Contacts of the helix formed by residues 82 - 93 (chain A) in PDB entry 2IWR
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 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A ALA 4.2 5.1 + - - -
80A ARG 3.2 5.5 + - - -
81A SER* 1.3 76.8 + - - +
83A LYS* 1.3 65.8 + - - +
84A SER 3.2 2.9 - - - -
85A SER* 3.4 12.6 + - - -
86A LEU* 2.9 23.9 + - - +
98A LEU 5.2 4.7 - - - -
142A VAL* 4.2 2.7 - - - -
179A THR* 4.4 8.7 - - - +
182A ARG* 6.1 0.9 - - - -
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Residues in contact with LYS 83 (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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75A VAL* 3.9 12.0 - - + +
76A LEU* 3.9 6.3 - - - -
77A GLY* 2.8 41.3 + - - +
78A ASP 3.3 13.5 + - - +
79A ALA* 4.4 1.2 + - - +
81A SER* 3.0 12.6 + - - +
82A GLY* 1.3 78.3 - - - +
84A SER* 1.3 66.2 + - - +
86A LEU* 3.4 3.3 + - - +
87A ILE* 3.1 28.2 + - - +
99A GLU 4.4 13.3 + - - -
123A GLU* 3.6 22.5 + - + +
124A GLU 3.3 24.5 + - - -
125A ALA* 4.2 8.5 + - - +
142A VAL* 3.8 28.4 - - + +
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Residues in contact with SER 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLY 3.2 0.8 - - - -
83A LYS* 1.3 78.7 - - - +
85A SER* 1.3 61.7 + - - +
87A ILE* 3.3 2.9 + - - +
88A HIS* 2.9 30.1 + - - +
98A LEU* 3.7 17.8 + - - +
99A GLU 3.5 5.0 + - - -
100A LYS* 3.2 40.0 + - - -
101A THR* 3.5 10.6 - - - +
123A GLU* 2.6 23.5 + - - -
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Residues in contact with SER 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLY* 3.4 12.6 + - - -
84A SER* 1.3 78.5 - - - +
86A LEU* 1.3 57.2 + - - +
88A HIS* 3.9 1.6 - - - +
89A ARG* 2.9 31.9 + - - +
94A SER 5.0 0.3 - - - +
95A TYR* 3.9 20.9 + - - -
96A GLN 2.7 28.7 + - - +
97A VAL* 3.7 3.1 - - - +
98A LEU* 3.1 22.8 + - - +
181A ASP* 6.3 0.2 - - - -
213A ALA* 4.0 4.4 - - - +
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Residues in contact with LEU 86 (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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75A VAL* 5.5 1.8 - - + -
82A GLY 2.9 17.3 + - - +
83A LYS 3.5 5.4 - - - +
85A SER* 1.3 76.2 - - - +
87A ILE* 1.3 64.9 + - - +
89A ARG* 3.7 2.3 - - - +
90A PHE* 3.0 22.7 + - - +
140A ILE* 4.7 4.7 - - + -
142A VAL* 4.0 26.7 - - + -
177A VAL* 4.1 20.6 - - + -
179A THR* 5.3 2.9 - - + -
211A THR* 4.0 21.8 - - + +
213A ALA* 4.4 9.6 - - + +
219A VAL* 3.8 31.3 - - + +
222A VAL* 5.1 3.1 - - + -
223A PHE* 3.9 20.9 - - + -
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Residues in contact with ILE 87 (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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75A VAL* 3.9 24.0 - - + -
83A LYS 3.1 16.2 + - - +
84A SER 3.7 4.9 - - - +
86A LEU* 1.3 76.8 - - + +
88A HIS* 1.3 63.6 + - - +
90A PHE* 3.2 2.8 + - - +
91A LEU* 2.9 45.0 + - + +
101A THR* 3.9 9.6 - - + -
106A TYR* 3.9 18.4 - - + -
121A ILE* 4.0 24.0 - - + -
123A GLU* 3.7 31.9 - - + +
223A PHE* 4.2 13.5 - - + -
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Residues in contact with HIS 88 (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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84A SER 2.9 18.5 + - - +
85A SER* 3.9 4.0 - - - +
87A ILE* 1.3 78.1 - - - +
89A ARG* 1.3 54.2 + - - +
91A LEU* 3.3 5.4 + - - -
92A THR* 2.8 69.6 + - + +
94A SER* 3.5 16.9 + - - -
96A GLN* 3.8 27.2 + - + +
98A LEU* 3.6 18.0 - - + +
101A THR* 4.9 2.2 - - + +
102A GLU* 3.5 27.8 + - - +
106A TYR* 4.6 15.1 + + - +
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Residues in contact with ARG 89 (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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85A SER 2.9 19.7 + - - +
86A LEU 3.7 3.8 - - - +
88A HIS* 1.3 74.9 - - - +
90A PHE* 1.3 61.8 + - - +
93A GLY* 2.8 53.5 + - - -
94A SER* 3.3 21.0 + - - +
95A TYR* 4.2 7.7 - - - +
213A ALA* 3.2 24.1 + - + +
214A THR 3.2 26.3 + - - -
215A TYR* 3.7 7.7 + - - +
216A GLY* 3.5 24.2 - - - +
219A VAL* 4.0 21.3 - - + +
220A ASP* 5.4 0.5 - - - +
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Residues in contact with PHE 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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86A LEU 3.0 14.0 + - - +
87A ILE 3.5 6.1 - - - +
89A ARG* 1.3 80.0 - - - +
91A LEU* 1.3 64.6 + - + +
93A GLY 4.4 1.4 + - - -
108A LYS* 2.8 60.4 + - + -
110A MET* 3.4 31.0 - - + -
119A VAL* 5.4 1.1 - - + -
121A ILE* 3.8 24.2 - - + -
219A VAL* 3.7 7.6 - - + +
220A ASP* 3.3 36.7 - - + +
223A PHE* 3.5 46.4 - + + -
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Residues in contact with LEU 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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87A ILE* 2.9 29.2 + - + +
88A HIS* 3.9 4.5 - - - +
90A PHE* 1.3 88.0 - - + +
92A THR* 1.3 66.0 + - + +
106A TYR* 2.8 66.0 - - + -
107A LYS 4.2 4.7 - - - +
108A LYS* 3.9 40.7 + - + +
121A ILE* 4.4 6.3 - - + -
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Residues in contact with THR 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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88A HIS* 2.8 44.2 + - + +
91A LEU* 1.3 86.3 - - + +
93A GLY* 1.3 59.1 + - - +
94A SER* 2.9 32.2 + - - -
106A TYR* 6.2 1.8 - - + -
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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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89A ARG* 2.8 44.9 + - - -
90A PHE 4.4 1.6 + - - -
91A LEU 3.8 0.6 - - - -
92A THR* 1.3 76.6 - - - +
94A SER* 1.3 57.2 + - - +
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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