.5 1.8 - - - -
9B GLN* 3.8 24.9 - - + +
60B GLN* 3.4 67.5 - - + +
63B ILE* 5.4 4.9 - - + -
64B VAL* 4.1 11.9 - - + +
90B HIS 3.2 0.2 + - - -
91B SER* 1.3 89.4 + - - +
93B GLY* 1.3 65.7 + - - +
95B ILE* 2.8 29.4 + - + +
96B ALA 3.8 1.4 + - - -
113B ALA* 4.1 8.1 - - + -
116B ARG* 3.1 11.1 - - - +
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Residues in contact with GLY 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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6B ALA* 3.2 20.7 - - - +
7B PRO 3.3 22.3 + - - -
64B VAL* 5.4 0.7 - - - -
89B GLY* 3.5 7.0 - - - -
90B HIS 2.9 12.4 + - - -
92B VAL* 1.3 78.5 - - - +
94B GLU* 1.3 49.5 + - - +
96B ALA* 3.2 6.9 + - - -
97B ALA* 2.7 31.9 + - - +
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Residues in contact with GLU 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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89B GLY* 3.5 14.7 - - - +
91B SER 3.1 11.2 + - - +
92B VAL 2.8 4.0 + - - -
93B GLY* 1.3 72.5 - - - +
95B ILE* 1.3 50.5 + - - +
97B ALA* 3.3 7.3 - - - +
98B TYR* 2.6 53.8 + - + -
222B LEU 4.0 3.4 - - - +
223B SER* 3.3 12.5 + - - -
224B ASN* 2.6 57.4 + - - +
239B THR* 5.8 0.5 - - - +
240B LEU* 3.4 27.3 - - + +
243B GLN* 3.8 17.0 - - - +
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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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64B VAL* 4.3 7.0 - - + -
92B VAL* 2.8 22.7 + - + +
94B GLU* 1.3 69.1 - - + +
96B ALA* 1.3 65.0 + - - +
98B TYR* 3.1 10.3 + - - +
99B ALA* 3.1 21.5 + - - +
104B ILE* 3.9 8.6 - - + +
109B ALA* 3.3 36.3 - - + +
112B LEU* 4.3 14.1 - - + -
113B ALA* 3.8 27.8 - - + +
116B ARG* 4.2 22.4 - - - +
205B PHE* 4.5 3.4 - - + -
240B LEU* 4.1 22.0 - - + -
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Residues in contact with ALA 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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6B ALA* 3.9 2.9 - - + -
63B ILE* 6.3 0.4 - - + -
64B VAL* 4.0 25.6 - - + +
67B THR* 3.8 32.3 - - + +
68B LEU* 3.5 14.3 - - + +
92B VAL 3.8 1.6 + - - -
93B GLY* 3.2 11.1 + - - +
95B ILE* 1.3 78.5 - - - +
97B ALA* 1.3 57.6 + - - +
99B ALA* 3.3 2.2 + - - -
100B ILE* 2.9 34.8 + - - +
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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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6B ALA* 4.0 2.8 - - + +
87B VAL* 3.9 20.7 - - + +
88B ALA 4.0 1.1 - - - -
89B GLY* 3.5 24.9 - - - +
93B GLY 2.7 21.4 + - - +
94B GLU* 3.3 7.9 - - - +
96B ALA* 1.3 72.0 - - - +
98B TYR* 1.3 59.1 + - + +
100B ILE* 3.3 6.0 + - - +
101B ALA* 2.8 33.4 + - - +
221B LEU* 3.8 10.9 - - + +
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Residues in contact with TYR 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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94B GLU* 2.6 52.0 + - + +
95B ILE* 3.1 7.2 + - - +
97B ALA* 1.3 73.0 - - - +
99B ALA* 1.3 54.9 + - - +
101B ALA 3.7 1.4 - - - -
102B GLY 3.4 2.8 + - - -
103B VAL* 2.7 44.0 + - + +
104B ILE* 3.8 15.9 - - + -
221B LEU* 3.8 27.8 - - + -
222B LEU 5.0 3.4 - - - -
223B SER* 4.8 8.6 - - - -
230B VAL* 5.0 2.3 - - + +
236B ALA* 2.8 48.4 + - + -
237B MET* 4.1 14.1 - - - -
239B THR* 4.4 5.0 - - - +
240B LEU* 3.7 35.2 + - + +
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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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68B LEU* 3.7 18.4 - - + -
71B HIS* 5.3 1.0 + - - -
95B ILE 3.1 11.0 + - - +
96B ALA 3.6 6.7 - - - +
98B TYR* 1.3 74.9 - - - +
100B ILE* 1.3 58.1 - - - +
102B GLY* 2.6 26.5 + - - -
104B ILE* 3.3 29.2 - - + +
105B ALA 4.6 1.6 - - - +
106B ALA* 4.6 4.3 - - + +
109B ALA* 4.1 11.7 - - + -
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Residues in contact with ILE 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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4B LEU* 3.7 20.4 - - + -
6B ALA* 4.4 4.9 - - + +
67B THR* 3.7 27.6 - - + -
68B LEU* 4.1 4.7 - - + +
71B HIS* 3.5 53.2 + - + -
85B VAL* 5.6 0.7 - - + -
87B VAL* 3.8 17.9 - - + +
96B ALA 2.9 27.7 + - - +
97B ALA* 3.6 8.3 - - - +
99B ALA* 1.3 71.0 - - - +
101B ALA* 1.3 58.7 + - - +
102B GLY* 3.0 5.4 + - - -
218B THR* 4.5 5.7 - - - +
219B ALA* 5.6 0.9 - - - +
268B PHE* 3.8 17.9 - - + -
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Residues in contact with ALA 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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87B VAL* 4.2 14.8 - - + -
97B ALA 2.8 21.4 + - - +
98B TYR 4.0 1.6 - - - +
100B ILE* 1.3 71.2 - - - +
102B GLY* 1.3 55.2 + - - +
103B VAL 3.4 2.0 + - - -
217B PRO* 3.5 2.6 - - - +
218B THR* 2.7 36.9 + - - -
219B ALA* 4.2 10.3 - - - +
221B LEU* 3.8 38.1 - - + -
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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