Contacts of the helix formed by residues 53 - 63 (chain B) in PDB entry 1WG8
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 53 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B ASP* 2.9 14.9 + - - +
52B GLN* 1.3 78.7 - - - +
54B PRO* 1.3 81.3 - - - +
55B GLU* 3.2 9.2 + - - +
56B ALA* 3.7 5.9 + - + +
57B VAL* 3.0 24.6 + - - +
100B SER* 4.3 1.7 + - - -
102B PHE* 3.7 15.8 - - - +
103B HIS* 3.3 17.3 + - - +
109B ARG* 2.5 38.4 + - - -
123B MET 3.6 9.2 - - - +
3141B SAM 3.7 7.4 - - - +
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Residues in contact with PRO 54 (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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52B GLN 3.4 10.0 - - - +
53B ASP* 1.3 92.2 - - - +
55B GLU* 1.3 57.4 + - + +
57B VAL* 3.5 2.4 + - + +
58B ALA* 3.0 30.5 + - - +
72B GLN* 4.0 29.3 + - - +
109B ARG* 5.4 2.7 - - - +
123B MET 4.7 2.9 - - - +
124B GLY* 4.7 5.4 - - - -
125B LEU* 4.9 20.6 - - + -
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Residues in contact with GLU 55 (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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53B ASP* 3.8 15.9 - - - +
54B PRO* 1.3 77.7 - - + +
56B ALA* 1.3 67.9 + - - +
58B ALA* 3.0 17.8 + - - +
59B ARG* 3.1 54.2 + - - +
102B PHE* 3.5 22.6 - - + +
109B ARG* 4.0 9.4 - - - +
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Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 5.7 0.7 - - - -
32B GLY* 3.5 23.7 - - - +
51B ASP* 3.8 22.7 - - + +
53B ASP* 3.3 13.6 + - + +
55B GLU* 1.3 78.1 - - - +
57B VAL* 1.3 64.8 + - - +
59B ARG* 3.4 1.0 + - - +
60B ALA* 3.0 26.2 + - - +
102B PHE* 4.0 25.5 - - + -
3141B SAM 4.7 2.0 - - - +
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Residues in contact with VAL 57 (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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31B LEU* 5.6 0.2 - - - -
51B ASP* 3.3 34.3 - - + +
53B ASP 3.0 14.1 + - - +
54B PRO 3.5 8.1 - - - +
55B GLU 3.2 0.2 - - - -
56B ALA* 1.3 76.9 - - - +
58B ALA* 1.3 65.7 + - - +
60B ALA* 3.3 2.2 + - - +
61B LYS* 3.1 40.6 + - + +
70B VAL* 4.0 19.6 - - + +
71B VAL 4.4 2.0 - - - +
72B GLN* 3.7 37.7 - - + +
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Residues in contact with ALA 58 (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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54B PRO 3.0 17.4 + - - +
55B GLU* 3.0 10.0 + - - +
57B VAL* 1.3 78.8 - - - +
59B ARG* 1.3 66.0 + - + +
61B LYS* 3.4 7.9 + - - +
62B GLY* 3.1 18.2 + - - -
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Residues in contact with ARG 59 (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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55B GLU* 3.1 42.9 + - - +
56B ALA 4.0 2.9 - - - +
58B ALA* 1.3 76.0 - - + +
60B ALA* 1.3 65.6 + - - +
62B GLY* 3.2 8.8 + - - +
63B LEU* 3.2 21.6 + - + +
102B PHE* 3.2 33.1 - - + -
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Residues in contact with ALA 60 (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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31B LEU* 3.4 35.2 - - + -
32B GLY 4.9 3.6 - - - +
33B GLY 5.7 0.4 - - - -
34B ALA* 4.8 3.1 - - + -
56B ALA 3.0 16.5 + - - +
57B VAL 3.9 2.9 - - - +
59B ARG* 1.3 76.8 - - - +
61B LYS* 1.3 62.6 + - - +
63B LEU* 3.2 30.6 + - + +
64B HIS 3.9 2.3 + - - -
65B LEU* 4.9 0.7 + - - +
68B LEU* 4.4 13.6 - - + +
70B VAL* 4.0 8.0 - - + +
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Residues in contact with LYS 61 (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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57B VAL* 3.1 31.4 + - + +
58B ALA* 3.6 7.6 - - - +
60B ALA* 1.3 78.7 - - - +
62B GLY* 1.3 60.5 + - - +
64B HIS* 3.2 26.0 + - - +
70B VAL* 2.7 52.9 + - + +
71B VAL* 4.7 0.8 - - - +
72B GLN 5.3 0.6 - - - +
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Residues in contact with GLY 62 (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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58B ALA 3.1 14.5 + - - -
59B ARG* 3.2 5.8 + - - -
60B ALA 3.2 0.4 - - - -
61B LYS* 1.3 76.9 - - - +
63B LEU* 1.3 58.3 + - - +
64B HIS* 2.8 26.4 + - - -
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Residues in contact with LEU 63 (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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33B GLY 4.4 5.6 - - - +
34B ALA* 4.3 12.6 - - + -
38B ARG* 3.8 22.7 - - - +
59B ARG 3.2 15.0 + - - +
60B ALA* 3.3 21.5 - - - +
61B LYS 3.1 0.6 - - - -
62B GLY* 1.3 78.7 - - - +
64B HIS* 1.3 68.8 + - - +
65B LEU* 2.9 39.9 + - + +
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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