Contacts of the strand formed by residues 1002 - 1007 (chain B) in PDB entry 1Y8Z
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 ARG1002 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1001B MET* 1.3 73.8 - - - +
1003B ILE* 1.3 62.6 + - - +
1033B GLU* 3.5 35.2 + - + +
1035B THR* 4.0 25.4 - - - +
1074B ASP* 2.6 54.8 + - - -
1075B CYS* 3.5 13.0 - - - +
1076B ASP* 2.8 44.5 + - - +
1077B ILE 3.1 8.0 + - - -
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Residues in contact with ILE1003 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001B MET* 4.1 16.6 - - + +
1002B ARG* 1.3 78.6 + - - +
1004B CYS* 1.3 60.8 + - - +
1005B ILE* 4.0 11.4 - - + -
1027B PHE* 3.6 40.2 - - + -
1032B HIS* 4.2 4.3 - - + -
1033B GLU 2.7 17.7 + - - +
1034B VAL* 3.3 8.9 - - + +
1035B THR* 2.9 28.0 + - - +
1075B CYS* 4.3 1.6 - - - -
1077B ILE* 3.4 35.2 - - + +
1079B ILE* 3.5 32.1 - - + -
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Residues in contact with CYS1004 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003B ILE* 1.3 72.8 - - - +
1005B ILE* 1.3 65.6 + - - +
1006B PHE* 4.6 0.7 - - - -
1035B THR* 3.3 19.5 - - - +
1037B VAL* 3.9 22.7 - - - -
1071B LEU 4.3 5.8 - - - +
1072B VAL* 4.2 17.0 - - - -
1075B CYS* 3.8 25.9 - - + +
1077B ILE 2.9 8.3 + - - -
1078B LEU* 3.5 17.3 - - + +
1079B ILE* 2.8 27.9 + - - +
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Residues in contact with ILE1005 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003B ILE* 4.3 13.2 - - + -
1004B CYS* 1.3 73.9 - - - +
1006B PHE* 1.3 60.9 + - - +
1007B MET* 4.2 0.7 - - + -
1020B SER* 3.7 14.1 - - - +
1023B GLN* 3.7 18.4 - - + +
1024B ARG* 3.6 36.8 - - + +
1027B PHE* 5.2 0.7 - - + -
1034B VAL* 3.7 17.7 - - + -
1035B THR 2.8 9.2 + - - +
1036B LEU* 3.5 22.4 - - + +
1037B VAL 2.8 29.8 + - - +
1079B ILE* 3.5 7.0 - - + +
1081B ASN* 3.3 30.1 - - - +
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Residues in contact with PHE1006 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004B CYS* 3.7 2.9 + - - -
1005B ILE* 1.3 73.0 - - - +
1007B MET* 1.3 64.0 + - - +
1008B ALA* 3.6 25.1 + - + -
1037B VAL* 3.3 33.4 - - + -
1039B ALA 4.5 6.7 - - - -
1059B VAL* 4.6 0.7 - - + -
1061B LEU* 4.0 24.5 - - + -
1068B ALA* 5.6 0.9 - - + -
1072B VAL* 4.1 16.4 - - + -
1078B LEU* 4.0 16.8 - - + -
1079B ILE 2.7 14.9 + - - +
1080B ILE* 3.5 16.7 - - + +
1081B ASN 3.0 26.7 + - - -
1082B SER 3.9 1.0 + - - +
1096B TYR* 3.9 24.2 - + - -
1099B LEU* 4.0 20.2 - - + -
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Residues in contact with MET1007 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005B ILE* 5.4 0.9 - - + -
1006B PHE* 1.3 74.3 - - - +
1008B ALA* 1.3 61.5 - - - +
1009B ARG 3.2 1.3 - - - -
1010B GLY 3.3 19.0 + - - +
1011B LEU* 4.1 18.6 - - + -
1016B VAL* 4.1 13.9 - - + -
1017B THR* 3.8 28.0 - - + +
1020B SER* 3.5 37.2 - - - +
1021B LEU* 5.6 1.6 - - + -
1036B LEU* 3.8 28.3 - - + -
1037B VAL 2.8 8.5 + - - -
1038B TYR* 3.2 7.9 - - + -
1039B ALA 3.1 21.8 + - - -
1081B ASN* 4.4 2.7 - - + -
1082B SER* 3.2 14.4 - - - +
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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