Contacts of the strand formed by residues 998 - 1007 (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 PHE 998 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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988A ILE* 3.7 22.9 - - + -
989A ASP 3.4 12.6 - - - +
990A GLY* 4.1 0.9 - - - -
991A ALA 3.5 22.4 - - - +
997A GLY* 1.3 74.1 - - - +
999A ASN* 1.3 60.5 + - - +
1000A LEU* 4.3 10.3 - - + -
1018A ALA* 4.1 13.2 - - + -
1025A TYR* 4.2 8.1 - - + -
1041A ILE 3.4 0.2 - - - +
1042A VAL* 3.2 7.7 - - - +
1043A GLY* 2.8 62.4 + - - -
1044A LYS 4.3 0.7 - - - -
1045A GLY 3.9 11.0 - - - -
1052A PHE* 3.3 60.8 - + + -
1067A ALA* 4.3 1.1 - - + -
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Residues in contact with ASN 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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988A ILE* 3.3 7.2 - - - -
989A ASP* 2.7 54.5 + - - +
990A GLY* 4.7 0.4 - - - -
998A PHE* 1.3 71.1 - - - +
1000A LEU* 1.3 60.6 + - - +
1001A VAL* 4.0 6.1 + - - +
1040A HIS* 2.9 37.6 + - - +
1041A ILE 3.4 4.1 + - - -
1042A VAL* 4.2 20.0 - - - +
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Residues in contact with LEU1000 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985A THR* 3.9 17.5 - - + -
987A SER 3.7 10.8 - - - +
988A ILE* 3.8 25.6 - - + -
998A PHE* 3.9 10.2 + - + -
999A ASN* 1.3 72.7 - - - +
1001A VAL* 1.3 62.2 + - - +
1002A CYS* 4.0 2.0 + - - -
1018A ALA* 3.9 17.7 - - + -
1039A ILE 3.7 0.9 - - - +
1040A HIS* 3.5 3.0 - - - -
1041A ILE* 2.8 48.1 + - + +
1052A PHE* 4.0 15.7 - - + +
1053A MET 3.8 31.6 - - - +
1054A CYS* 3.9 18.2 - - - +
1065A LEU* 4.5 1.3 - - + -
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Residues in contact with VAL1001 (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 3.9 0.2 - - - -
986A ALA* 2.9 37.1 + - + -
987A SER* 2.7 39.5 + - - +
988A ILE* 5.5 0.2 - - - -
989A ASP* 6.0 1.1 - - - +
999A ASN* 4.3 6.3 - - - +
1000A LEU* 1.3 73.5 - - - +
1002A CYS* 1.3 64.8 + - - +
1038A THR* 3.5 28.9 - - + -
1039A ILE 3.5 4.5 - - - +
1040A HIS* 3.7 28.5 - - + +
1054A CYS* 3.8 4.7 - - - -
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Residues in contact with CYS1002 (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 3.6 0.9 - - - +
1000A LEU* 4.4 4.3 - - - -
1001A VAL* 1.3 78.3 - - - +
1003A THR* 1.3 59.7 + - - +
1004A VAL* 3.8 16.3 + - + -
1016A ILE* 4.2 2.9 - - + -
1037A ASN 3.3 3.8 - - - +
1038A THR* 3.4 3.2 - - - +
1039A ILE* 2.7 46.0 + - + +
1041A ILE* 3.4 29.6 - - - -
1054A CYS* 2.0 51.4 - - + -
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Residues in contact with THR1003 (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 ASP 3.8 0.9 - - - +
983A LEU* 3.5 4.3 - - - -
984A ALA* 2.8 50.5 + - + +
986A ALA* 4.0 14.9 - - - +
1001A VAL* 4.3 0.4 - - - +
1002A CYS* 1.3 71.0 - - - +
1004A VAL* 1.3 61.1 + - - +
1005A SER* 4.2 1.1 + - - +
1036A GLN* 3.7 36.1 - - + +
1037A ASN 3.3 8.3 - - - +
1038A THR* 4.9 5.6 + - - +
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Residues in contact with VAL1004 (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* 4.3 12.1 - - + -
982A ASP 3.5 5.8 - - - +
983A LEU* 4.7 6.5 - - + -
1002A CYS* 4.1 16.2 - - + +
1003A THR* 1.3 77.6 - - - +
1005A SER* 1.3 67.0 + - - +
1016A ILE* 4.3 20.9 - - + -
1032A LEU* 3.7 34.5 - - + -
1036A GLN* 4.1 1.3 - - - -
1037A ASN* 2.7 49.4 + - - +
1039A ILE* 4.0 20.2 - - + -
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Residues in contact with SER1005 (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* 3.2 12.6 - - - +
982A ASP* 2.9 46.4 + - - +
1003A THR* 4.2 1.9 + - - +
1004A VAL* 1.3 72.1 - - - +
1006A LEU* 1.3 60.9 + - - +
1007A THR* 4.2 7.4 - - - -
1035A GLY* 3.4 8.3 - - - -
1036A GLN* 2.7 23.0 + - - -
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Residues in contact with LEU1006 (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* 4.1 7.0 - - + -
980A GLN 3.6 9.0 - - - +
981A ILE* 4.1 3.6 - - + -
1004A VAL 3.8 0.2 + - - -
1005A SER* 1.3 72.8 - - - +
1007A THR* 1.3 79.2 + - - +
1009A CYS* 3.7 16.6 - - + +
1011A ALA 3.9 11.9 - - - -
1012A PHE* 3.6 45.3 - - + -
1032A LEU* 3.9 11.2 - - + +
1033A VAL 3.6 33.2 - - - +
1034A ARG* 3.6 9.4 - - - +
1035A GLY* 2.9 30.1 + - - +
1037A ASN* 4.3 4.3 - - - +
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Residues in contact with THR1007 (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* 3.9 0.3 - - - -
980A GLN* 2.9 46.1 + - - +
982A ASP* 5.1 5.8 + - - +
1005A SER* 5.3 8.0 + - - -
1006A LEU* 1.3 84.0 - - - +
1008A GLU* 1.3 70.3 + - - +
1009A CYS 3.2 10.7 + - - +
1034A ARG* 4.7 5.4 - - + +
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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