Contacts of the strand formed by residues 980 - 990 (chain A) in PDB entry 5J9H
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 GLN 980 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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978A PRO 3.6 1.8 + - - +
979A CYS* 1.3 74.6 - - - +
981A ILE* 1.3 76.4 + - - +
982A ASP* 4.9 7.4 + - - +
1006A LEU* 3.6 1.2 - - - +
1007A THR* 2.9 52.0 + - - +
1008A GLU* 4.1 13.7 - - + +
1059A LYS* 4.7 14.8 - - - +
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Residues in contact with ILE 981 (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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979A CYS 4.5 0.2 + - - -
980A GLN* 1.3 89.0 + - - +
982A ASP* 1.3 71.2 + - - +
983A LEU* 3.4 38.6 - - + +
1004A VAL* 4.3 9.2 - - + -
1005A SER 3.2 12.1 - - - +
1006A LEU* 4.1 3.1 - - + -
1007A THR* 5.7 0.2 - - - -
1012A PHE* 3.7 33.4 - - + -
1014A THR* 4.8 0.7 - - + -
1016A ILE* 4.7 1.1 - - + -
1032A LEU* 4.1 13.7 - - + -
1056A HIS* 3.4 41.5 - - + +
1059A LYS* 5.7 4.9 - - + +
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Residues in contact with ASP 982 (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 GLN* 4.9 8.9 + - - +
981A ILE* 1.3 81.3 - - - +
983A LEU* 1.3 64.2 + - - +
1003A THR 3.8 0.5 - - - +
1004A VAL* 3.5 4.5 - - - +
1005A SER* 2.9 49.1 + - - +
1007A THR* 5.1 5.9 + - - +
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Residues in contact with LEU 983 (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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981A ILE* 3.4 26.9 - - + +
982A ASP* 1.3 76.2 - - - +
984A ALA* 1.3 61.8 + - - +
1003A THR 3.5 5.8 - - - +
1004A VAL* 4.7 6.3 - - + -
1016A ILE* 4.0 17.7 - - + -
1054A CYS* 3.8 16.6 - - + +
1055A CYS 3.5 35.9 - - - +
1056A HIS* 3.8 9.6 - - + +
1059A LYS* 3.8 28.7 - - + +
1060A CYS 5.1 0.4 - - - -
1061A SER* 3.7 17.6 + - - +
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Residues in contact with ALA 984 (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 LEU* 1.3 75.3 - - - +
985A THR* 1.3 65.5 + - - +
986A ALA* 3.3 0.6 + - - -
1002A CYS* 3.6 2.4 - - - -
1003A THR* 2.8 53.0 + - + +
1054A CYS* 4.4 2.7 - - - -
1061A SER* 3.8 6.1 - - - -
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Residues in contact with THR 985 (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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984A ALA* 1.3 70.9 - - - +
986A ALA* 1.3 62.4 + - - +
1000A LEU* 3.9 21.3 - - + -
1001A VAL 4.5 0.2 - - - +
1052A PHE 3.9 6.5 - - - +
1054A CYS* 2.9 33.6 + - - -
1061A SER* 3.2 10.5 + - - -
1063A THR* 2.9 44.1 + - + +
1065A LEU* 3.6 27.5 - - + +
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Residues in contact with ALA 986 (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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984A ALA* 3.3 2.5 + - - +
985A THR* 1.3 74.6 - - - +
987A SER* 1.3 63.7 + - - +
1001A VAL* 2.9 35.2 + - + +
1003A THR* 4.0 20.0 - - - +
1065A LEU* 4.3 4.8 - - - +
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Residues in contact with SER 987 (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 THR 3.8 0.6 - - - -
986A ALA* 1.3 82.9 - - - +
988A ILE* 1.3 61.8 + - - +
1000A LEU* 3.7 3.1 - - - +
1001A VAL* 2.7 50.9 + - - +
1065A LEU* 3.6 12.4 - - - +
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Residues in contact with ILE 988 (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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987A SER* 1.3 79.4 - - - +
989A ASP* 1.3 75.6 + - - +
998A PHE* 3.7 22.9 - - + -
999A ASN 3.3 14.4 - - - +
1000A LEU* 3.8 17.0 - - + -
1001A VAL* 5.5 0.7 - - - -
1052A PHE* 3.9 8.1 - - + -
1065A LEU* 3.7 35.2 - - + +
1066A VAL 3.6 17.5 - - - +
1067A ALA* 4.1 14.8 - - + -
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Residues in contact with ASP 989 (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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988A ILE* 1.3 79.3 - - - +
990A GLY* 1.3 62.4 + - - +
998A PHE* 3.4 6.1 - - - +
999A ASN* 2.7 58.2 + - - +
1001A VAL* 6.0 1.4 - - - +
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Residues in contact with GLY 990 (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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989A ASP* 1.3 83.8 + - - +
991A ALA* 1.3 60.8 + - - -
997A GLY 3.9 7.6 - - - -
998A PHE* 4.1 3.1 - - - -
1067A ALA* 3.8 2.4 - - - +
1068A ALA* 3.1 28.1 + - - +
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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