Contacts of the helix formed by residues 89 - 98 (chain A) in PDB entry 2W3S
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 HIS 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A ILE* 3.9 23.6 - - + +
82A ALA* 4.5 1.4 - - - +
87A ARG 3.8 2.0 + - - -
88A LEU* 1.3 73.6 - - - +
90A PRO* 1.3 76.3 - - + +
91A VAL* 2.8 43.6 + - + +
92A GLN* 2.8 39.2 + - + +
93A GLN* 3.0 11.8 + - - +
115A ALA* 4.1 8.0 + - + +
118A HIS* 3.8 27.8 + + + +
119A ASP 5.8 0.2 + - - -
155A ALA* 3.9 17.0 + - + +
157A TRP* 4.2 5.6 - + + -
158A LEU* 3.6 32.5 - - + +
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Residues in contact with PRO 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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88A LEU 3.8 3.6 - - - +
89A HIS* 1.3 99.7 - - + +
91A VAL* 1.3 54.9 + - - +
93A GLN* 3.9 6.0 - - + +
94A ALA* 2.9 33.1 + - - +
118A HIS* 4.4 4.0 - - - +
149A ALA* 3.6 12.9 - - + +
152A GLU* 3.5 42.6 - - + +
153A PRO* 4.2 13.0 - - + +
155A ALA* 5.5 2.2 - - + +
157A TRP* 4.9 6.7 - - + -
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Residues in contact with VAL 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 HIS* 2.8 26.1 + - + +
90A PRO* 1.3 78.0 - - - +
92A GLN* 1.3 58.0 + - + +
94A ALA* 3.6 2.0 - - - +
95A MET* 3.2 33.3 + - - +
111A ILE* 3.6 42.8 - - + +
114A MET* 3.6 41.4 - - + +
115A ALA* 4.2 1.6 - - + +
118A HIS* 4.4 5.2 - - + -
145A ALA* 5.2 0.6 - - - +
146A ALA* 6.0 2.9 - - - -
149A ALA* 4.0 15.9 - - + -
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Residues in contact with GLN 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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78A ILE* 4.2 6.3 + - - +
81A ILE* 3.7 25.1 - - - +
82A ALA* 3.3 23.7 - - - +
88A LEU* 3.6 11.8 - - + +
89A HIS* 2.8 41.3 + - + +
91A VAL* 1.3 70.9 - - - +
93A GLN* 1.3 64.2 + - - +
96A ILE* 3.2 21.3 + - - +
111A ILE* 3.8 26.2 - - + -
16B VAL* 3.1 44.0 + - + +
17B THR* 4.2 7.5 - - - +
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Residues in contact with GLN 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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88A LEU* 3.4 28.4 - - + +
89A HIS 3.0 12.7 + - - +
90A PRO* 4.0 6.7 - - + +
92A GLN* 1.3 73.5 - - - +
94A ALA* 1.3 56.9 + - - +
96A ILE* 3.2 15.8 + - - +
97A ASP* 2.8 66.8 + - - +
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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 PRO 2.9 21.0 + - - +
91A VAL 3.6 5.4 - - - +
93A GLN* 1.3 75.1 - - - +
95A MET* 1.3 51.8 + - - +
97A ASP* 2.7 17.2 + - - +
98A HIS* 2.7 36.3 + - - +
145A ALA* 3.4 32.8 - - - +
148A ALA* 4.4 8.3 - - + -
149A ALA* 3.8 7.0 - - + +
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Residues in contact with MET 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 VAL 3.2 16.2 + - - +
92A GLN 3.7 0.2 - - - +
93A GLN 3.4 0.2 - - - -
94A ALA* 1.3 78.7 - - - +
96A ILE* 1.3 60.9 + - - +
99A HIS* 3.1 1.6 + - - -
100A GLY* 2.6 60.6 + - - +
101A SER* 4.4 2.5 + - - -
106A CYS* 6.4 0.2 - - - -
107A THR* 3.5 27.8 - - + -
110A PHE* 4.3 8.1 - - + -
111A ILE* 3.7 3.8 - - + -
114A MET* 3.5 34.8 - - + +
142A ILE* 4.0 13.5 - - + -
145A ALA* 3.8 22.6 - - + +
16B VAL* 3.5 21.5 - - + -
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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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88A LEU* 3.9 27.1 - - + -
92A GLN 3.2 9.1 + - - +
93A GLN* 3.2 16.0 + - - +
94A ALA 3.2 0.6 - - - -
95A MET* 1.3 75.8 - - - +
97A ASP* 1.3 71.1 + - - +
99A HIS* 2.9 22.1 + - - +
8B PRO* 4.4 16.0 - - + +
12B ALA* 4.0 35.6 - - + +
13B ARG* 3.8 27.6 - - + +
16B VAL* 4.3 4.7 - - + -
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Residues in contact with ASP 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 GLN* 2.8 48.2 + - - +
94A ALA* 2.7 13.9 + - - +
96A ILE* 1.3 74.2 - - - +
98A HIS* 1.3 75.3 + - + +
99A HIS* 3.7 14.0 + - - -
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Residues in contact with HIS 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* 2.7 20.4 + - - +
97A ASP* 1.3 83.9 - - + +
99A HIS* 1.3 77.7 + - - +
100A GLY 3.1 2.3 + - - -
141A PRO* 3.4 30.3 - - - +
144A ARG* 3.6 35.8 + - + +
145A ALA* 4.1 6.8 - - + +
148A ALA* 3.7 30.4 - - + +
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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