Contacts of the strand formed by residues 50 - 55 (chain A) in PDB entry 1WGY
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 50 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 3.4 18.3 - - + +
40A ALA* 3.7 20.2 - - + +
43A ILE* 3.1 28.5 - - + -
45A TYR* 3.5 19.5 - - + -
46A ALA 2.8 8.2 + - - +
47A GLU 2.7 16.6 + - - +
48A GLU 3.9 5.0 - - - +
49A ASP* 1.3 83.3 - - - +
51A ALA* 1.3 65.1 + - - +
83A VAL* 3.7 13.2 - - + -
84A TYR 3.1 24.9 - - - +
85A ARG* 3.7 23.3 - - + -
86A LYS* 4.2 4.2 - - - +
95A PHE* 4.2 7.2 - - + -
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Residues in contact with ALA 51 (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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36A LEU* 3.5 12.3 - - - +
50A LEU* 1.3 82.4 - - - +
52A LEU* 1.3 63.2 + - - +
53A VAL* 3.4 2.0 + - - +
63A GLU* 4.6 7.9 - - + -
64A LEU 5.7 4.0 - - - +
83A VAL* 3.2 23.6 - - - -
84A TYR 3.2 8.8 + - - +
86A LYS* 4.8 10.5 - - + -
92A LEU* 4.2 22.0 - - + -
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Residues in contact with LEU 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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14A VAL* 4.5 15.5 - - + -
32A ALA* 3.1 41.3 - - + +
33A GLN* 4.1 1.1 - - - +
35A ILE* 5.4 0.4 - - + -
36A LEU* 3.5 50.0 - - + +
39A VAL* 5.6 0.2 - - + -
51A ALA* 1.3 72.0 - - - +
53A VAL* 1.3 61.7 + - - +
63A GLU* 3.8 3.8 - - - +
64A LEU* 3.0 40.8 + - + +
65A GLN 5.1 3.8 - - - +
66A PRO* 5.2 3.6 - - + -
70A VAL* 4.6 4.0 - - + -
81A ILE* 3.9 18.6 - - + -
82A TYR 3.2 10.1 - - - +
83A VAL* 4.5 3.6 - - + -
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Residues in contact with VAL 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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51A ALA 4.0 2.2 - - - +
52A LEU* 1.3 72.6 - - - +
54A ALA* 1.3 58.7 + - - +
55A ILE* 3.7 17.5 - - + -
61A LYS* 3.9 7.6 - - + -
62A HIS 3.0 8.1 - - - +
63A GLU* 2.7 35.2 - - + +
81A ILE* 3.3 2.1 - - - -
82A TYR* 2.5 44.6 + - - +
84A TYR* 2.9 56.8 - - + -
92A LEU* 3.6 6.1 - - + -
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Residues in contact with ALA 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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52A LEU 3.7 2.8 + - - -
53A VAL* 1.3 70.8 - - - +
55A ILE* 1.3 61.7 + - - +
62A HIS* 2.5 47.3 + - + +
64A LEU* 3.8 29.6 - - + -
80A ARG 4.4 0.2 - - - -
81A ILE* 4.3 19.1 - - + +
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Residues in contact with ILE 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 VAL* 3.7 9.9 - - + -
54A ALA* 1.3 80.3 - - - +
56A THR* 1.3 78.3 + - - +
59A GLY* 4.2 4.3 - - - -
60A GLU 3.1 29.2 - - - +
61A LYS* 3.2 29.8 - - + -
76A GLU* 5.3 0.7 - - - +
79A GLY* 4.5 4.0 - - - -
80A ARG* 3.4 27.8 + - + +
82A TYR* 3.5 35.2 - - + -
84A TYR* 3.6 11.4 - - - +
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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