Contacts of the helix formed by residues 103 - 115 (chain B) in PDB entry 1WVA
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 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B ALA* 3.5 18.6 - - + +
15B PHE* 3.7 38.4 - - + -
55B PHE* 4.3 7.9 - - + -
76B ALA* 4.1 20.4 - - + +
77B SER* 4.6 4.7 - - - +
80B LEU* 3.0 39.7 - - + +
96B VAL* 5.4 0.4 - - + -
99B GLY* 3.4 24.9 - - - +
100B ASP 3.3 17.0 - - - +
101B HIS 3.0 0.2 - - - -
102B SER* 1.3 79.0 + - - +
104B ALA* 1.3 63.8 + - - +
105B ILE 3.1 0.4 - - - -
106B GLY 3.1 3.6 + - - -
107B SER* 3.1 6.6 + - - -
276B MET* 3.5 15.5 - - + -
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Residues in contact with ALA 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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101B HIS* 3.1 35.8 + - + +
102B SER 2.9 0.4 - - - -
103B LEU* 1.3 78.1 - - - +
105B ILE* 1.3 56.4 + - - +
107B SER* 4.0 7.9 - - - -
108B ILE* 2.8 42.1 + - + +
122B TRP* 3.7 24.5 - - + -
144B PRO* 4.1 2.7 - - + -
148B LEU* 4.7 0.4 - - + -
274B ASP* 4.4 8.3 - - - +
276B MET* 4.6 2.2 - - - +
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Residues in contact with ILE 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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73B VAL* 4.9 4.5 - - + -
77B SER* 3.9 12.6 - - - +
102B SER* 3.0 20.6 - - - +
104B ALA* 1.3 78.2 - - - +
106B GLY* 1.3 54.2 + - - +
109B SER* 2.6 37.2 + - - +
140B LEU* 5.2 3.4 - - + +
143B GLN 5.2 0.2 - - - -
144B PRO* 3.4 33.8 - - + +
147B PHE* 4.3 26.7 - - + -
148B LEU* 3.6 16.4 - - + +
162B PHE* 4.0 24.0 - - + -
164B TRP* 4.2 12.8 - - + -
165B VAL* 4.4 9.4 - - + -
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Residues in contact with GLY 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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77B SER* 2.9 35.3 - - - -
80B LEU* 3.9 2.0 - - - -
81B ALA* 2.8 35.2 - - - +
84B VAL* 4.5 0.2 - - - +
103B LEU 3.1 4.8 + - - -
105B ILE* 1.3 76.9 - - - +
107B SER* 1.3 59.6 + - - +
109B SER* 4.0 0.2 - - - -
110B GLY 3.0 9.5 + - - -
164B TRP* 4.0 3.4 - - - -
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Residues in contact with SER 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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80B LEU* 3.7 10.2 - - - +
84B VAL* 3.5 18.1 - - - +
94B SER* 5.6 1.0 + - - -
96B VAL* 3.9 11.2 - - - +
103B LEU 3.1 16.7 + - - -
104B ALA* 3.6 4.7 - - - -
106B GLY* 1.3 79.0 - - - +
108B ILE* 1.3 60.6 + - - +
111B HIS* 3.3 24.3 + - - +
228B HIS* 3.4 9.0 - - - -
274B ASP* 2.6 34.0 + - - -
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Residues in contact with ILE 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 ALA* 2.8 22.6 + - + +
107B SER* 1.3 71.7 - - - +
109B SER* 1.3 61.4 + - - +
111B HIS* 4.0 3.7 - - - +
112B ALA* 3.3 22.3 + - - +
118B LEU* 4.2 8.9 - - + +
120B VAL* 4.1 24.0 - - + -
122B TRP* 3.7 18.2 - - + -
148B LEU* 3.6 31.2 - - + -
168B CYS* 3.7 13.2 - - - -
169B ILE* 4.5 4.9 - - + -
228B HIS* 3.3 27.6 - - + +
230B SER* 3.6 19.7 - - - +
274B ASP* 4.3 0.9 - - - +
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Residues in contact with SER 109 (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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81B ALA* 4.1 2.2 - - - -
105B ILE* 2.6 25.6 + - - +
106B GLY 3.7 4.3 - - - -
107B SER 3.2 0.6 - - - -
108B ILE* 1.3 76.8 - - - +
110B GLY* 1.3 64.9 + - - +
112B ALA* 3.2 4.9 + - - +
113B ARG* 3.2 26.6 + - - +
148B LEU* 3.6 12.1 - - - +
164B TRP* 4.0 24.5 - - - -
165B VAL* 5.0 5.4 - - - +
166B THR 5.0 3.6 + - - -
168B CYS* 4.4 8.7 - - - +
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Residues in contact with GLY 110 (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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81B ALA* 3.2 29.5 - - - +
84B VAL* 3.9 7.0 - - - -
85B ALA* 3.5 15.0 - - - -
106B GLY 3.0 13.7 + - - -
109B SER* 1.3 76.8 - - - +
111B HIS* 1.3 61.3 + - - +
113B ARG* 3.4 23.8 - - - +
114B VAL* 3.7 2.4 - - - +
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Residues in contact with HIS 111 (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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84B VAL* 3.5 10.6 - - + +
88B LYS* 3.7 18.8 - - + -
94B SER* 4.7 0.6 + - - +
107B SER 3.3 19.4 + - - +
108B ILE 4.0 2.7 - - - +
109B SER 3.2 0.4 - - - -
110B GLY* 1.3 76.7 - - - +
112B ALA* 1.3 57.5 + - - +
114B VAL* 3.1 6.6 + - - +
115B HIS* 2.8 29.8 + - + -
118B LEU* 3.4 20.5 - - + +
226B PRO* 4.1 6.7 - - - +
227B ILE 3.6 8.1 - - - -
228B HIS* 3.1 25.8 + - + +
271B SER* 2.5 43.9 + - - -
272B GLY* 3.4 16.8 - - - -
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Residues in contact with ALA 112 (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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108B ILE 3.3 17.3 + - - +
109B SER 3.2 6.1 + - - +
111B HIS* 1.3 75.8 - - - +
113B ARG* 1.3 65.9 + - - +
114B VAL 3.1 0.2 - - - -
115B HIS 3.6 4.7 - - - +
116B PRO* 2.9 34.5 - - + +
118B LEU* 3.4 17.0 - - + +
168B CYS* 3.7 27.4 - - + +
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Residues in contact with ARG 113 (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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78B GLU* 4.6 5.7 + - - +
81B ALA* 3.5 27.5 + - - +
82B GLY* 3.5 26.7 - - - +
85B ALA* 4.0 15.3 - - + +
109B SER* 3.2 14.6 + - - +
110B GLY* 3.4 10.7 - - - +
111B HIS 3.2 0.8 - - - -
112B ALA* 1.3 77.1 - - - +
114B VAL* 1.3 65.0 + - + +
116B PRO* 4.3 4.5 - - - +
164B TRP* 4.5 16.0 - - - -
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Residues in contact with VAL 114 (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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85B ALA* 3.7 18.6 - - + +
88B LYS* 3.6 31.4 - - + +
89B LYS* 4.5 9.9 - - + +
110B GLY 3.7 12.8 - - - +
111B HIS 3.1 2.4 + - - +
113B ARG* 1.3 82.0 - - + +
115B HIS* 1.3 90.0 + - + +
116B PRO* 3.5 7.0 - - - +
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Residues in contact with HIS 115 (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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88B LYS* 3.7 27.9 + - + -
111B HIS* 2.8 22.4 + + + +
112B ALA* 3.3 3.4 - - - -
114B VAL* 1.3 108.5 + - + +
116B PRO* 1.3 59.1 - - - +
117B ASP* 2.9 15.3 + - - +
118B LEU* 3.1 22.7 + - - +
226B PRO* 3.5 40.6 - - + -
271B SER* 4.5 2.1 + - - -
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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