Contacts of the helix formed by residues 92 - 107 (chain A) in PDB entry 2E7G
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 ARG 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A GLU* 2.7 36.5 + - + +
89A ASP* 3.8 7.4 + - - +
91A ALA* 1.3 70.6 - - - +
93A LEU* 1.3 58.2 + - - +
95A ALA* 4.4 4.0 - - + -
96A LEU* 2.7 45.6 + - + +
133A PHE* 3.5 42.1 - - + +
174A ARG* 5.1 23.5 - - + +
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Residues in contact with LEU 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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89A ASP* 3.1 35.6 + - - +
90A HIS* 3.7 16.8 - - + +
92A ARG* 1.3 77.8 - - - +
94A ARG* 1.3 57.5 + - - +
96A LEU* 4.2 0.3 - - - +
97A ASN* 2.9 32.7 + - - +
129A LEU* 3.9 16.0 - - + +
130A THR 4.2 9.6 - - - +
131A PRO* 4.7 12.1 - - + +
133A PHE* 3.1 39.3 - - + -
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Residues in contact with ARG 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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90A HIS* 2.9 49.2 + - - +
91A ALA* 4.1 3.4 - - - +
93A LEU* 1.3 74.6 - - - +
95A ALA* 1.3 60.9 + - - +
97A ASN* 3.9 8.4 + - - +
98A GLY* 2.8 28.4 + - - -
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Residues in contact with ALA 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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91A ALA 2.9 21.8 + - - +
92A ARG* 4.1 3.6 - - + +
94A ARG* 1.3 79.1 - - - +
96A LEU* 1.3 51.3 + - - +
98A GLY* 5.2 0.2 - - - -
99A LEU* 2.7 55.7 + - + +
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Residues in contact with LEU 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 ARG* 2.7 30.9 + - + +
93A LEU 4.2 0.7 - - - +
95A ALA* 1.3 71.3 - - - +
97A ASN* 1.3 60.0 + - - +
99A LEU* 4.2 7.2 - - - -
100A LEU* 3.0 65.7 + - + +
129A LEU* 3.9 16.8 - - + -
133A PHE* 3.4 34.1 - - + -
173A LEU* 4.5 13.2 - - + -
175A ASN* 3.9 20.4 - - - +
177A PRO* 4.3 8.5 - - + -
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Residues in contact with ASN 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 LEU 2.9 22.3 + - - +
94A ARG* 3.9 9.5 + - - +
96A LEU* 1.3 80.8 - - - +
98A GLY* 1.3 61.0 + - - +
100A LEU* 4.1 2.6 - - - +
101A TYR* 3.1 27.8 + - - +
127A VAL* 3.6 33.4 + - - +
129A LEU* 4.7 14.5 - - + +
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Residues in contact with GLY 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 ARG 2.8 16.6 + - - -
95A ALA 4.0 0.2 - - - -
97A ASN* 1.3 81.2 - - - +
99A LEU* 1.3 60.6 + - - +
101A TYR* 3.7 8.2 - - - +
102A LYS* 2.8 34.6 + - - +
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Residues in contact with LEU 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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95A ALA* 2.7 44.8 + - + +
96A LEU 3.8 3.8 - - - +
98A GLY* 1.3 73.6 - - - +
100A LEU* 1.3 52.7 + - - +
102A LYS* 3.8 11.2 - - - +
103A ALA* 2.8 38.4 + - - +
170A GLN* 4.2 10.2 - - - +
172A THR* 4.9 14.1 - - + -
173A LEU* 3.4 46.0 - - + -
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Residues in contact with LEU 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 LEU* 3.0 44.8 + - + +
97A ASN* 4.1 2.9 - - - +
99A LEU* 1.3 77.4 - - + +
101A TYR* 1.3 55.6 + - - +
103A ALA* 4.4 2.7 - - - -
104A LEU* 2.7 47.9 + - + +
127A VAL* 5.2 3.4 - - + -
136A CYS* 3.4 31.0 - - + -
167A LEU* 3.6 26.5 - - + -
173A LEU* 5.3 7.0 - - + -
176A VAL* 4.4 17.5 - - + -
177A PRO* 4.7 7.4 - - + -
179A ILE* 4.3 14.8 - - + -
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Residues in contact with TYR 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 ASN* 3.1 22.7 + - - +
98A GLY* 3.7 8.1 - - - +
100A LEU* 1.3 77.8 - - - +
102A LYS* 1.3 60.2 + - + +
104A LEU* 4.5 1.1 - - - -
105A THR* 2.8 39.0 + - + +
124A LEU* 3.9 33.4 + - + +
125A SER* 4.2 21.8 + - - -
126A LYS* 4.8 0.9 - - - -
127A VAL* 3.6 32.2 - - + +
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Residues in contact with LYS 102 (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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98A GLY 2.8 21.3 + - - +
99A LEU* 3.9 11.9 - - - +
101A TYR* 1.3 75.7 - - + +
103A ALA* 1.3 64.3 + - - +
105A THR* 3.0 6.8 - - + +
106A ASP* 2.6 58.2 + - - +
170A GLN* 5.7 6.7 - - - +
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Residues in contact with ALA 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 LEU 2.8 23.1 + - - +
100A LEU* 4.1 0.4 - - - +
102A LYS* 1.3 75.8 - - - +
104A LEU* 1.3 64.5 + - - +
106A ASP* 3.3 7.7 + - - +
107A LEU* 3.1 27.2 + - - +
167A LEU* 3.4 32.0 - - + +
170A GLN* 4.2 22.0 - - - +
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Residues in contact with LEU 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 LEU* 2.7 43.1 + - + +
101A TYR* 4.3 1.8 - - - +
103A ALA* 1.3 73.6 - - - +
105A THR* 1.3 62.1 + - - +
107A LEU* 3.3 10.4 + - - +
108A LEU* 3.2 25.7 - - + +
124A LEU* 3.5 21.8 - - + -
127A VAL* 4.7 6.1 - - + -
136A CYS* 5.5 0.9 - - - -
138A ALA* 4.7 17.9 - - + -
163A MET* 4.4 20.6 - - + -
167A LEU* 4.1 13.2 - - + +
179A ILE* 3.5 37.2 - - + -
181A PHE* 5.0 8.3 - - + -
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Residues in contact with THR 105 (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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101A TYR* 2.8 34.8 + - + +
102A LYS* 3.0 20.6 - - + +
104A LEU* 1.3 79.5 - - - +
106A ASP* 1.3 65.4 + - - +
108A LEU* 3.3 15.9 + - - +
109A CYS* 2.8 25.8 + - - -
123A GLU* 5.2 7.3 - - - +
124A LEU* 3.6 22.0 + - - +
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Residues in contact with ASP 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 LYS* 2.6 49.4 + - - +
103A ALA* 3.4 9.0 - - - +
104A LEU 3.2 0.4 - - - -
105A THR* 1.3 83.0 - - - +
107A LEU* 1.3 58.2 + - + +
109A CYS* 3.0 32.2 + - - +
110A THR* 3.8 6.2 + - - -
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Residues in contact with LEU 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 ALA 3.1 14.3 + - - +
104A LEU* 3.3 8.5 + - - +
106A ASP* 1.3 72.6 - - + +
108A LEU* 1.3 64.3 + - + +
109A CYS 3.0 9.1 + - - -
110A THR* 3.1 23.8 + - - +
113A VAL* 4.1 14.1 - - + +
114A SER* 3.7 6.2 + - - -
163A MET* 3.8 36.6 - - + +
166A LEU* 3.6 30.3 - - + -
167A LEU* 3.4 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