Contacts of the strand formed by residues 49 - 55 (chain A) in PDB entry 1WGP
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 GLU 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A LEU 4.9 4.9 - - - +
41A VAL* 5.4 0.5 - - - +
47A VAL* 3.4 13.7 - - - +
48A ASN* 1.3 102.4 + - - +
50A MET* 1.3 57.4 + - - +
51A LEU* 3.6 25.3 - - + +
86A LEU* 3.8 7.0 - - - -
116A ALA* 4.8 7.2 - - + -
117A LEU 2.9 24.5 - - - +
118A ILE* 3.9 5.6 - - + -
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Residues in contact with MET 50 (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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13A LEU* 4.9 2.2 - - + -
41A VAL* 6.1 1.1 - - - -
47A VAL* 4.9 2.2 - - - -
49A GLU* 1.3 74.0 - - - +
51A LEU* 1.3 74.8 + - - +
52A PHE* 3.2 37.9 + - + -
81A PHE* 4.3 12.8 - - + -
82A CYS 3.4 13.2 - - - +
83A GLY 3.2 24.9 - - - +
84A ASP* 3.6 20.9 - - + -
86A LEU* 3.4 21.9 - - + +
87A LEU* 4.3 17.5 - - + -
116A ALA 3.4 1.0 - - - -
117A LEU* 2.5 48.9 + - + +
122A LEU* 5.4 1.1 - - + -
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Residues in contact with LEU 51 (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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34A PHE* 3.1 43.1 - - + -
40A LEU* 3.8 42.3 - - + +
41A VAL* 4.9 5.3 - - + +
49A GLU* 3.6 23.3 - - + +
50A MET* 1.3 94.7 - - - +
52A PHE* 1.3 64.0 + - - +
53A ILE* 3.6 6.7 + - + +
81A PHE* 4.6 1.9 - - - -
82A CYS* 4.2 19.9 + - + +
115A PHE 3.4 9.6 - - - +
116A ALA* 3.4 18.2 - - + -
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Residues in contact with PHE 52 (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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8A VAL* 5.1 3.1 - - + -
13A LEU* 5.7 0.9 - - + -
14A PHE* 3.6 32.3 - + - -
25A ILE* 4.8 6.3 - - + -
29A LEU* 4.2 18.2 - - + -
50A MET* 3.2 37.9 - - + -
51A LEU* 1.3 71.2 - - - +
53A ILE* 1.3 67.7 + - - +
54A ILE* 3.0 18.5 + - + +
81A PHE* 5.2 7.2 - - + -
87A LEU* 3.9 17.5 - - + -
114A ALA* 2.9 18.4 - - - +
115A PHE 3.4 13.0 + - - +
117A LEU* 3.4 42.0 - - + -
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Residues in contact with ILE 53 (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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7A GLY* 5.7 2.6 - - - -
34A PHE* 4.6 0.4 - - + -
40A LEU* 4.0 20.9 - - + -
51A LEU 3.6 6.6 + - - +
52A PHE* 1.3 71.4 - - - +
54A ILE* 1.3 65.6 + - - +
55A ARG 4.2 5.8 - - - +
56A GLY* 4.5 13.2 - - - +
58A LEU* 3.7 28.7 - - + -
77A LYS 5.0 0.7 - - - +
78A GLU* 3.9 17.9 - - - +
79A GLY* 4.1 13.8 - - - +
80A ASP* 2.9 50.1 + - - +
81A PHE* 5.0 0.8 - - - +
82A CYS* 5.6 3.4 - - - -
112A VAL* 4.1 11.0 - - + -
114A ALA* 3.7 8.1 - - + -
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Residues in contact with ILE 54 (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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5A SER 5.1 7.6 - - - +
6A SER* 5.0 7.6 - - - +
7A GLY* 4.6 28.7 - - - +
8A VAL* 6.0 4.0 - - + -
29A LEU* 6.2 2.0 - - + -
52A PHE* 3.0 25.8 + - + +
53A ILE* 1.3 77.1 - - - +
55A ARG* 1.3 73.9 + - + +
78A GLU* 2.9 15.5 - - - +
113A GLU* 3.2 12.7 + - + +
114A ALA* 3.5 15.0 - - - -
115A PHE* 3.8 27.6 - - + -
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Residues in contact with ARG 55 (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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53A ILE* 3.8 1.7 - - - +
54A ILE* 1.3 88.4 - - + +
56A GLY* 1.3 58.5 + - - +
78A GLU* 3.3 17.0 + - + +
112A VAL* 5.1 0.2 - - - -
113A GLU* 3.1 38.1 + - + +
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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