Contacts of the helix formed by residues 98 - 107 (chain A) in PDB entry 2H3W
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 LEU 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A LEU* 3.4 22.2 - - + -
96A ASN* 2.8 10.3 + - - +
97A TRP* 1.3 107.3 - - + +
99A SER* 1.3 64.1 + - - +
100A GLU 3.5 1.6 - - - -
101A TRP* 3.1 11.0 + - + +
102A TRP* 2.9 43.0 + - + +
457A LEU* 6.2 2.0 - - + -
464A ARG* 6.1 4.3 - - + +
465A THR 4.5 7.4 - - - +
518A ARG* 3.8 43.7 - - + +
521A LEU* 4.8 8.7 - - + -
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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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96A ASN* 3.0 42.4 + - - +
98A LEU* 1.3 76.1 - - - +
100A GLU* 1.3 65.1 + - - +
102A TRP* 3.4 3.8 + - - +
103A LEU* 3.1 23.5 + - - +
462A LEU* 3.6 22.2 + - - +
464A ARG* 5.8 6.4 - - - +
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Residues in contact with GLU 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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90A ARG* 5.1 10.3 - - - +
94A MET* 4.4 18.9 - - + +
96A ASN 4.9 1.4 + - - -
97A TRP 5.5 0.4 + - - -
98A LEU 3.5 0.8 - - - -
99A SER* 1.3 76.5 - - - +
101A TRP* 1.3 68.8 + - + +
103A LEU* 3.9 9.0 - - + +
104A LYS* 3.0 37.6 + - + +
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Residues in contact with TRP 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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87A LEU* 3.5 22.0 - - + -
90A ARG* 3.2 57.2 - - - +
97A TRP* 3.7 18.4 + + - -
98A LEU* 3.1 13.0 + - + +
100A GLU* 1.3 80.4 - - + +
102A TRP* 1.3 58.6 + - - +
104A LYS* 3.5 21.2 - - - +
105A THR* 2.9 36.3 + - - +
521A LEU* 5.8 0.2 - - - -
522A GLY* 3.6 20.6 - - - -
525A LEU* 3.4 45.8 + - + +
526A GLN* 3.5 20.2 - - - -
529A GLU* 3.7 13.1 + - - +
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Residues in contact with TRP 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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98A LEU* 2.9 29.5 + - + +
99A SER* 3.8 4.5 - - - +
101A TRP* 1.3 77.4 - - - +
103A LEU* 1.3 60.3 + - - +
105A THR* 4.1 4.0 - - - -
106A ALA* 2.8 54.1 + - + +
107A TYR* 4.0 20.7 + + - -
347A GLU* 4.8 2.2 + - - -
452A TYR* 4.5 5.6 - + - -
464A ARG* 4.3 29.2 - - + +
465A THR* 4.3 5.3 + - - -
518A ARG* 3.3 55.9 - - - -
521A LEU* 3.8 21.3 - - + -
1602A HC5 3.6 18.0 + - - -
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Residues in contact with LEU 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 SER 3.1 14.0 + - - +
100A GLU* 3.9 9.4 - - + +
102A TRP* 1.3 82.2 - - - +
104A LYS* 1.3 57.7 + - - +
107A TYR* 3.1 18.1 + - + +
108A LEU* 3.0 52.6 + - + -
190A VAL* 5.3 5.8 - - + -
344A ALA* 3.6 37.9 - - + +
464A ARG* 5.5 5.6 - - - +
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Residues in contact with LYS 104 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A GLU* 3.0 28.7 + - + +
101A TRP* 3.5 21.0 - - - +
103A LEU* 1.3 76.9 - - - +
105A THR* 1.3 76.7 + - - +
108A LEU* 3.5 11.6 + - + -
109A GLN* 2.7 73.2 + - + +
187A GLN* 3.9 17.0 - - - +
525A LEU* 5.5 4.2 - - - +
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Residues in contact with THR 105 (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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101A TRP 2.9 24.7 + - - +
102A TRP* 3.7 8.7 + - - -
104A LYS* 1.3 90.4 - - - +
106A ALA* 1.3 63.0 + - - +
109A GLN* 4.1 14.8 - - - +
110A PHE* 4.5 10.0 + - - +
521A LEU* 4.2 18.0 - - + +
525A LEU* 4.1 28.3 - - + -
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Residues in contact with ALA 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 TRP* 2.8 59.4 + - + +
105A THR* 1.3 76.4 + - - +
107A TYR* 1.3 80.7 + - + +
110A PHE* 3.7 17.3 - - - +
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Residues in contact with TYR 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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102A TRP* 4.0 12.5 + + - -
103A LEU* 3.1 20.2 + - + +
105A THR 3.5 1.2 - - - -
106A ALA* 1.3 107.4 - - + +
108A LEU* 1.3 63.4 + - - +
109A GLN 3.1 2.0 - - - -
110A PHE* 2.8 24.5 + + - +
118A SER* 3.9 19.3 - - - -
181A ARG* 2.9 24.0 + - - +
343A HIS* 3.3 47.3 + + + -
344A ALA* 3.9 30.3 - - + -
347A GLU* 4.3 1.2 + - - -
464A ARG* 3.8 18.6 - - - -
1602A HC5 3.8 20.6 + - - +
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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