Contacts of the strand formed by residues 1058 - 1067 (chain A) in PDB entry 4BQ9
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 PRO1058 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1027A THR* 3.8 20.0 - - - +
1056A ASP 4.5 0.7 - - - +
1057A THR* 1.4 94.4 - - + +
1059A TYR* 1.3 58.4 + - - +
1060A TYR* 3.9 13.8 - - + +
1079A GLN* 3.2 26.2 - - - +
1080A PHE 3.5 7.4 - - - +
1081A ARG* 3.9 31.0 - - + +
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Residues in contact with TYR1059 (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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1025A TYR* 3.8 26.5 - + - -
1026A SER* 3.5 7.0 - - - -
1027A THR* 3.4 23.3 - - + +
1052A GLU 5.1 0.2 + - - -
1053A LEU* 3.7 29.1 - - + +
1054A THR* 3.0 51.6 + - - -
1057A THR* 3.4 27.6 + - + -
1058A PRO* 1.3 71.7 - - - +
1060A TYR* 1.3 62.6 + - - +
1061A PHE* 3.6 22.0 - + + -
1079A GLN* 3.5 4.9 - - - +
1080A PHE* 2.8 34.3 + - + +
1082A THR* 3.9 11.4 - - + -
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Residues in contact with TYR1060 (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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1025A TYR* 3.1 29.5 - - - +
1026A SER 2.8 18.7 + - - +
1027A THR 3.8 17.9 - - - -
1029A VAL* 3.8 47.9 - - + +
1036A TRP* 3.4 24.0 - - + -
1058A PRO* 3.9 19.6 - - + +
1059A TYR* 1.3 71.3 - - - +
1061A PHE* 1.3 62.9 + - - +
1077A ALA* 4.6 6.3 - - + -
1078A VAL 3.5 3.8 - - - -
1079A GLN* 3.6 49.9 + - + -
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Residues in contact with PHE1061 (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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992A VAL* 5.0 9.1 - - + +
994A VAL* 3.8 22.2 - - + -
1004A ILE* 3.5 31.4 - - + -
1006A VAL* 4.7 5.8 - - + -
1023A ILE* 4.3 15.7 - - + -
1024A TYR 3.3 4.5 - - - -
1025A TYR* 3.4 30.7 - + + -
1050A ILE* 4.1 5.8 - - + -
1053A LEU* 4.8 2.9 - - + -
1059A TYR* 3.6 38.8 - + + -
1060A TYR* 1.3 73.4 - - - +
1062A LYS* 1.3 63.6 + - - +
1063A ILE* 5.2 1.6 - - + -
1075A SER* 4.1 1.6 + - - -
1076A GLU 3.9 2.6 - - - +
1077A ALA* 3.2 5.3 - - - +
1078A VAL* 2.9 46.4 + - + +
1080A PHE* 4.1 17.3 - + + -
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Residues in contact with LYS1062 (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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1023A ILE* 3.4 2.6 - - - +
1024A TYR* 2.7 47.5 + - + +
1029A VAL* 5.5 2.4 + - - -
1031A ALA 5.7 1.2 + - - -
1033A ILE* 3.8 18.1 - - + +
1036A TRP* 3.7 32.0 - - + +
1061A PHE* 1.3 76.4 - - - +
1063A ILE* 1.3 63.2 + - - +
1074A MET* 3.9 28.7 - - + -
1075A SER* 3.5 21.5 - - - +
1077A ALA* 4.0 16.8 - - + +
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Residues in contact with ILE1063 (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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989A PRO* 3.3 23.0 - - + +
992A VAL* 3.7 34.8 - - + -
1006A VAL* 3.9 10.1 - - + -
1008A TRP* 3.5 33.7 - - + -
1021A TYR* 3.9 24.5 - - + -
1022A ILE 3.3 10.8 - - - +
1023A ILE* 4.0 18.6 - - + -
1061A PHE* 5.2 1.1 - - + -
1062A LYS* 1.3 80.1 - - - +
1064A GLN* 1.3 63.9 + - - +
1074A MET* 3.3 3.7 - - - -
1075A SER* 2.8 33.9 + - - +
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Residues in contact with GLN1064 (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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989A PRO* 3.9 5.8 - - - -
1021A TYR* 3.1 6.1 - - - +
1022A ILE* 2.9 35.6 + - + +
1024A TYR* 2.7 38.8 + - + +
1063A ILE* 1.3 74.1 - - - +
1065A ALA* 1.3 59.3 + - - +
1071A MET* 3.6 35.5 - - + +
1072A GLY 2.7 22.6 + - - +
1073A PRO 3.7 9.9 - - - +
1074A MET* 3.7 24.3 - - + +
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Residues in contact with ALA1065 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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985A PRO* 3.9 8.4 - - + +
987A SER 5.2 0.9 - - - +
989A PRO* 3.9 7.1 - - + +
1011A PRO* 3.9 25.4 - - + -
1018A ILE* 4.0 11.0 - - + -
1021A TYR* 3.7 26.5 - - + -
1064A GLN* 1.3 73.2 - - - +
1066A ARG* 1.3 60.0 + - - +
1071A MET* 3.4 7.9 - - - +
1072A GLY* 2.9 27.0 + - - +
1073A PRO 4.4 3.0 + - - -
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Residues in contact with ARG1066 (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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985A PRO* 4.4 3.1 - - - -
1018A ILE* 3.3 9.7 - - - +
1019A THR* 2.8 49.0 + - - +
1020A GLY* 2.8 21.0 + - - +
1021A TYR 5.8 0.2 - - - -
1022A ILE* 4.2 20.4 - - - +
1065A ALA* 1.3 74.4 - - - +
1067A ASN* 1.3 64.4 + - - +
1070A GLY* 3.5 11.7 - - - +
1071A MET* 3.6 28.5 - - + +
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Residues in contact with ASN1067 (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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982A GLU* 3.8 8.0 + - - +
983A LEU 2.8 25.4 + - - +
984A VAL* 4.0 1.0 - - - -
985A PRO* 3.4 13.0 - - + +
1014A ALA 3.0 20.4 + - - -
1016A GLY* 3.9 7.0 - - - +
1017A LYS 3.3 23.1 - - - +
1018A ILE* 4.3 2.5 - - + -
1019A THR* 3.4 11.4 + - - -
1066A ARG* 1.3 82.3 - - - +
1068A SER* 1.4 65.0 + - - +
1069A LYS* 2.8 22.3 + - - +
1070A GLY* 3.0 23.9 + - - +
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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