Contacts of the helix formed by residues 102 - 110 (chain 4) in PDB entry 2WSC
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 102 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504 TRP* 4.7 14.1 - - + -
984 SER* 3.2 42.2 + - - +
994 HIS* 2.8 9.6 + - - +
1004 TYR 3.6 0.2 - - - -
1014 VAL* 1.3 82.5 - - + +
1034 ILE* 1.3 57.7 + - - +
1044 ARG* 2.8 18.4 + - - +
1054 ARG* 3.0 30.1 + - - +
1064 TRP 3.9 1.2 + - - -
12074 CLA 3.1 71.3 - - + +
12084 CLA 5.8 1.2 - - - +
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Residues in contact with ILE 103 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994 HIS* 3.0 53.7 + - + +
1004 TYR* 3.6 8.1 - - + -
1024 GLU* 1.3 73.1 - - - +
1044 ARG* 1.3 51.0 - - - +
1054 ARG 3.3 1.1 - - - -
1064 TRP* 3.3 16.4 - - + +
1074 GLN* 2.5 34.8 + - + +
11964 CLA 3.9 8.5 - - - +
11974 CLA 3.3 41.1 - - + +
11984 CLA 3.9 23.1 - - + -
12074 CLA 3.7 23.8 - - + +
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Residues in contact with ARG 104 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004 TYR 4.6 2.9 - - - +
1014 VAL* 2.6 50.7 + - + +
1024 GLU* 2.8 9.0 + - - +
1034 ILE* 1.3 77.9 - - - +
1054 ARG* 1.3 119.3 + - - +
1074 GLN* 2.8 50.9 - - + +
1084 ASP* 3.3 5.0 - - - +
1134 GLY 4.8 1.2 - - - +
12064 CLA 3.0 76.1 + - + +
40144 CLA 6.3 0.4 - - - -
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Residues in contact with ARG 105 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424 GLN* 3.8 31.0 - - - +
464 VAL* 4.1 20.4 - - - +
504 TRP* 5.2 7.5 - - - -
1024 GLU* 3.0 16.4 + - - +
1044 ARG* 1.3 118.2 - - - +
1064 TRP* 1.3 55.3 + - - +
1084 ASP* 3.0 9.5 - - - +
1094 ILE* 2.6 45.6 + - + +
12064 CLA 3.9 24.9 - - + +
12074 CLA 3.1 63.6 + - + +
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Residues in contact with TRP 106 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1024 GLU 3.9 1.4 + - - -
1034 ILE* 3.3 11.2 + - - +
1054 ARG* 1.3 74.1 - - - +
1074 GLN* 1.3 50.8 + - - +
1084 ASP 2.7 16.5 + - - -
1094 ILE* 3.5 30.7 + - + +
1104 LYS* 4.3 10.9 + - + +
1114 ASN 5.3 0.2 + - - -
11964 CLA 2.6 48.3 - - + +
11984 CLA 4.0 25.4 - - + -
12074 CLA 3.0 50.2 - + + +
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Residues in contact with GLN 107 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004 TYR 5.0 1.8 + - - -
1034 ILE* 2.5 24.2 + - + +
1044 ARG* 2.8 42.7 - - + +
1054 ARG 3.3 0.2 - - - -
1064 TRP* 1.3 64.9 - - - +
1084 ASP* 1.3 52.7 + - - +
1134 GLY* 3.7 9.5 - - - +
11964 CLA 2.1 81.1 + - + +
11974 CLA 3.6 51.3 + - + +
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Residues in contact with ASP 108 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1044 ARG 3.3 8.3 - - - +
1054 ARG* 3.0 19.0 - - - +
1064 TRP 2.7 9.9 + - - -
1074 GLN* 1.3 74.4 - - - +
1094 ILE* 1.3 56.4 + - - -
1104 LYS 3.3 2.0 - - - -
1114 ASN 2.8 35.4 - - - -
1124 PRO* 2.9 11.1 - - - +
1134 GLY 2.4 41.8 + - - +
1144 SER* 2.8 20.4 + - - -
1204 ILE* 2.9 25.0 - - - +
11964 CLA 2.8 1.8 - - - +
12064 CLA 4.8 6.1 - - - +
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Residues in contact with ILE 109 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384 ARG* 3.4 45.3 - - + +
394 TRP 5.7 1.6 - - - +
424 GLN* 4.1 26.5 - - + +
1054 ARG* 2.6 31.5 + - + +
1064 TRP* 3.5 41.7 - - + +
1084 ASP* 1.3 72.4 - - - +
1104 LYS* 1.3 72.6 + - + +
1124 PRO* 4.7 3.6 - - - +
1204 ILE* 4.0 22.3 - - + +
12074 CLA 5.9 2.2 - - + -
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Residues in contact with LYS 110 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384 ARG* 5.0 3.6 - - - +
1064 TRP* 4.3 12.9 + - + +
1084 ASP 3.3 0.2 - - - -
1094 ILE* 1.3 89.9 - - + +
1114 ASN* 1.3 100.5 + - + +
1124 PRO* 3.5 6.6 - - - +
11964 CLA 5.1 13.2 - - + -
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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