Contacts of the helix formed by residues 93 - 106 (chain A) in PDB entry 2A79
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 GLY 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A ALA 5.2 0.2 - - - -
88A GLU 3.1 19.8 + - - -
90A TYR 3.1 4.1 + - - -
92A ALA* 1.3 73.9 - - - +
94A LYS* 1.3 63.8 + - - +
95A ALA 3.3 2.0 - - - -
96A GLU* 3.1 20.0 + - - +
97A VAL* 3.1 11.2 + - - +
146A ARG* 3.4 30.4 - - - -
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Residues in contact with LYS 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLY* 3.8 23.7 + - - +
91A ALA* 2.9 28.8 + - + +
92A ALA* 3.4 8.0 + - - +
93A GLY* 1.3 74.6 - - - +
95A ALA* 1.3 66.4 + - - +
97A VAL* 2.9 21.5 + - + +
98A VAL* 3.0 18.8 + - + +
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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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56A THR* 4.0 6.1 - - - +
60A PHE* 3.6 35.7 + - + +
86A THR* 3.8 12.1 - - - +
87A ALA 5.0 0.4 - - - +
90A TYR* 3.4 35.4 + - + +
91A ALA* 3.8 2.0 - - - +
93A GLY 3.3 0.4 - - - -
94A LYS* 1.3 77.4 - - - +
96A GLU* 1.3 58.5 + - - +
98A VAL* 3.3 1.9 + - - +
99A LEU* 2.9 31.0 + - - +
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Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A THR* 3.6 24.9 - - + +
87A ALA 3.8 2.6 + - - +
88A GLU* 3.2 17.7 + - - -
90A TYR 4.8 0.4 + - - -
93A GLY* 3.1 9.5 + - - +
95A ALA* 1.3 79.8 - - - +
97A VAL* 1.3 61.0 + - - +
99A LEU* 4.6 0.7 - - - -
100A GLY* 3.0 19.1 + - - -
117A THR* 2.8 23.7 + - - -
143A SER* 2.8 25.9 + - - -
146A ARG* 2.7 48.5 + - + -
147A LEU* 3.6 24.8 - - + +
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Residues in contact with VAL 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLY 3.1 14.0 + - - +
94A LYS* 2.9 13.6 + - - +
96A GLU* 1.3 77.4 - - - +
98A VAL* 1.3 58.7 + - + +
100A GLY* 3.1 2.4 + - - -
101A ASN* 2.9 49.4 + - - +
146A ARG* 3.9 32.4 - - + +
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Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PHE* 3.8 9.4 - - + -
61A GLY* 3.6 20.2 - - - +
66A ASP* 3.6 33.9 - - + +
69A ALA* 3.6 31.9 - - + -
94A LYS* 3.0 13.8 + - + +
95A ALA 3.7 5.4 - - - +
97A VAL* 1.3 77.5 - - + +
99A LEU* 1.3 64.8 + - - +
101A ASN* 3.1 11.1 + - + +
102A ILE* 2.9 31.6 + - + +
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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
----------------------------------------------------------
56A THR* 4.8 6.5 - - + -
60A PHE* 3.9 19.0 - - + -
73A MET* 3.2 37.7 - - + -
84A PHE* 4.4 18.6 - - + +
86A THR* 4.2 20.0 - - - -
95A ALA 2.9 18.3 + - - +
96A GLU 4.0 2.5 - - - +
98A VAL* 1.3 76.6 - - - +
100A GLY* 1.3 65.3 + - - +
102A ILE* 3.3 3.1 + - - +
103A ILE* 3.1 29.9 + - + +
115A ILE* 4.3 16.6 - - + -
147A LEU* 3.8 20.2 - - + -
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Residues in contact with GLY 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 GLU 3.0 15.8 + - - -
97A VAL 3.1 3.6 + - - -
99A LEU* 1.3 76.8 - - - +
101A ASN* 1.3 57.9 + - - +
103A ILE* 3.2 9.4 + - - +
104A LYS* 2.9 29.8 + - - +
146A ARG 4.8 0.4 - - - -
147A LEU* 3.3 32.4 - - - +
148A GLN* 4.5 4.2 - - - +
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Residues in contact with ASN 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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66A ASP* 5.3 5.7 + - - -
97A VAL* 2.9 37.3 + - - +
98A VAL* 3.4 10.5 - - + +
100A GLY* 1.3 72.2 - - - +
102A ILE* 1.3 58.0 + - + +
104A LYS* 3.1 6.4 + - - +
105A LYS* 2.7 38.5 + - + +
146A ARG 5.6 0.3 - - - +
148A GLN* 3.2 17.5 - - - +
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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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60A PHE* 3.7 22.7 - - + -
66A ASP 5.0 1.1 - - - +
69A ALA* 3.5 14.6 - - + +
70A GLU* 3.5 44.6 - - + +
73A MET* 3.8 26.9 - - + -
98A VAL* 2.9 18.4 + - + +
99A LEU 3.6 5.6 - - - +
101A ASN* 1.3 76.2 - - + +
103A ILE* 1.3 57.4 + - - +
105A LYS* 3.1 6.5 + - - +
106A LYS* 2.9 43.4 + - + +
108A TRP* 4.0 11.4 - - + -
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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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73A MET* 4.4 14.4 - - + -
99A LEU* 3.1 25.8 + - + +
100A GLY* 3.5 9.0 - - - +
101A ASN 3.2 0.2 - - - -
102A ILE* 1.3 77.8 - - - +
104A LYS* 1.3 68.9 + - - +
106A LYS 3.8 0.3 + - - -
107A GLY* 3.3 19.8 + - - -
108A TRP* 3.9 17.3 + - + +
110A ARG* 5.6 1.8 - - - -
113A LEU* 3.8 26.7 - - + -
115A ILE* 3.8 35.0 - - + -
147A LEU* 5.6 0.2 - - + -
149A LEU* 4.5 27.6 - - + -
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Residues in contact with LYS 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 GLY 2.9 17.3 + - - +
101A ASN* 3.7 6.1 - - - +
103A ILE* 1.3 84.5 - - - +
105A LYS* 1.3 63.2 + - - +
107A GLY* 3.6 9.1 + - - -
147A LEU 5.2 0.2 + - - -
148A GLN* 3.4 54.7 + - - +
149A LEU* 5.0 4.9 - - - +
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Residues in contact with LYS 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLU* 2.8 42.2 + - - +
101A ASN* 2.7 20.7 + - + +
102A ILE* 3.6 5.8 - - - +
104A LYS* 1.3 72.4 - - - +
106A LYS* 1.3 62.1 + - + +
107A GLY* 2.9 10.7 + - - -
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Residues in contact with LYS 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLU* 4.1 24.7 + - + +
74A THR* 3.1 40.5 + - - +
102A ILE* 2.9 24.0 + - + +
105A LYS* 1.3 73.5 - - + +
107A GLY* 1.3 64.6 + - - +
108A TRP* 2.9 50.1 + - + +
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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