Contacts of the helix formed by residues 95 - 104 (chain A) in PDB entry 2NVT
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 PHE 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A LEU* 3.5 34.1 - - + -
92A HIS* 2.6 50.1 + + + +
94A GLY* 1.3 80.0 - - - -
96A ILE* 1.3 54.1 + - - +
97A ALA 3.4 2.2 - - - -
98A LYS* 3.7 9.6 - - + -
99A ILE* 2.5 39.7 + - + +
233A TRP 5.7 0.2 - - - -
234A MET* 3.6 48.2 - - + +
1410A PHE* 4.0 33.0 - + + -
1411A GLU* 4.8 0.7 - - - -
1414A ALA* 3.8 22.7 - - + -
1212B ILE* 5.0 1.6 - - + -
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Residues in contact with ILE 96 (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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91A PHE* 3.4 51.1 - - + -
92A HIS 4.0 0.6 + - - -
93A VAL* 3.5 25.2 + - - +
94A GLY 3.6 0.2 - - - -
95A PHE* 1.3 74.1 - - - +
97A ALA* 1.3 71.6 + - - +
99A ILE* 3.3 7.8 - - + +
100A LYS* 3.0 25.4 + - + +
176A LYS* 3.3 44.2 - - + +
179A LEU* 4.3 17.7 - - + +
181A LEU* 4.9 9.4 - - + -
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Residues in contact with ALA 97 (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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93A VAL 5.0 0.6 + - - -
94A GLY 5.3 4.9 - - - +
95A PHE 5.1 0.4 - - - -
96A ILE* 1.3 81.3 - - - +
98A LYS* 1.3 56.9 + - - +
100A LYS* 3.6 8.6 - - - +
101A LYS* 3.0 38.9 + - - +
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Residues in contact with LYS 98 (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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94A GLY 5.4 0.9 - - - +
95A PHE* 3.2 15.0 + - + +
96A ILE 3.1 0.6 - - - -
97A ALA* 1.3 73.9 - - - +
99A ILE* 1.3 55.8 + - - +
100A LYS 3.1 1.1 - - - -
101A LYS* 2.7 13.7 + - + -
102A VAL* 2.6 46.8 + - + +
132A LYS* 5.2 5.9 - - - +
135A PHE* 4.8 24.2 - - + -
224A PHE* 4.7 10.5 - - + -
234A MET* 3.9 20.4 - - + -
1411A GLU* 4.1 24.1 + - + +
1414A ALA* 4.6 17.3 - - + -
1415A SER* 4.0 18.3 + - - -
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Residues in contact with ILE 99 (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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91A PHE* 4.3 12.8 - - + -
95A PHE* 2.5 18.3 + - + +
96A ILE* 3.3 19.3 - - + +
98A LYS* 1.3 71.0 - - - +
100A LYS* 1.3 59.6 + - - +
102A VAL* 3.7 4.0 + - - +
103A CYS* 3.1 33.0 + - - -
181A LEU* 3.9 22.2 - - + -
207A ILE* 5.4 4.7 - - + -
211A PHE* 4.0 13.9 - - + -
231A PRO 4.4 2.5 - - - +
234A MET* 3.3 49.6 - - + +
235A ILE* 3.7 30.5 - - + +
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Residues in contact with LYS 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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96A ILE* 3.0 14.2 + - + +
97A ALA* 3.6 7.9 - - - +
98A LYS 2.9 0.4 + - - -
99A ILE* 1.3 81.2 - - - +
101A LYS* 1.3 63.3 + - + +
103A CYS* 2.8 24.4 + - - +
104A GLU* 3.0 36.1 + - - +
174A ILE* 3.8 30.9 + - + -
175A ARG* 4.2 12.6 - - - +
176A LYS* 4.3 10.1 - - + +
181A LEU* 3.9 26.7 - - + -
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Residues in contact with LYS 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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97A ALA* 3.0 25.3 + - + +
98A LYS* 2.7 14.4 + - + +
100A LYS* 1.3 75.3 - - + +
102A VAL* 1.3 59.7 + - - +
104A GLU* 3.6 11.6 + - - +
105A CYS* 3.6 9.0 - - - -
135A PHE* 4.1 25.4 - - + -
139A TRP* 3.2 55.5 - - + +
5N T 3.3 27.4 + - - -
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Residues in contact with VAL 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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98A LYS* 2.6 27.6 + - + +
99A ILE* 3.9 1.6 - - - +
101A LYS* 1.3 71.2 - - - +
103A CYS* 1.3 58.8 + - - +
105A CYS* 3.1 16.4 + - + +
106A VAL* 3.0 26.3 + - + +
135A PHE* 4.0 23.3 - - + -
211A PHE* 3.1 34.3 - - + -
214A ILE* 5.7 0.4 - - + -
222A LEU* 5.0 11.7 - - + -
224A PHE* 4.2 12.3 - - + -
231A PRO* 5.1 1.6 - - + -
234A MET* 4.2 15.3 - - + -
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Residues in contact with CYS 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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99A ILE* 3.1 22.8 + - - +
100A LYS* 2.8 12.5 + - - +
102A VAL* 1.3 73.4 - - - +
104A GLU* 1.3 58.9 + - - +
105A CYS 3.0 5.8 + - - -
106A VAL* 3.3 20.6 + - - +
108A MET* 4.2 22.6 - - + +
171A GLN* 5.2 0.5 - - - +
174A ILE* 3.3 26.5 - - + +
181A LEU* 5.7 5.6 - - + -
202A LEU* 5.6 1.6 - - - -
207A ILE* 4.3 15.0 - - - -
211A PHE* 3.5 23.6 - - - -
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Residues in contact with GLU 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 LYS* 3.0 50.2 + - - +
101A LYS* 3.6 6.1 - - - +
102A VAL 3.4 0.2 - - - -
103A CYS* 1.3 74.8 - - - +
105A CYS* 1.3 58.6 - - - +
106A VAL 4.9 0.9 - - - -
114A LEU* 4.4 5.2 - - - +
139A TRP* 3.6 32.8 + - + +
142A CYS* 3.5 23.7 - - - +
143A LYS* 4.0 29.0 - - + +
172A PRO 5.8 1.3 - - - +
174A ILE* 4.6 20.8 - - + +
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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