Contacts of the helix formed by residues 53 - 63 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ASP* 2.9 14.4 + - - +
52A GLN* 1.3 78.8 - - - +
54A PRO* 1.3 71.8 - - - +
55A GLU* 3.0 15.9 + - - +
56A ALA* 2.9 24.4 + - + +
57A VAL* 3.0 14.2 + - - +
100A SER* 2.8 23.2 + - - -
102A PHE* 4.0 2.6 - - - -
103A HIS* 3.2 11.9 + - + +
109A ARG* 3.0 24.5 + - - -
123A MET 3.2 9.9 - - - +
3142A SAM 3.4 11.4 - - - +
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Residues in contact with PRO 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 GLN 3.3 10.0 - - - +
53A ASP* 1.3 90.3 - - - +
55A GLU* 1.3 57.0 + - + +
57A VAL* 3.4 5.8 + - + +
58A ALA* 3.0 28.9 + - - +
72A GLN* 3.8 20.6 - - - +
109A ARG* 4.5 6.3 - - - +
123A MET 4.0 5.8 - - - +
124A GLY* 4.4 5.4 - - - -
125A LEU* 4.2 26.2 - - + -
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Residues in contact with GLU 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 ASP* 3.0 17.9 + - - +
54A PRO* 1.3 81.0 - - + +
56A ALA* 1.3 61.2 + - - +
58A ALA* 4.4 10.5 - - - +
59A ARG* 3.1 22.2 + - - +
102A PHE* 3.2 43.1 - - + -
109A ARG* 4.1 8.1 - - - +
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Residues in contact with ALA 56 (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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31A LEU* 6.1 0.4 - - - -
32A GLY* 3.8 16.8 - - - +
51A ASP* 3.7 29.6 - - - +
53A ASP* 2.9 20.3 + - + +
55A GLU* 1.3 75.0 - - - +
57A VAL* 1.3 68.8 + - - +
59A ARG* 3.8 0.8 - - - +
60A ALA* 2.8 27.7 + - - +
100A SER* 4.7 4.5 - - - -
102A PHE* 4.1 10.1 - - + -
3142A SAM 4.2 5.2 - - - +
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Residues in contact with VAL 57 (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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31A LEU* 6.0 0.2 - - - -
51A ASP* 3.3 33.9 - - + +
53A ASP 3.0 15.2 + - - +
54A PRO* 3.7 8.3 - - + +
56A ALA* 1.3 76.9 - - - +
58A ALA* 1.3 65.0 + - - +
60A ALA* 3.3 2.1 + - - +
61A LYS* 3.0 35.0 + - + +
70A VAL* 3.7 23.8 - - + -
71A VAL 4.6 2.2 - - - +
72A GLN* 3.8 36.6 - - + +
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Residues in contact with ALA 58 (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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54A PRO 3.0 17.4 + - - +
55A GLU* 3.9 13.5 - - - +
57A VAL* 1.3 80.4 - - - +
59A ARG* 1.3 63.2 + - - +
61A LYS* 3.2 8.2 + - - +
62A GLY* 3.0 19.2 + - - -
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Residues in contact with ARG 59 (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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32A GLY 4.4 4.2 + - - -
33A GLY* 3.7 32.5 - - - +
55A GLU* 3.1 21.8 + - - +
56A ALA 3.8 2.0 - - - +
58A ALA* 1.3 80.0 - - - +
60A ALA* 1.3 62.0 + - - +
62A GLY* 3.0 13.5 + - - -
63A LEU* 3.3 30.4 + - + +
100A SER* 5.7 1.0 - - - -
101A SER* 2.7 30.9 + - - +
102A PHE* 3.0 37.2 - - + -
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Residues in contact with ALA 60 (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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31A LEU* 3.6 33.7 - - + -
32A GLY 4.6 4.7 - - - +
33A GLY 5.9 0.2 - - - -
34A ALA* 5.2 2.7 - - + -
56A ALA 2.8 21.9 + - - +
57A VAL* 3.6 5.2 - - - +
59A ARG* 1.3 74.0 - - - +
61A LYS* 1.3 63.0 + - - +
63A LEU* 3.1 30.7 + - + +
64A HIS 4.0 1.7 + - - -
65A LEU 5.1 0.9 + - - -
68A LEU* 4.7 10.6 - - + +
70A VAL* 4.0 8.1 - - + -
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Residues in contact with LYS 61 (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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57A VAL* 3.0 33.8 + - + +
58A ALA* 3.6 9.2 - - - +
60A ALA* 1.3 71.0 - - - +
62A GLY* 1.3 58.7 + - - +
63A LEU 3.0 5.2 - - - -
64A HIS* 3.0 34.4 + - - +
70A VAL* 3.9 27.2 + - + +
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Residues in contact with GLY 62 (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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58A ALA 3.0 13.6 + - - -
59A ARG* 3.0 8.2 + - - -
61A LYS* 1.3 76.3 - - - +
63A LEU* 1.3 59.6 + - - +
64A HIS* 3.2 23.5 + - - -
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Residues in contact with LEU 63 (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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33A GLY 3.9 21.5 - - - +
34A ALA* 4.0 14.8 - - + -
38A ARG* 4.1 23.7 + - - +
59A ARG* 3.5 24.2 - - + +
60A ALA* 3.2 18.2 - - - +
61A LYS 3.0 1.0 - - - -
62A GLY* 1.3 80.2 - - - +
64A HIS* 1.3 69.4 + - - +
65A LEU* 3.3 23.6 + - + +
68A LEU* 5.9 0.2 - - + -
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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