Contacts of the helix formed by residues 89 - 99 (chain A) in PDB entry 1IN7
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 LYS 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A VAL* 1.3 80.8 - - + +
90A GLN* 1.3 55.5 + - - +
91A GLY* 2.7 23.0 + - - +
92A ASP* 2.8 43.7 + - - +
117A ALA* 5.7 1.1 - - - -
118A VAL* 3.6 6.6 - - - +
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Residues in contact with GLN 90 (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 LYS* 1.3 71.6 - - - +
91A GLY* 1.3 61.3 + - - +
92A ASP 3.2 0.2 - - - -
93A MET 3.3 1.5 + - - -
94A ALA* 3.0 21.1 + - - +
117A ALA* 3.9 40.3 - - + +
118A VAL* 3.8 11.3 - - - +
121A LEU* 3.3 28.3 + - + +
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Residues in contact with GLY 91 (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 LYS* 2.7 15.4 + - - +
90A GLN* 1.3 79.2 - - - +
92A ASP* 1.3 59.7 - - - -
94A ALA* 3.3 6.5 + - - +
95A ALA* 3.1 24.1 + - - +
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Residues in contact with ASP 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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86A VAL* 4.3 5.0 - - + +
87A LEU* 4.1 23.6 - - + -
88A VAL* 3.3 10.8 + - - +
89A LYS* 2.8 49.6 + - - +
91A GLY* 1.3 73.8 - - - +
93A MET* 1.3 60.2 + - - +
94A ALA 3.4 0.2 + - - -
95A ALA* 3.4 5.1 + - - +
96A ILE* 3.3 27.7 + - + +
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Residues in contact with MET 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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87A LEU* 3.5 32.8 - - + +
89A LYS 3.8 1.4 + - - -
90A GLN 3.3 2.3 + - - +
92A ASP* 1.3 78.8 - - - +
94A ALA* 1.3 58.2 + - - +
96A ILE* 3.4 6.6 + - - +
97A LEU* 3.0 54.7 + - + +
106A LEU* 5.0 6.1 - - - -
108A ILE* 4.5 2.2 - - + -
114A LEU* 4.4 4.7 - - + -
118A VAL* 3.5 39.5 - - + +
121A LEU* 3.5 27.4 - - + -
122A LEU* 3.6 31.6 - - + +
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Residues in contact with ALA 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 GLN 3.0 17.2 + - - +
91A GLY* 3.6 8.1 - - - +
92A ASP 3.2 0.2 - - - -
93A MET* 1.3 75.3 - - - +
95A ALA* 1.3 66.2 + - - +
96A ILE 3.1 0.2 + - - -
97A LEU* 3.1 2.1 + - - +
98A THR* 3.0 31.6 + - + +
121A LEU* 3.7 7.8 - - + +
131A ILE* 4.1 22.0 - - + -
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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 GLY 3.1 13.5 + - - +
92A ASP* 3.8 6.1 - - - +
94A ALA* 1.3 79.0 - - - +
96A ILE* 1.3 59.8 + - + +
98A THR* 3.1 17.8 + - - -
99A SER* 3.4 14.9 + - - -
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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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80A HIS* 4.7 8.5 - - + +
82A THR* 4.1 16.8 - - + +
87A LEU* 3.5 32.8 - - + -
92A ASP* 3.3 11.1 + - + +
93A MET* 3.8 9.2 - - - +
94A ALA 3.1 0.8 - - - -
95A ALA* 1.3 78.1 - - + +
97A LEU* 1.3 65.5 + - + +
99A SER* 3.0 24.8 + - - +
100A LEU* 3.2 13.8 - - + +
106A LEU* 3.6 29.8 - - + -
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Residues in contact with LEU 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 MET* 3.0 47.7 + - + +
94A ALA* 3.1 4.5 + - - +
96A ILE* 1.3 76.8 - - - +
98A THR* 1.3 61.9 + - + +
100A LEU* 3.5 22.3 + - + +
106A LEU* 4.1 13.9 - - + -
121A LEU* 3.9 25.4 - - + +
122A LEU* 4.4 2.7 - - + -
125A ALA* 4.0 9.2 - - + -
131A ILE* 4.7 4.9 - - + -
148A ILE* 3.2 46.3 - - + +
149A GLN 5.0 0.3 + - - -
151A PHE* 4.0 28.3 - - + -
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Residues in contact with THR 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 ALA* 3.0 15.7 + - + +
95A ALA* 3.1 18.4 + - - -
97A LEU* 1.3 74.3 - - + +
99A SER* 1.3 57.7 - - - +
100A LEU 3.2 10.5 + - - +
131A ILE* 4.6 15.5 - - + -
147A ASP 5.0 13.7 - - - +
148A ILE* 5.4 1.8 - - + +
149A GLN* 6.0 0.5 - - - +
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Residues in contact with SER 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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80A HIS* 3.4 27.9 + - - -
95A ALA 3.4 12.9 + - - -
96A ILE* 3.0 17.9 + - - +
98A THR* 1.3 79.7 + - - +
100A LEU* 1.3 61.7 + - - +
101A GLU* 3.7 8.2 + - - +
104A ASP* 4.3 0.5 - - - +
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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