Contacts of the strand formed by residues 1059 - 1062 (chain C) in PDB entry 4UVL
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 ILE1059 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1031C HIS* 3.9 12.3 - - + -
1044C PHE* 3.8 27.4 - - + -
1045C ASP 4.2 9.9 - - - +
1048C HIS* 4.0 17.9 - - + +
1049C ALA* 4.1 7.0 - - - +
1058C GLY* 1.3 73.9 - - - -
1060C TYR* 1.3 63.3 + - - +
1061C PHE* 3.6 29.2 - - + -
1115C MET* 4.1 13.0 - - + -
1140C VAL* 3.3 3.3 - - - -
1141C ILE* 2.7 42.1 + - + +
1143C ARG 4.4 2.9 - - - -
1144C GLY* 3.8 31.6 - - - +
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Residues in contact with TYR1060 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031C HIS* 2.8 34.1 + - - -
1048C HIS 5.2 0.6 + - - -
1050C TYR* 3.8 17.0 - - + +
1053C GLY* 3.0 16.3 - - - -
1054C MET* 4.3 1.8 - - + -
1055C PHE* 2.9 37.8 + + - -
1056C GLY 2.6 30.0 + - - -
1058C GLY 3.2 20.6 - - - -
1059C ILE* 1.3 76.7 - - - +
1061C PHE* 1.3 58.5 + - - +
1138C GLU* 5.2 3.1 - - + -
1139C TYR 3.3 4.7 - - - -
1140C VAL* 3.4 25.6 - - + -
2165C 32X 3.3 58.9 - + + -
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Residues in contact with PHE1061 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029C LEU* 3.7 25.4 - - + -
1030C PHE 3.2 19.3 - - - +
1031C HIS* 3.7 21.5 - - + -
1044C PHE* 3.8 14.1 - + - -
1059C ILE* 3.6 35.0 - - + -
1060C TYR* 1.3 74.8 - - - +
1062C ALA* 1.3 61.9 + - - +
1099C CYS* 3.8 12.3 - - + -
1101C VAL* 3.8 21.8 - - + -
1138C GLU* 3.2 7.8 - - - +
1139C TYR* 2.8 37.2 + - - +
1141C ILE* 3.7 20.0 - - + -
1147C ALA* 3.5 22.2 - - + -
2165C 32X 3.8 3.5 - - - -
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Residues in contact with ALA1062 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029C LEU* 3.8 6.7 - - - -
1030C PHE* 2.9 33.9 + - - -
1061C PHE* 1.3 74.5 - - - +
1063C GLU* 1.3 61.2 + - - +
1064C ASN 3.5 16.4 - - - +
1067C LYS* 3.8 15.3 - - + -
1068C SER* 3.4 18.6 - - - +
1137C ALA 3.9 4.9 - - - -
1138C GLU* 4.6 1.8 - - + -
2165C 32X 3.7 14.1 - - + -
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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