Contacts of the helix formed by residues 53 - 63 (chain B) in PDB entry 1WRL
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 THR 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 ASN 4.9 4.0 - - - +
52B PRO* 1.3 76.0 - - - +
54B PRO* 1.3 77.3 - - + +
55B GLU* 3.5 13.1 + - - +
56B GLU* 3.1 40.3 + - - +
57B LEU* 3.0 25.0 + - - +
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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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38B THR* 4.7 2.6 - - - +
52B PRO 4.8 0.7 - - - +
53B THR* 1.3 87.0 - - - +
55B GLU* 1.3 72.1 + - - +
57B LEU* 3.2 12.5 + - + +
58B GLN* 3.0 43.6 + - + +
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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 THR* 3.1 16.2 + - - +
54B PRO* 1.3 90.3 - - - +
56B GLU* 1.3 62.4 + - + +
58B GLN* 3.3 16.7 + - - +
59B GLU* 3.1 25.4 + - - +
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Residues in contact with GLU 56 (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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51B ASN 4.6 0.5 - - - +
52B PRO* 3.5 22.9 - - + +
53B THR* 3.1 30.5 + - - +
55B GLU* 1.3 77.5 - - + +
57B LEU* 1.3 57.7 + - - +
59B GLU* 3.2 17.4 - - - +
60B MET* 3.0 35.2 + - + +
201B TFP 3.2 40.8 - - - +
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Residues in contact with LEU 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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38B THR* 3.6 34.8 - - + +
41B LEU* 3.6 33.7 - - + +
42B GLY* 3.8 16.2 - - - +
45B MET* 4.1 5.4 - - - -
46B ARG* 6.4 0.2 - - - +
52B PRO* 3.8 30.1 - - + +
53B THR 3.0 21.4 + - - +
54B PRO* 3.5 10.3 - - + +
56B GLU* 1.3 76.0 - - - +
58B GLN* 1.3 64.2 + - - +
60B MET* 3.4 4.4 + - - +
61B ILE* 3.2 27.9 + - - +
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Residues in contact with GLN 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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38B THR* 3.9 19.1 - - + +
54B PRO* 3.0 30.9 + - + +
55B GLU* 3.7 15.0 - - - +
56B GLU 3.3 0.2 - - - -
57B LEU* 1.3 76.5 - - - +
59B GLU* 1.3 58.0 + - - +
61B ILE* 3.9 4.6 - - - +
62B ASP* 2.9 30.7 + - - +
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Residues in contact with GLU 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 15.4 + - - +
56B GLU* 3.2 20.1 - - - +
57B LEU 3.1 0.2 - - - -
58B GLN* 1.3 75.1 - - - +
60B MET* 1.3 68.4 + - + +
62B ASP* 3.1 6.7 + - - +
63B GLU* 3.1 40.0 + - + +
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Residues in contact with MET 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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41B LEU* 4.0 18.8 - - + -
45B MET* 3.7 36.8 - - + +
52B PRO* 5.6 1.6 - - - -
56B GLU* 3.0 18.1 + - + +
57B LEU* 3.4 10.1 + - - +
59B GLU* 1.3 80.4 - - + +
61B ILE* 1.3 62.8 + - - +
63B GLU* 3.6 21.8 + - - +
64B VAL* 3.9 2.8 - - - +
80B MET* 3.8 18.2 - - + +
201B TFP 3.7 51.8 - - + -
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Residues in contact with ILE 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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36B ILE* 4.0 10.8 - - + +
37B SER 3.8 7.6 - - - +
38B THR* 3.6 42.0 - - + +
41B LEU* 4.0 14.6 - - + -
57B LEU 3.2 11.9 + - - +
58B GLN* 3.9 5.2 - - - +
59B GLU 3.2 0.6 - - - -
60B MET* 1.3 74.8 - - - +
62B ASP* 1.3 65.3 + - - +
64B VAL* 3.1 7.3 + - - +
65B ASP* 2.9 24.2 + - + -
70B GLY* 3.7 31.4 - - - +
71B THR 3.8 2.7 - - - +
72B VAL* 3.8 25.6 - - + -
80B MET* 4.5 0.7 - - + -
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Residues in contact with ASP 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 GLN 2.9 20.2 + - - +
59B GLU* 3.1 6.3 + - - +
61B ILE* 1.3 78.1 - - - +
63B GLU* 1.3 60.2 + - - +
64B VAL 2.9 5.5 + - - -
65B ASP* 3.3 20.7 + - - +
66B GLU* 5.4 1.0 - - - +
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Residues in contact with GLU 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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59B GLU* 3.1 33.1 + - + +
60B MET* 3.7 15.8 + - - +
61B ILE 3.2 0.6 - - - -
62B ASP* 1.3 77.2 + - + +
64B VAL* 1.3 62.0 + - + +
66B GLU* 4.4 6.1 - - - +
79B VAL* 5.6 0.3 - - - +
83B ARG* 3.1 53.0 + - - +
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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