Contacts of the strand formed by residues 1077 - 1080 (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 ILE1077 (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* 3.8 35.0 - - + -
1002B ARG 3.1 3.6 + - - -
1003B ILE* 3.4 24.0 - - + +
1004B CYS 2.9 25.8 + - - +
1027B PHE* 5.3 5.2 - - + -
1075B CYS* 3.4 5.8 - - - -
1076B ASP* 1.3 83.3 - - - +
1078B LEU* 1.3 60.3 + - - +
1079B ILE* 3.8 26.5 - - + -
1108B ARG* 3.4 22.9 - - + +
1110B VAL* 4.1 13.5 - - + -
1395B PHE* 5.5 1.1 - - + -
1398B ILE* 4.2 20.4 - - + -
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Residues in contact with LEU1078 (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* 3.5 35.2 - - + +
1006B PHE* 4.0 13.5 - - + -
1072B VAL* 4.0 31.0 - - + +
1075B CYS* 3.8 3.8 - - - -
1077B ILE* 1.3 71.9 - - - +
1079B ILE* 1.3 61.6 + - - +
1080B ILE* 3.9 23.7 + - + -
1100B LEU* 5.5 2.5 - - + -
1103B ILE* 3.9 26.9 - - + -
1107B ILE* 3.8 16.3 - - + +
1108B ARG 2.8 9.2 + - - +
1109B VAL* 3.4 6.3 - - + +
1110B VAL* 2.8 27.5 + - - +
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Residues in contact with ILE1079 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003B ILE* 3.5 27.1 - - + -
1004B CYS 2.8 12.5 + - - +
1005B ILE* 3.5 6.4 - - + +
1006B PHE* 2.7 33.8 + - - +
1023B GLN* 3.7 25.8 - - - +
1027B PHE* 3.9 18.8 - - + -
1077B ILE* 3.8 15.5 - - + -
1078B LEU* 1.3 74.4 - - - +
1080B ILE* 1.3 59.5 + - - +
1081B ASN* 3.6 11.0 + - - +
1110B VAL* 3.3 10.8 - - + +
1112B TYR* 3.5 34.3 - - + -
1398B ILE* 5.1 4.0 - - + -
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Residues in contact with ILE1080 (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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1006B PHE* 3.5 17.7 - - + +
1078B LEU* 4.1 20.6 - - + -
1079B ILE* 1.3 71.5 - - - +
1081B ASN* 1.3 60.8 + - - +
1082B SER 3.6 24.2 - - - +
1083B VAL* 4.4 4.5 - - + -
1096B TYR* 3.7 20.0 - - + +
1100B LEU* 3.7 29.4 - - + -
1109B VAL* 3.9 21.8 - - + -
1110B VAL 2.8 10.8 + - - +
1111B VAL* 3.5 7.5 - - + +
1112B TYR 3.1 24.6 + - - +
1130B THR* 4.3 11.7 - - + +
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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