Contacts of the strand formed by residues 1051 - 1055 (chain A) in PDB entry 5WBL
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 ILE1051 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1043A VAL* 3.8 18.6 - - + -
1044A ALA 3.6 7.4 - - - +
1045A ALA* 4.8 6.3 - - + -
1049A GLU 3.6 3.6 - - - +
1050A ARG* 1.3 80.2 - - - +
1052A ARG* 1.3 74.8 + - - +
1053A VAL* 4.5 2.5 - - + -
1064A GLY* 3.2 7.6 - - - -
1065A PHE* 3.0 59.4 + - + +
1067A ASN* 3.8 21.8 - - + +
1078A LEU* 4.8 3.1 - - + -
1089A LEU* 3.9 11.2 - - + -
1091A VAL* 3.5 36.1 - - + -
1101A TRP* 4.8 1.1 - - - +
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Residues in contact with ARG1052 (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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1022A TRP* 3.5 32.1 - - + -
1024A THR 4.2 12.5 + - - +
1025A ARG* 5.2 3.2 + - - +
1026A PHE* 3.3 37.3 - - + -
1043A VAL* 3.4 8.0 - - - +
1044A ALA* 3.2 28.8 + - + -
1050A ARG* 3.5 33.1 - - - +
1051A ILE* 1.3 74.3 - - - +
1053A VAL* 1.3 68.0 + - - +
1054A TRP 3.8 0.7 - - - -
1061A LEU* 4.0 12.3 - - + -
1063A ASN 3.4 4.3 - - - -
1064A GLY* 4.3 7.7 - - - -
1065A PHE 3.8 28.3 + - - +
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Residues in contact with VAL1053 (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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1041A ILE* 3.5 27.1 - - + -
1042A VAL 3.3 4.0 - - - +
1043A VAL* 4.5 3.8 - - + -
1051A ILE* 4.5 11.7 - - + -
1052A ARG* 1.3 77.8 - - - +
1054A TRP* 1.3 62.0 + - - +
1061A LEU* 4.3 1.1 - - - +
1062A LEU* 2.8 40.2 + - + +
1063A ASN* 3.0 24.6 + - + +
1065A PHE* 5.0 1.1 - - + -
1104A TYR* 3.5 36.3 - - + +
1105A ALA* 4.1 14.8 - - + -
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Residues in contact with TRP1054 (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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1020A ALA* 3.4 36.1 - - + -
1022A TRP* 3.2 80.4 - + + +
1041A ILE* 3.7 1.5 - - - -
1042A VAL* 2.7 48.6 + - + +
1052A ARG 3.8 1.4 - - - -
1053A VAL* 1.3 73.9 - - - +
1055A ASN* 1.3 81.4 + - - +
1056A TYR* 3.9 17.9 - - + -
1059A ALA* 3.7 33.1 + - + -
1060A THR 3.5 15.2 - - - -
1061A LEU* 3.9 9.5 - - + +
1062A LEU* 5.4 0.4 - - - -
1333A VAL* 4.8 2.0 - - + -
1335A ILE* 4.1 8.7 - - + -
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Residues in contact with ASN1055 (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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1040A PRO* 3.0 37.6 + - - +
1041A ILE* 4.5 2.3 - - - +
1053A VAL 3.6 1.4 + - - -
1054A TRP* 1.3 85.0 - - - +
1056A TYR* 1.3 57.6 + - - +
1057A GLU* 3.0 23.7 + - - -
1058A GLU* 3.0 26.5 + - + +
1059A ALA 3.4 3.2 + - - -
1060A THR* 2.6 48.8 + - + +
1062A LEU* 3.6 24.1 - - + +
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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