Contacts of the helix formed by residues 96 - 108 (chain B) in PDB entry 5VXA
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 PRO 96 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94B THR 4.6 1.6 - - - +
95B LEU* 1.3 95.9 - - + +
97B LYS* 1.3 66.6 + - - +
98B LEU* 3.3 6.1 - - + +
99B GLU* 3.0 16.0 + - + +
100B ARG* 3.0 19.0 + - - +
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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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95B LEU 3.7 0.4 + - - -
96B PRO* 1.3 73.0 - - - +
98B LEU* 1.3 75.4 + - + +
100B ARG* 3.2 30.4 + - - +
101B LYS* 3.0 41.9 + - + +
202B NDP 3.5 26.7 - - - +
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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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96B PRO* 3.3 4.4 - - + +
97B LYS* 1.3 90.4 - - + +
99B GLU* 1.3 57.8 + - - +
101B LYS* 3.4 13.4 + - + +
102B ARG* 3.0 26.9 + - - +
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Residues in contact with GLU 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 LEU* 4.1 26.0 - - + -
96B PRO* 3.0 26.0 + - + +
98B LEU* 1.3 76.6 - - - +
100B ARG* 1.3 59.4 + - - +
102B ARG* 2.9 43.2 + - - -
103B LEU* 2.9 42.1 + - + +
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Residues in contact with ARG 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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91B ASP* 3.8 32.4 + - + +
92B ASP 3.3 26.7 - - - +
93B LYS* 3.7 23.4 + - - +
95B LEU* 2.5 33.8 + - + +
96B PRO* 3.0 12.7 + - - +
97B LYS* 3.4 35.8 - - - +
99B GLU* 1.3 75.6 - - - +
101B LYS* 1.3 63.6 + - + +
103B LEU* 3.6 8.0 + - - +
104B GLN* 3.1 29.7 + - - +
202B NDP 4.4 17.0 + - - -
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Residues in contact with LYS 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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97B LYS* 3.0 37.0 + - + +
98B LEU* 3.8 14.4 - - + +
99B GLU 3.2 0.2 - - - -
100B ARG* 1.3 73.1 - - + +
102B ARG* 1.3 67.8 + - - +
104B GLN* 3.3 8.5 + - - +
105B VAL* 3.3 5.9 + - - +
146B TYR* 4.0 12.9 - - - +
149B TRP* 2.9 75.4 + - + +
202B NDP 2.9 33.7 + - - -
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Residues in contact with ARG 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 LEU 3.0 17.6 + - - +
99B GLU* 2.9 37.4 + - - +
101B LYS* 1.3 75.9 - - - +
103B LEU* 1.3 76.0 + - - +
105B VAL* 2.9 26.3 + - + +
106B GLU* 2.9 43.5 + - + +
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Residues in contact with LEU 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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92B ASP* 5.6 2.2 - - + -
95B LEU* 3.6 31.2 - - + -
99B GLU* 2.9 29.2 + - - +
100B ARG* 3.9 6.5 - - - +
102B ARG* 1.3 90.7 - - - +
104B GLN* 1.3 56.6 + - - +
106B GLU* 3.7 26.2 - - - +
107B GLN* 2.8 60.0 + - - +
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Residues in contact with GLN 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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91B ASP* 3.0 36.5 + - - +
100B ARG* 3.1 19.1 + - - +
101B LYS* 3.5 10.0 - - - +
102B ARG 3.1 0.4 - - - -
103B LEU* 1.3 75.9 - - - +
105B VAL* 1.3 62.0 + - - +
107B GLN* 4.1 3.0 - - - +
108B ALA* 3.2 24.8 + - - +
119B LYS* 5.2 8.8 + - - +
123B LYS* 3.0 29.2 + - - +
149B TRP* 3.3 25.4 - - + -
153B VAL* 4.0 13.4 - - + +
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Residues in contact with VAL 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 LYS 3.3 13.2 + - - +
102B ARG* 2.9 11.7 + - + +
104B GLN* 1.3 79.5 - - - +
106B GLU* 1.3 63.8 + - - +
107B GLN 3.5 0.2 + - - -
108B ALA* 3.5 8.5 + - - +
109B PRO* 3.7 8.8 - - - +
149B TRP* 3.8 7.0 - - + +
152B GLN* 3.7 45.3 - - + +
153B VAL* 3.7 22.9 - - + +
156B GLY* 5.5 1.0 - - - -
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Residues in contact with GLU 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 ARG* 2.9 49.4 + - + +
103B LEU* 3.3 21.4 + - - +
105B VAL* 1.3 79.2 - - - +
107B GLN* 1.3 64.6 + - + +
109B PRO* 3.6 11.8 - - - +
110B HIS* 3.6 17.3 + - + +
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Residues in contact with GLN 107 (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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88B GLU 4.9 8.1 - - - +
103B LEU* 2.8 55.9 + - + +
104B GLN* 4.6 2.0 - - - +
106B GLU* 1.3 79.1 + - + +
108B ALA* 1.3 65.0 + - - +
109B PRO 3.5 0.4 - - - -
110B HIS* 3.3 18.8 + - + +
111B SER* 3.0 14.8 + - - -
119B LYS* 4.4 9.6 + - - +
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Residues in contact with ALA 108 (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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104B GLN 3.2 18.4 + - - +
105B VAL 3.8 4.0 - - - +
106B GLU 3.4 0.2 - - - -
107B GLN* 1.3 76.2 - - - +
109B PRO* 1.3 70.7 - - + +
111B SER* 3.1 20.6 + - - -
116B LYS* 3.5 11.4 - - - -
119B LYS* 4.3 3.8 - - - +
153B VAL* 3.6 28.3 - - + +
156B GLY* 3.8 5.6 - - - -
157B LEU* 3.6 18.1 - - + +
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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