Contacts of the strand formed by residues 992 - 1002 (chain A) in PDB entry 4YOC
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 ARG 992 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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939A VAL 3.7 1.2 - - - +
940A TYR* 3.7 0.2 - - - -
941A LEU* 2.9 45.0 + - + +
942A PRO 3.3 18.6 - - - +
943A PRO* 3.3 25.2 + - + +
946A PHE* 2.8 56.1 + - + +
947A THR* 4.9 5.1 - - - +
948A PHE* 3.7 32.5 - - - -
989A GLU* 3.1 36.2 + - - -
990A PRO 3.4 8.7 + - - -
991A TYR* 1.3 75.6 + - - +
993A ILE* 1.3 62.3 + - - +
994A GLY 4.2 0.2 - - - -
1026A ASN* 4.7 4.0 + - - +
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Residues in contact with ILE 993 (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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939A VAL 3.5 1.8 - - - -
940A TYR* 4.4 10.3 - - + -
946A PHE* 4.1 7.3 - - - -
991A TYR 3.7 7.8 + - - +
992A ARG* 1.3 80.7 - - - +
994A GLY* 1.3 62.1 + - - +
1020A LYS 4.0 0.3 - - - -
1021A PHE* 3.0 37.9 + - + +
1023A ARG* 3.8 11.7 - - + +
1042A LEU* 3.6 27.6 - - + -
1060A CYS* 3.9 12.3 - - - -
1062A VAL* 3.8 26.5 - - + -
1083A PHE* 3.6 42.4 - - + -
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Residues in contact with GLY 994 (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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938A GLY* 3.6 3.1 - - - -
939A VAL* 2.9 37.3 + - - +
941A LEU* 4.9 2.5 - - - +
946A PHE* 5.0 2.9 - - - -
992A ARG 4.2 0.4 - - - -
993A ILE* 1.3 76.1 - - - +
995A ARG* 1.3 60.7 + - - -
1018A VAL* 4.2 16.8 - - - -
1019A ASN 3.1 11.7 - - - -
1020A LYS* 4.8 0.9 - - - -
1021A PHE* 3.9 5.8 - - - -
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Residues in contact with ARG 995 (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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936A GLY* 3.2 39.0 + - - +
937A ASP 3.8 4.5 - - - +
938A GLY* 4.8 1.6 - - - -
994A GLY* 1.3 73.5 - - - -
996A ILE* 1.3 69.3 + - - +
997A LYS* 3.1 1.1 + - - +
1018A VAL* 3.1 6.1 - - - -
1019A ASN* 2.9 42.4 + - + +
1021A PHE* 3.5 19.5 - - + -
1044A TRP* 3.4 22.8 - - - -
1062A VAL* 3.8 17.9 + - + +
1063A GLU* 5.4 0.8 - - - +
1064A TYR 5.5 0.4 - - - +
1085A PHE* 3.7 22.4 - - - -
1102A HIS 5.7 1.5 + - - -
1103A ALA* 3.1 27.9 + - - +
1105A SER* 4.4 19.5 - - - +
1106A PRO* 5.3 3.6 - - - +
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Residues in contact with ILE 996 (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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933A TYR* 3.8 22.7 - - + -
934A ARG 3.6 13.7 - - - +
935A VAL* 3.6 15.4 - - - +
936A GLY* 2.7 34.0 + - - +
937A ASP* 3.1 20.5 + - + +
939A VAL* 3.7 30.3 - - + -
995A ARG* 1.3 72.7 - - - +
997A LYS* 1.3 60.5 + - - +
998A GLU 4.2 4.3 - - - +
999A ILE* 3.6 30.1 - - + -
1016A ILE* 3.9 22.2 - - + -
1017A ARG 3.9 3.8 - - - -
1018A VAL* 4.1 1.3 - - + -
1053A PHE* 5.8 0.4 - - + -
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Residues in contact with LYS 997 (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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935A VAL* 3.4 21.5 - - - +
995A ARG 3.1 2.1 + - - +
996A ILE* 1.3 73.7 - - - +
998A GLU* 1.3 74.0 + - + +
1017A ARG* 2.9 24.4 + - + +
1018A VAL* 4.7 0.7 - - - -
1019A ASN* 3.9 24.7 - - - +
1048A GLU* 2.3 47.6 + - + +
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Residues in contact with GLU 998 (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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920A ARG* 2.8 45.3 + - - -
922A LEU* 4.1 17.0 - - + +
935A VAL* 5.1 1.3 - - - -
996A ILE* 4.4 0.4 - - - -
997A LYS* 1.3 95.3 - - + +
999A ILE* 1.3 63.7 + - - +
1000A PHE* 4.1 6.9 - - + -
1015A LYS 3.9 0.2 - - - +
1016A ILE* 3.4 8.7 - - - +
1017A ARG* 2.8 60.7 + - + +
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Residues in contact with ILE 999 (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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910A VAL* 4.9 0.9 - - + -
922A LEU* 3.4 4.4 - - - +
923A TYR* 2.9 50.6 + - + +
924A TYR 3.6 24.2 - - - +
925A SER* 3.9 1.1 - - - -
926A ALA* 3.7 26.7 - - + +
933A TYR* 3.7 19.1 - - + +
934A ARG 4.4 1.3 - - - +
935A VAL* 4.1 5.0 - - + +
996A ILE* 3.6 28.3 - - + -
998A GLU* 1.3 72.9 - - - +
1000A PHE* 1.3 65.1 + - - +
1014A ILE* 4.1 10.5 - - + -
1015A LYS 3.5 2.5 - - - -
1016A ILE* 3.9 19.3 - - + -
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Residues in contact with PHE1000 (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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920A ARG* 4.0 35.4 - - + -
921A VAL 3.1 12.3 - - - +
922A LEU* 3.5 15.5 - - + -
923A TYR* 4.4 1.8 - - - -
998A GLU* 4.1 17.9 - - + -
999A ILE* 1.3 78.9 - - - +
1001A CYS* 1.3 67.3 + - - +
1002A PRO* 4.5 7.6 - - + -
1015A LYS* 2.7 82.1 + - + +
1017A ARG* 4.2 12.6 - - + -
1050A VAL* 4.0 28.9 - - + -
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Residues in contact with CYS1001 (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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910A VAL* 3.5 31.6 - - - -
920A ARG* 3.6 0.2 - - - -
921A VAL* 2.9 34.4 + - - +
923A TYR* 3.6 13.0 - - + -
1000A PHE* 1.3 80.1 - - - +
1002A PRO* 1.3 66.4 - - - +
1003A LYS 3.7 0.2 + - - -
1009A PRO* 4.4 8.2 - - + +
1010A ASN 3.2 26.2 - - - +
1011A GLU* 4.1 7.6 - - - -
1013A ASP 3.9 0.2 - - - -
1014A ILE* 3.8 18.4 - - - -
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Residues in contact with PRO1002 (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 SER 3.8 9.9 - - - +
920A ARG* 4.3 3.8 - - + -
1000A PHE* 4.2 16.4 - - + +
1001A CYS* 1.3 84.0 - - + +
1003A LYS* 1.3 68.1 + - - +
1009A PRO* 4.3 0.2 - - - -
1010A ASN* 2.8 28.6 + - + +
1013A ASP* 3.2 40.6 - - + +
1015A LYS* 4.6 8.1 - - + +
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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