Contacts of the strand formed by residues 989 - 998 (chain A) in PDB entry 3QCF
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 TYR 989 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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986A HIS* 2.8 60.7 + + + +
987A ALA 3.7 0.6 - - - -
988A CYS* 1.3 92.1 - - + +
990A THR* 1.3 67.3 + - - +
991A VAL* 3.5 28.9 - - + -
1021A TYR* 4.1 11.7 - + - -
1022A HIS 3.2 13.7 - - - +
1023A TYR* 3.6 9.4 - - + -
1024A THR* 3.5 5.9 + - - -
1037A PRO 5.5 0.7 - - - -
1040A THR* 4.7 10.5 - - + -
1041A PHE* 3.6 35.0 - + + -
1044A ARG* 2.9 43.8 + - - +
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Residues in contact with THR 990 (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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983A THR* 3.7 25.4 - - + -
984A LYS 3.1 14.1 - - - +
985A ILE* 3.9 20.3 - - + +
989A TYR* 1.3 77.2 + - - +
991A VAL* 1.3 72.1 + - - +
992A ARG* 4.2 22.5 + - - +
1020A GLN 3.7 0.5 - - - +
1021A TYR* 3.8 0.2 - - - -
1022A HIS* 2.8 40.7 + - - +
1024A THR* 3.9 14.4 + - - +
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Residues in contact with VAL 991 (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 SER* 3.9 0.7 + - - +
983A THR* 3.3 3.1 - - - -
984A LYS* 2.7 50.6 + - + +
986A HIS* 4.2 11.9 - - + +
989A TYR* 3.5 26.7 - - + -
990A THR* 1.3 79.6 - - - +
992A ARG* 1.3 65.9 - - - +
993A ARG* 5.2 0.9 - - + +
1019A ILE* 3.7 27.1 - - + -
1020A GLN 3.4 4.7 - - - +
1021A TYR* 3.8 22.4 - - + +
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Residues in contact with ARG 992 (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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965A TRP* 3.5 36.5 - - - +
980A LEU* 4.0 9.6 - - + +
982A SER 3.2 5.4 - - - +
983A THR* 4.0 17.8 + - - +
990A THR* 4.2 19.7 + - + +
991A VAL* 1.3 80.3 - - - +
993A ARG* 1.3 60.1 + - - +
994A PHE* 3.5 26.3 - - + -
1019A ILE* 3.5 5.3 - - - +
1020A GLN* 2.9 59.7 + - - +
1022A HIS* 3.3 33.1 - - - +
1024A THR* 6.2 0.2 - - - +
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Residues in contact with ARG 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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980A LEU* 3.7 2.6 - - - +
981A LYS* 2.7 68.5 + - - +
982A SER* 2.9 44.3 + - - +
991A VAL* 4.3 0.8 - - + +
992A ARG* 1.3 71.7 - - - +
994A PHE* 1.3 64.2 + - - +
1017A VAL* 4.3 24.2 - - + +
1018A VAL 4.0 2.0 - - - -
1019A ILE* 4.3 16.2 - - + +
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Residues in contact with PHE 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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936A TRP* 4.9 9.6 - + + -
947A ILE* 5.8 0.7 - - + -
964A TYR* 6.3 0.7 - + - -
965A TRP* 3.6 45.5 - + + -
966A PRO* 4.0 6.5 - - + -
978A VAL* 3.5 26.7 - - + -
979A THR 3.1 12.8 - - - +
980A LEU* 3.7 20.0 - - + -
981A LYS* 4.6 3.8 - - - -
992A ARG* 3.5 36.1 - - + -
993A ARG* 1.3 76.2 + - - +
995A SER* 1.3 61.5 + - - +
996A ILE* 4.9 2.0 - - + -
1017A VAL* 3.6 10.0 - - - +
1018A VAL* 2.9 46.8 + - + +
1020A GLN* 3.9 17.3 - - + -
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Residues in contact with SER 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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977A ILE 3.7 2.1 - - - +
979A THR* 2.9 41.2 + - - -
981A LYS* 4.1 16.8 - - - +
994A PHE* 1.3 75.6 - - - +
996A ILE* 1.3 63.5 + - - +
997A ARG* 5.5 1.0 - - - +
1014A ASN* 3.3 32.3 - - - +
1016A ARG 3.1 11.0 - - - -
1017A VAL* 5.4 3.1 - - - -
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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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936A TRP* 3.9 26.9 - - + +
939A ILE* 4.2 16.4 - - + +
940A TRP* 3.4 30.9 - - + -
944A THR 5.3 0.7 - - - +
976A ILE* 4.0 12.3 - - + -
977A ILE 3.4 3.1 - - - -
978A VAL* 4.0 15.7 - - + -
994A PHE* 4.9 1.3 - - + -
995A SER* 1.3 80.5 - - - +
997A ARG* 1.3 60.4 + - - +
1014A ASN* 4.7 0.2 - - - -
1015A GLU* 3.2 3.9 + - - +
1016A ARG* 2.9 49.9 + - + +
1018A VAL* 3.8 26.2 - - + -
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Residues in contact with ARG 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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940A TRP* 4.5 2.2 - - - -
975A ASN 3.5 0.9 - - - +
976A ILE* 3.5 5.7 - - - -
977A ILE* 3.1 72.2 + - + +
979A THR* 6.1 0.9 - - - -
995A SER* 5.5 1.3 - - - +
996A ILE* 1.3 75.6 - - - +
998A ASN* 1.3 65.0 + - - +
999A THR* 3.7 16.2 + - + +
1014A ASN* 3.2 32.6 - - - +
1015A GLU* 4.0 9.0 - - + +
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Residues in contact with ASN 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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940A TRP* 3.2 51.7 - - + +
975A ASN* 3.6 16.3 - - - +
976A ILE* 4.1 11.8 - - - +
997A ARG* 1.3 75.0 + - - +
999A THR* 1.3 61.0 + - - +
1000A LYS* 2.8 63.3 + - - +
1015A GLU* 5.1 1.2 - - - +
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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