Contacts of the strand formed by residues 929 - 940 (chain A) in PDB entry 5ES4
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 SER 929 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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927A LYS 3.5 4.3 + - - -
928A GLU* 1.3 80.2 + - - +
930A HIS* 1.3 63.3 + - - +
965A MET* 4.3 13.5 - - - -
1031A ASN* 3.0 37.5 + - - +
1032A LEU 3.5 10.1 - - - -
1033A SER* 4.0 12.1 - - - +
1034A PHE* 4.7 1.3 - - - -
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Residues in contact with HIS 930 (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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919A LEU* 3.8 28.6 - - + +
920A ASN* 5.9 1.8 - - - -
929A SER* 1.3 77.9 + - - +
931A VAL* 1.3 98.3 + - + +
932A ALA* 3.1 1.0 + - - +
1031A ASN* 3.5 5.6 - - - -
1032A LEU* 2.5 36.4 + - - +
1034A PHE* 3.7 24.9 - + + -
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Residues in contact with VAL 931 (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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916A THR* 4.5 9.9 + - - +
919A LEU* 4.7 0.9 - - - +
930A HIS* 1.3 99.8 + - + +
932A ALA* 1.3 59.5 + - - +
933A MET* 4.6 13.0 - - + -
1029A LYS* 4.5 22.4 - - + -
1030A GLY 4.1 1.6 - - - +
1031A ASN* 3.1 20.8 + - - +
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Residues in contact with ALA 932 (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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916A THR* 3.7 12.1 - - - +
919A LEU* 4.0 15.7 - - + -
930A HIS 3.1 6.0 + - - +
931A VAL* 1.3 74.3 - - - +
933A MET* 1.3 63.8 + - - +
964A TRP* 3.5 26.6 - - + -
1029A LYS* 3.3 4.7 - - - -
1030A GLY 3.0 35.6 + - - +
1032A LEU* 4.0 7.0 - - + -
1076A THR* 5.2 2.5 - - - +
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Residues in contact with MET 933 (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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914A GLN 5.2 7.4 - - - +
915A PHE* 3.6 5.4 - - - -
916A THR* 3.4 39.5 + - + +
931A VAL* 4.6 11.7 - - + -
932A ALA* 1.3 80.9 - - - +
934A HIS* 1.3 66.9 + - - +
935A ARG* 6.4 0.4 - - + -
1027A THR* 5.3 15.0 - - + -
1028A LEU 3.2 6.3 - - - +
1029A LYS* 3.5 43.7 - - + +
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Residues in contact with HIS 934 (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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915A PHE* 4.3 5.8 - - + -
916A THR* 4.9 0.4 - - - -
933A MET* 1.3 82.1 - - - +
935A ARG* 1.3 61.4 + - - +
936A TYR* 4.4 6.0 - - + -
964A TRP* 4.1 22.5 - + + -
1027A THR* 3.3 4.7 - - - -
1028A LEU* 2.7 43.3 + - + +
1047A VAL 4.0 6.5 - - - -
1049A SER* 3.2 31.7 + - - +
1074A THR* 3.0 44.6 + - + +
1075A THR* 3.7 3.3 - - - -
1076A THR* 2.8 37.8 + - - -
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Residues in contact with ARG 935 (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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911A SER* 3.8 0.7 - - - -
912A HIS* 2.9 79.8 + - + +
914A GLN* 4.3 21.7 - - - +
915A PHE* 4.8 5.3 - - - +
933A MET* 6.4 0.4 - - + -
934A HIS* 1.3 76.4 - - - +
936A TYR* 1.3 73.6 + - - +
937A GLN* 5.8 0.2 - - - +
1023A GLU* 5.6 0.8 + - - -
1025A ASP* 2.8 40.1 + - - +
1026A PHE 3.5 5.2 - - - +
1027A THR* 3.6 23.7 - - + +
1074A THR* 4.0 4.4 + - - +
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Residues in contact with TYR 936 (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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909A VAL* 4.3 9.9 - - + -
910A SER 3.3 11.7 - - - +
911A SER* 4.0 2.7 - - - -
912A HIS* 4.3 0.7 - - - +
934A HIS* 4.4 6.3 - - + -
935A ARG* 1.3 80.4 + - - +
937A GLN* 1.3 61.0 + - - +
938A VAL 4.3 0.4 - - - -
952A PHE* 3.7 32.1 - + + -
1024A LEU 4.2 0.5 - - - +
1025A ASP* 3.8 3.5 - - - +
1026A PHE* 2.9 37.2 + - + +
1028A LEU* 3.6 19.7 - - + -
1049A SER* 2.2 51.9 + - - -
1050A VAL 4.4 0.9 - - - -
1051A ALA* 3.9 17.3 - - + -
1072A ALA* 4.3 4.9 - - + -
1073A GLN 3.8 18.6 - - - -
1074A THR* 3.1 31.4 + - - -
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Residues in contact with GLN 937 (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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482A TRP* 6.1 2.6 - - - +
483A ARG* 4.8 7.5 - - - +
908A VAL* 4.0 0.7 - - - +
909A VAL* 3.1 3.0 - - - +
910A SER* 2.7 55.8 + - - +
911A SER 5.3 0.5 - - - +
912A HIS* 3.6 30.3 - - + +
913A GLU* 5.0 1.4 - - - +
935A ARG* 6.1 0.2 - - - -
936A TYR* 1.3 75.6 - - - +
938A VAL* 1.3 61.5 + - - +
939A ASN* 3.7 14.4 + - - +
1023A GLU* 2.9 31.4 + - - +
1024A LEU 3.9 3.8 - - - -
1025A ASP* 4.0 6.1 - - - +
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Residues in contact with VAL 938 (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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908A VAL 3.2 12.8 - - - +
909A VAL* 3.7 11.2 - - + -
937A GLN* 1.3 73.4 - - - +
939A ASN* 1.3 72.2 + - - +
950A ILE* 4.1 15.5 - - + -
1018A PHE* 4.1 18.1 - - + -
1022A GLU 4.0 0.3 - - - +
1023A GLU* 3.5 0.7 - - - +
1024A LEU* 3.1 61.5 + - + +
1026A PHE* 3.9 17.9 - - + -
1053A ILE* 3.7 20.0 - - + -
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Residues in contact with ASN 939 (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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481A GLY* 5.2 6.7 - - - -
482A TRP 5.4 0.7 + - - -
483A ARG* 3.0 42.6 + - - +
907A THR* 3.8 1.0 - - - -
908A VAL* 2.8 37.3 + - + +
910A SER* 5.4 0.4 + - - -
937A GLN* 3.7 26.3 + - - +
938A VAL* 1.3 84.3 + - - +
940A ASN* 1.3 59.4 + - - +
941A LEU* 3.3 13.0 + - + -
1018A PHE* 3.7 5.6 - - - -
1021A GLN* 4.8 3.1 - - - +
1022A GLU 3.7 5.6 - - - +
1023A GLU* 3.1 31.4 - - - +
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Residues in contact with ASN 940 (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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906A TYR 3.9 5.8 + - - +
907A THR* 4.9 1.3 - - - +
939A ASN* 1.3 68.4 - - - +
941A LEU* 1.3 60.1 + - - +
942A GLY* 3.2 17.2 + - - -
944A ARG 3.2 21.6 + - - +
946A LEU* 3.8 12.4 - - - +
1018A PHE* 2.4 50.9 + - + -
1019A SER 3.2 18.1 + - - +
1020A VAL* 3.3 11.0 - - - +
1021A GLN* 2.6 34.4 + - - +
1022A GLU 3.4 4.6 + - - +
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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