Contacts of the helix formed by residues 99 - 110 (chain A) in PDB entry 2VWI
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 SER 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A GLY 4.6 0.5 - - - +
98A GLY* 1.3 75.5 - - - -
100A VAL* 1.3 63.0 + - - +
101A LEU* 3.5 9.2 + - - +
102A ASP* 2.9 46.1 + - - +
103A ILE* 3.6 4.0 + - - +
149A ALA 3.8 3.6 - - - -
150A GLY* 3.6 22.8 + - - -
152A ILE 3.2 12.6 - - - -
153A LEU* 4.0 7.4 - - - -
154A LEU* 3.8 10.4 - - - +
1294A ANP 5.2 3.4 - - - -
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Residues in contact with VAL 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A SER* 1.3 70.6 - - - +
101A LEU* 1.3 64.7 + - - +
103A ILE* 3.2 10.5 + - + +
104A ILE* 3.1 24.2 + - + +
118A LEU* 4.3 11.9 - - + -
126A ILE* 4.0 17.3 - - + -
149A ALA* 3.4 9.4 + - + +
152A ILE* 2.9 38.9 + - + +
154A LEU* 3.9 22.9 - - + -
220A LEU* 3.6 35.9 - - + -
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Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A SER* 3.2 8.2 - - - +
100A VAL* 1.3 77.6 - - - +
102A ASP* 1.3 52.8 + - - +
104A ILE* 3.2 15.2 + - + +
105A LYS* 2.8 69.3 + - + +
148A LYS* 6.1 2.7 - - - -
149A ALA* 3.3 9.6 + - + -
150A GLY* 3.7 27.4 - - - +
219A GLU* 3.7 21.3 - - - +
223A GLY 5.2 4.9 - - - +
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Residues in contact with ASP 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A GLY 5.7 0.7 - - - +
98A GLY* 3.5 9.9 - - - -
99A SER* 2.9 38.8 + - - +
101A LEU* 1.3 78.9 - - - +
103A ILE* 1.3 56.7 + - + +
105A LYS* 3.5 13.3 + - - +
106A HIS* 2.7 47.8 + - + -
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Residues in contact with ILE 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A GLY 5.9 1.1 - - - +
99A SER 3.6 6.2 + - - +
100A VAL* 3.2 14.5 + - + +
102A ASP* 1.3 73.2 - - + +
104A ILE* 1.3 66.9 + - - +
106A HIS* 3.3 11.5 + - + +
107A ILE* 3.2 39.2 + - + +
118A LEU* 4.0 14.4 - - + -
126A ILE* 5.5 6.7 - - + -
154A LEU* 3.6 27.8 - - + -
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Residues in contact with ILE 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A VAL* 3.1 16.8 + - + +
101A LEU* 3.2 14.8 + - + +
103A ILE* 1.3 76.6 - - - +
105A LYS* 1.3 58.0 + - + +
107A ILE* 3.2 3.3 + - - +
108A VAL* 2.9 35.4 + - + +
117A VAL* 4.1 20.6 - - + -
118A LEU* 4.1 10.5 - - + -
149A ALA* 3.8 25.4 - - + -
219A GLU* 3.8 16.4 - - + +
220A LEU* 3.8 19.1 - - + -
223A GLY* 3.6 32.5 - - - +
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Residues in contact with LYS 105 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A LEU* 2.8 57.0 + - + +
102A ASP* 3.8 13.9 + - - +
104A ILE* 1.3 73.9 - - + +
106A HIS* 1.3 59.1 + - + +
108A VAL* 3.9 5.9 - - - +
109A ALA* 3.0 30.5 + - - +
109B ALA 5.6 3.7 - - - +
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Residues in contact with HIS 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ASP* 2.7 34.8 + - + -
103A ILE* 3.6 10.6 - - + +
104A ILE 3.3 0.2 - - - -
105A LYS* 1.3 75.8 - - + +
107A ILE* 1.3 66.5 + - + +
109A ALA* 3.4 5.7 + - - +
110A LYS* 3.1 45.8 + - - +
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Residues in contact with ILE 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ILE* 3.2 24.7 + - + +
104A ILE 3.6 5.4 - - - +
106A HIS* 1.3 78.1 - - + +
108A VAL* 1.3 60.3 - - - +
110A LYS* 3.2 22.8 + - - +
112A GLU* 3.7 42.6 + - + +
113A HIS* 3.9 19.5 + - + -
117A VAL* 3.8 27.4 - - + +
118A LEU* 3.8 28.3 - - + -
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Residues in contact with VAL 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ILE* 2.9 34.7 + - + +
105A LYS* 4.1 5.4 - - - +
107A ILE* 1.3 73.0 - - - +
109A ALA* 1.3 60.7 + - - +
110A LYS 2.9 13.0 - - - +
113A HIS* 3.6 25.3 - - + +
117A VAL* 4.5 6.7 - - + -
222A THR 5.0 0.9 - - - +
223A GLY* 4.5 13.9 - - - +
109B ALA 3.7 13.7 - - - +
110B LYS 3.8 4.5 - - - +
111B GLY* 3.6 27.4 - - - +
113B HIS* 3.1 12.8 - - - -
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Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A LYS 3.0 20.1 + - - +
106A HIS* 3.7 7.2 - - - +
108A VAL* 1.3 75.3 - - - +
110A LYS* 1.3 61.0 + - + +
108B VAL* 3.7 27.4 - - + +
109B ALA* 5.2 4.2 + - - +
113B HIS* 3.1 17.0 + - - -
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Residues in contact with LYS 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A HIS* 3.1 31.3 + - - +
107A ILE* 3.2 14.7 + - - +
108A VAL 2.9 16.5 - - - +
109A ALA* 1.3 77.3 - - + +
111A GLY* 1.3 60.2 + - - +
112A GLU* 3.3 28.0 + - + +
113A HIS* 3.7 3.3 + - - -
113B HIS* 3.1 13.5 + - - -
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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