Contacts of the helix formed by residues 99 - 108 (chain D) in PDB entry 4WNP
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 ASP 99 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97D GLY 4.7 0.7 - - - +
98D GLY* 1.3 76.9 - - - -
100D LEU* 1.3 58.1 + - - +
101D ALA* 3.1 12.9 + - - +
102D ASP* 3.0 33.6 + - - +
103D TYR* 3.0 24.9 + - - +
141D PRO 3.9 1.3 - - - +
142D GLN* 3.5 27.3 - - - +
144D ILE 3.3 14.4 - - - +
145D LEU* 4.1 9.5 - - + +
146D LEU* 3.9 2.6 - - - +
401D 3RJ 3.7 22.8 + - - -
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Residues in contact with LEU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D ASP* 1.3 70.9 - - - +
101D ALA* 1.3 59.7 + - - +
103D TYR* 4.0 10.8 - - + -
104D LEU* 2.9 42.9 + - + +
110D LEU* 4.5 0.9 - - + -
118D PHE* 4.1 31.9 - - + -
122D ILE* 5.8 2.5 - - + -
141D PRO* 3.3 24.4 + - + +
144D ILE* 2.8 30.6 + - + +
146D LEU* 3.7 10.5 - - + +
210D ILE* 3.9 28.5 - - + -
214D CYS* 4.0 13.7 - - - -
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Residues in contact with ALA 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D ASP* 3.1 11.1 + - - +
100D LEU* 1.3 78.6 - - - +
102D ASP* 1.3 62.9 + - - +
104D LEU* 3.4 4.5 + - - +
105D HIS* 3.2 41.2 + - + +
141D PRO* 3.4 12.9 + - + +
142D GLN* 3.7 38.6 - - + +
213D GLN* 5.5 4.0 - - - +
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Residues in contact with ASP 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D GLY 5.9 0.7 - - - +
98D GLY* 5.1 3.1 - - - -
99D ASP* 3.0 34.3 + - - +
101D ALA* 1.3 75.2 - - - +
103D TYR* 1.3 63.1 + - - +
105D HIS* 3.2 17.2 + - - +
106D ALA* 3.2 20.5 + - - +
401D 3RJ 5.2 11.3 + - - -
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Residues in contact with TYR 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D GLY 5.3 4.0 - - - +
99D ASP 3.0 14.5 + - - +
100D LEU* 3.5 20.4 - - + +
101D ALA 3.3 0.2 - - - -
102D ASP* 1.3 76.0 - - - +
104D LEU* 1.3 57.5 + - - +
106D ALA* 3.2 8.3 + - + +
107D MET* 2.9 58.1 + - + +
110D LEU* 3.7 29.5 - - + +
114D THR* 5.2 1.3 - - + +
118D PHE* 4.0 13.9 - + - -
146D LEU* 3.4 28.7 - - + -
156D PRO* 4.1 15.2 - - - +
159D ILE* 3.4 26.9 - - + +
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Residues in contact with LEU 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D LEU* 2.9 29.9 + - + +
101D ALA* 3.9 3.8 - - - +
102D ASP 3.3 0.2 - - - -
103D TYR* 1.3 73.8 - - - +
105D HIS* 1.3 62.2 + - + +
107D MET* 4.3 1.6 - - - +
108D ARG* 2.5 48.6 + - - +
109D THR* 4.6 0.9 - - - -
110D LEU* 3.5 40.2 - - + -
141D PRO* 4.9 3.8 - - + -
210D ILE 5.3 0.2 - - - +
213D GLN* 3.9 41.7 - - + +
214D CYS* 3.8 26.0 - - - +
217D GLY* 5.8 1.3 - - - -
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Residues in contact with HIS 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D ALA* 3.2 31.3 + - + +
102D ASP* 3.2 16.6 + - - +
104D LEU* 1.3 81.5 - - + +
106D ALA* 1.3 59.7 + - - +
108D ARG* 3.6 18.2 + - - +
142D GLN* 6.2 0.7 - - - -
213D GLN* 5.6 7.2 + - - -
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Residues in contact with ALA 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ASP 3.2 8.4 + - - +
103D TYR* 3.2 12.9 + - + +
104D LEU 3.1 0.2 - - - -
105D HIS* 1.3 82.5 - - - +
107D MET* 1.3 69.0 + - + +
108D ARG* 4.5 4.7 - - - +
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Residues in contact with MET 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D TYR* 2.9 57.6 + - + +
104D LEU 4.4 0.7 - - - +
106D ALA* 1.3 83.5 - - + +
108D ARG* 1.3 70.3 + - - +
109D THR 3.0 12.6 + - - +
110D LEU* 3.9 20.2 - - + -
156D PRO* 5.7 6.1 - - + -
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Residues in contact with ARG 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D LEU* 2.5 29.9 + - - +
105D HIS* 3.6 18.6 + - - +
106D ALA 4.5 4.3 - - - +
107D MET* 1.3 76.4 - - - +
109D THR* 1.3 69.4 + - + +
217D GLY* 3.7 18.5 - - - -
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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