Contacts of the helix formed by residues 99 - 108 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLY* 1.3 75.0 - - - -
100B LEU* 1.3 62.3 + - - +
101B ALA* 3.0 12.1 + - - +
102B ASP* 2.6 50.1 + - - +
103B TYR* 3.2 20.1 + - - +
141B PRO 3.9 0.9 - - - +
142B GLN* 3.5 23.8 - - - +
144B ILE 3.2 13.0 - - - +
145B LEU* 3.8 12.4 - - + +
146B LEU* 3.9 2.5 - - - -
401B 3RJ 3.5 22.8 + - + -
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ASP* 1.3 70.2 - - - +
101B ALA* 1.3 56.5 + - - +
103B TYR* 4.2 9.2 - - + -
104B LEU* 2.8 43.1 + - + +
110B LEU* 4.3 13.2 - - + -
118B PHE* 4.1 31.6 - - + -
122B ILE* 5.7 3.4 - - + -
141B PRO* 3.2 24.8 + - + +
144B ILE* 2.7 30.8 + - + +
146B LEU* 3.6 11.8 - - + +
210B ILE* 4.0 27.6 - - + -
214B CYS* 4.1 12.1 - - - -
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Residues in contact with ALA 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ASP* 3.0 9.5 + - - +
100B LEU* 1.3 76.9 - - - +
102B ASP* 1.3 68.5 + - - +
103B TYR 3.0 0.2 + - - -
104B LEU* 3.9 2.6 - - - +
105B HIS* 3.0 37.3 + - + +
141B PRO* 3.3 9.5 + - + -
142B GLN* 3.3 48.5 - - + +
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Residues in contact with ASP 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLY* 5.6 2.2 - - - -
99B ASP* 2.6 36.2 + - - +
101B ALA* 1.3 74.0 - - - +
103B TYR* 1.3 57.7 + - - +
105B HIS* 3.6 25.8 - - - +
106B ALA* 3.8 8.8 + - - +
401B 3RJ 4.4 15.5 + - + -
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Residues in contact with TYR 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B GLY 4.9 8.3 - - - +
99B ASP 3.2 17.1 + - - +
100B LEU* 3.8 13.7 - - + +
101B ALA 3.0 0.8 - - - -
102B ASP* 1.3 74.3 - - - +
104B LEU* 1.3 66.8 + - - +
105B HIS 3.1 1.6 - - - -
106B ALA* 3.2 6.9 + - + +
107B MET* 3.2 65.5 + - + +
110B LEU* 4.1 17.2 - - + +
114B THR* 5.6 0.7 - - + -
118B PHE* 4.5 10.8 - + - -
146B LEU* 3.5 30.3 - - + -
156B PRO* 4.6 12.0 - - - +
159B ILE* 4.1 18.1 - - + +
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B LEU* 2.8 29.5 + - + +
101B ALA* 3.9 3.6 - - - +
103B TYR* 1.3 73.0 - - - +
105B HIS* 1.3 65.9 + - - +
107B MET* 4.5 3.1 - - - +
108B ARG* 3.0 38.9 + - - +
109B THR* 4.2 3.4 - - - -
110B LEU* 3.9 29.2 - - + -
141B PRO* 5.1 6.5 - - + -
213B GLN* 3.9 37.5 - - + +
214B CYS* 3.9 29.2 - - - +
217B GLY* 5.7 1.1 - - - -
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Residues in contact with HIS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ALA* 3.0 31.8 + - + +
102B ASP* 3.6 22.4 - - - +
103B TYR 3.1 0.2 - - - -
104B LEU* 1.3 79.5 - - - +
106B ALA* 1.3 62.6 + - + +
108B ARG* 3.7 8.8 + - - +
142B GLN* 5.4 4.6 + - - -
213B GLN* 6.2 2.0 - - - -
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ASP 3.8 7.8 + - - +
103B TYR* 3.2 10.2 + - + +
105B HIS* 1.3 80.2 - - - +
107B MET* 1.3 70.3 + - + +
108B ARG* 3.7 9.2 + - - +
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Residues in contact with MET 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B TYR* 3.2 61.5 + - + +
104B LEU 3.4 2.7 + - - +
106B ALA* 1.3 81.2 - - + +
108B ARG* 1.3 75.8 + - - +
109B THR* 2.8 24.4 + - - +
110B LEU* 4.1 11.9 - - + -
156B PRO* 6.5 0.4 - - + -
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Residues in contact with ARG 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B LEU* 3.0 22.4 + - - +
105B HIS 3.7 6.4 + - - +
106B ALA 3.4 10.7 + - - +
107B MET* 1.3 83.3 + - - +
109B THR* 1.3 70.1 + - + +
217B GLY* 3.6 16.1 - - - -
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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