Contacts of the helix formed by residues 91 - 106 (chain B) in PDB entry 2V5Q
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 LYS 91 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88B LEU 5.3 0.8 + - - +
89B LEU 3.3 1.6 - - - +
90B LEU* 1.3 80.5 - - + +
92B PRO* 1.4 58.5 - - + +
93B HIS* 3.2 36.8 - - + +
94B GLN* 2.7 35.5 + - + +
95B ARG 3.2 7.3 + - - -
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Residues in contact with PRO 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 LEU 3.3 9.8 - - - +
91B LYS* 1.4 85.0 - - + +
93B HIS* 1.3 66.2 + - + +
95B ARG* 3.7 12.0 - - + +
96B GLU* 2.9 43.7 + - - +
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Residues in contact with HIS 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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91B LYS* 3.2 45.0 - - + +
92B PRO* 1.3 80.3 - - + +
94B GLN* 1.3 69.1 + - + +
96B GLU* 3.3 7.5 + - - +
97B LYS* 2.9 39.6 + - + +
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Residues in contact with GLN 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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64B PHE* 3.2 37.7 - - + -
88B LEU 4.1 16.6 - - - +
89B LEU* 3.7 8.6 - - + +
91B LYS* 2.7 19.6 + - + +
93B HIS* 1.3 82.8 - - + +
95B ARG* 1.3 62.1 + - - +
97B LYS* 3.5 18.2 + - - +
98B MET* 3.2 23.6 + - - +
212B CYS* 5.4 6.7 + - - +
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Residues in contact with ARG 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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89B LEU* 3.6 27.9 + - + +
91B LYS 3.2 5.7 + - - -
92B PRO* 3.7 14.8 - - + +
93B HIS 3.4 0.2 - - - -
94B GLN* 1.3 75.4 - - - +
96B GLU* 1.3 68.9 + - - +
98B MET* 3.5 8.2 + - + +
99B SER* 3.1 49.3 + - - -
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Residues in contact with GLU 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 PRO* 2.9 27.2 + - - +
93B HIS* 3.7 6.8 - - - +
94B GLN 3.3 0.2 - - - -
95B ARG* 1.3 87.2 - - + +
97B LYS* 1.3 65.3 + - + +
99B SER* 3.1 18.5 + - - +
100B MET* 3.1 15.4 + - - +
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Residues in contact with LYS 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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93B HIS* 2.9 29.3 + - + +
94B GLN* 4.0 22.0 - - - +
95B ARG 3.4 0.4 - - - -
96B GLU* 1.3 78.8 - - + +
98B MET* 1.3 59.3 + - - +
100B MET* 3.4 5.6 + - + +
101B GLU* 3.0 33.8 + - - +
196B GLY 5.1 5.3 - - - +
212B CYS* 3.7 41.3 - - + -
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Residues in contact with MET 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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82B LYS* 5.1 4.9 - - - -
84B VAL* 4.1 31.4 - - + -
89B LEU* 3.9 21.8 - - + -
94B GLN 3.2 16.7 + - - +
95B ARG* 3.7 5.8 - - + +
96B GLU 3.3 0.2 - - - -
97B LYS* 1.3 80.9 - - - +
99B SER* 1.3 61.5 + - - +
101B GLU* 3.4 27.8 - - - +
102B ILE* 3.3 48.6 + - + +
126B VAL* 4.4 15.3 - - + -
128B VAL* 4.5 10.1 - - + -
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Residues in contact with SER 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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95B ARG* 3.1 36.7 + - - -
96B GLU* 3.1 16.6 + - - +
98B MET* 1.3 75.4 - - - +
100B MET* 1.3 62.3 + - - +
102B ILE* 3.9 7.7 - - - +
103B SER* 2.9 30.0 + - - -
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Residues in contact with MET 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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96B GLU 3.1 16.2 + - - +
97B LYS* 3.7 6.7 - - - +
98B MET 3.3 0.2 - - - -
99B SER* 1.3 79.1 + - - +
101B GLU* 1.3 66.2 + - - +
103B SER* 3.3 13.3 + - - +
104B ILE* 2.9 49.9 + - + +
198B ALA 4.5 7.6 - - - +
199B THR* 5.8 0.7 - - - -
200B LYS* 5.6 5.4 - - - -
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Residues in contact with GLU 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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82B LYS* 3.8 22.3 + - - -
97B LYS 3.0 15.0 + - - +
98B MET* 3.4 31.7 - - + +
100B MET* 1.3 76.4 - - - +
102B ILE* 1.3 54.4 + - + +
104B ILE* 3.2 3.0 + - - +
105B HIS* 2.8 43.0 + - - +
194B ASP* 4.9 2.3 - - - +
195B PHE* 3.3 40.2 + - - +
196B GLY* 3.4 19.7 - - - +
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Residues in contact with ILE 102 (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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98B MET* 3.3 47.2 + - + +
99B SER* 3.9 7.0 - - - +
101B GLU* 1.3 77.3 - - + +
103B SER* 1.3 66.4 + - - +
105B HIS* 4.6 0.7 - - - -
106B ARG* 3.0 37.4 + - - +
116B PHE* 3.8 18.2 - - + -
119B PHE* 3.7 49.1 - - + -
126B VAL* 4.4 4.7 - - + -
128B VAL* 4.2 21.1 - - + -
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Residues in contact with SER 103 (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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99B SER 2.9 20.6 + - - -
100B MET* 3.3 22.1 + - - +
102B ILE* 1.3 78.3 - - - +
104B ILE* 1.3 61.2 + - - +
106B ARG* 3.8 24.4 + - - +
107B SER* 4.0 9.2 + - - -
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Residues in contact with ILE 104 (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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100B MET* 2.9 40.7 + - + +
101B GLU 3.7 2.9 - - - +
103B SER* 1.3 76.9 - - - +
105B HIS* 1.3 63.7 + - - +
107B SER* 2.7 24.6 + - - -
108B LEU* 3.3 8.4 - - + +
172B VAL* 4.0 32.8 - - + -
195B PHE* 4.2 9.4 - - + +
198B ALA* 3.4 44.4 - - + +
199B THR* 3.9 11.9 - - - -
200B LYS* 4.2 13.2 - - + +
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Residues in contact with HIS 105 (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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101B GLU* 2.8 27.2 + - - +
102B ILE 4.2 1.1 - - - +
104B ILE* 1.3 73.3 - - - +
106B ARG* 1.3 63.8 + - - +
108B LEU* 3.2 25.4 + - + +
113B VAL* 4.8 1.1 - - + -
114B VAL* 2.7 40.8 + - + +
116B PHE* 3.7 23.7 - + + +
128B VAL* 6.0 0.2 - - - +
130B LEU* 3.7 28.7 - - + +
193B GLY* 4.8 4.5 - - - -
194B ASP* 4.8 3.3 + - - -
195B PHE* 3.6 39.1 + + + +
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Residues in contact with ARG 106 (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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102B ILE* 3.0 27.5 + - - +
103B SER* 3.8 19.7 - - - +
105B HIS* 1.3 76.2 - - - +
107B SER* 1.3 62.9 + - - +
108B LEU 3.2 5.8 + - - +
116B PHE* 3.4 38.9 - - + +
119B PHE* 3.5 34.0 - - - -
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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