Contacts of the helix formed by residues 91 - 104 (chain A) in PDB entry 2ENV
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 CYS 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A CYS* 3.4 6.7 - - + -
77A CYS* 3.8 5.8 - - - -
79A ASP* 4.1 8.3 - - + +
80A LYS 3.3 22.9 - - - +
82A SER* 4.0 9.4 - - - +
85A HIS* 5.2 0.2 - - - -
90A ALA* 1.3 75.6 - - - +
92A GLU* 1.3 67.1 + - - +
93A GLY* 3.7 7.2 - - - -
94A CYS* 3.4 16.2 - - - -
95A LYS* 2.9 26.8 + - - +
122A ARG* 5.6 2.5 - - - -
200A ZN 2.2 35.4 - - - -
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Residues in contact with GLU 92 (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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82A SER* 3.7 25.6 + - - +
91A CYS* 1.3 73.7 - - - +
93A GLY* 1.3 66.6 + - - +
95A LYS* 2.9 33.9 + - - +
96A GLY* 3.0 18.5 + - - -
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Residues in contact with GLY 93 (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 CYS* 3.3 7.1 - - - -
92A GLU* 1.3 82.1 - - - +
94A CYS* 1.3 65.4 + - - +
96A GLY* 3.1 6.6 + - - -
97A PHE* 3.3 9.8 + - - +
122A ARG* 6.3 2.5 - - - -
129A ARG* 5.3 3.4 + - - -
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Residues in contact with CYS 94 (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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74A CYS* 4.3 1.6 - - - -
76A VAL* 3.3 42.4 - - + -
77A CYS* 3.6 11.4 - - - -
90A ALA* 4.5 0.7 - - + -
91A CYS* 3.4 6.2 - - - +
93A GLY* 1.3 70.5 - - - +
95A LYS* 1.3 68.9 + - - +
97A PHE* 2.7 22.7 + - - +
98A PHE* 3.1 11.0 + - - +
117A ILE* 5.3 1.3 - - - -
122A ARG* 5.2 4.9 - - - +
129A ARG* 5.6 9.9 - - + +
133A CYS* 5.4 2.4 - - - -
138A MET* 6.0 0.2 - - + -
200A ZN 2.4 35.9 - - - -
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Residues in contact with LYS 95 (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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82A SER* 5.1 0.2 + - - -
85A HIS* 3.4 47.9 + - + +
86A TYR* 3.8 24.5 - - + +
90A ALA* 4.4 11.0 - - + +
91A CYS 2.9 23.0 + - - +
92A GLU* 2.9 29.4 + - - +
94A CYS* 1.3 73.3 - - - +
96A GLY* 1.3 68.9 + - - +
98A PHE* 3.1 7.1 + - - +
99A ARG* 3.1 34.6 + - + +
138A MET* 4.9 2.2 - - - -
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Residues in contact with GLY 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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92A GLU 3.0 14.9 + - - -
93A GLY 3.6 4.5 - - - -
94A CYS 3.0 0.2 + - - -
95A LYS* 1.3 77.5 - - - +
97A PHE* 1.3 62.3 + - - +
99A ARG* 4.0 5.2 - - - +
100A ARG* 2.9 26.8 + - - +
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Residues in contact with PHE 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 GLY 3.3 7.3 + - - +
94A CYS 2.7 15.3 + - - +
96A GLY* 1.3 71.6 - - - +
98A PHE* 1.3 72.8 + - + +
100A ARG* 3.1 17.4 + - - +
101A THR* 2.9 35.7 + - - -
108A TYR* 3.8 16.6 - + - -
126A GLN* 2.9 46.9 - - - -
129A ARG* 3.1 51.6 - - + +
130A PHE* 3.4 29.8 - + + -
133A CYS* 5.2 3.4 - - - -
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Residues in contact with PHE 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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86A TYR* 4.1 22.4 - + - -
94A CYS 3.1 4.6 + - - +
95A LYS 3.4 7.9 - - - +
97A PHE* 1.3 83.8 - - - +
99A ARG* 1.3 79.1 + - - +
101A THR* 2.7 19.7 + - - -
102A ILE* 3.1 30.8 + - + +
130A PHE* 3.8 24.5 - + - -
133A CYS* 3.5 23.1 - - + -
134A LEU* 4.5 9.4 - - + -
138A MET* 3.3 58.6 - - + -
139A SER 4.0 16.4 - - - -
140A HIS* 4.5 5.8 - - + -
143A ILE* 4.7 0.9 - - + -
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Residues in contact with ARG 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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86A TYR* 2.8 32.6 + - - +
95A LYS* 3.1 26.7 + - + +
96A GLY* 4.0 4.5 - - - +
98A PHE* 1.3 79.3 - - - +
100A ARG* 1.3 57.2 + - - +
102A ILE* 2.8 4.3 + - - +
103A ARG* 2.8 44.2 + - + +
143A ILE* 3.8 40.3 + - + +
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Residues in contact with ARG 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 GLY 2.9 20.3 + - - +
97A PHE* 3.2 21.9 + - - +
98A PHE 2.9 0.2 + - - -
99A ARG* 1.3 76.0 - - - +
101A THR* 1.3 57.1 + - - +
103A ARG* 3.9 12.3 - - + +
104A MET* 2.8 59.3 + - - +
106A LEU* 3.9 23.0 - - + +
108A TYR* 4.4 10.7 + - - -
126A GLN* 4.9 5.3 - - - +
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Residues in contact with THR 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 PHE* 2.9 36.9 + - - -
98A PHE 2.7 14.3 + - - -
100A ARG* 1.3 73.5 + - - +
102A ILE* 1.3 56.8 + - - +
105A LYS* 2.9 20.1 + - - -
106A LEU* 3.0 37.5 + - + +
108A TYR* 4.2 9.4 + - + -
130A PHE* 3.4 39.7 - - + -
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Residues in contact with ILE 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 PHE* 3.4 40.6 - - + +
99A ARG* 2.8 9.1 + - - +
101A THR* 1.3 75.3 - - - +
103A ARG* 1.3 61.9 + - - +
104A MET 3.0 1.3 - - - -
105A LYS* 2.7 34.1 + - - +
130A PHE* 3.8 28.7 - - + -
134A LEU* 6.0 0.4 - - + -
140A HIS* 4.5 19.5 - - + +
143A ILE* 3.7 26.2 - - + -
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Residues in contact with ARG 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 ARG* 2.8 28.1 + - + +
100A ARG* 3.5 19.3 - - - +
102A ILE* 1.3 75.1 - - - +
104A MET* 1.3 75.4 + - + +
105A LYS* 3.2 21.1 + - - +
143A ILE* 5.0 10.1 - - + +
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Residues in contact with MET 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 ARG* 2.8 51.8 + - + +
103A ARG* 1.3 94.3 - - + +
105A LYS* 1.3 73.8 + - - +
106A LEU* 3.3 29.8 + - + +
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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