Contacts of the strand formed by residues 1026 - 1031 (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 GLU1026 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1009C TYR* 2.5 29.1 + - - +
1013C ARG* 2.8 32.2 + - - -
1024C ALA* 4.3 13.7 - - + +
1025C ASN* 1.3 74.8 - - - +
1027C ARG* 1.3 70.7 + - - +
1100C ARG* 2.9 40.7 + - + -
1101C VAL 3.4 6.7 - - - +
1102C THR* 4.5 0.9 - - - +
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Residues in contact with ARG1027 (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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1025C ASN* 3.0 35.1 + - - +
1026C GLU* 1.3 82.9 + - - +
1028C MET* 1.3 63.2 - - - +
1029C LEU* 3.9 26.0 - - + -
1063C GLU* 4.2 4.4 + - - -
1099C CYS 3.4 1.0 - - - +
1100C ARG* 3.5 3.8 - - - -
1101C VAL* 2.8 34.2 + - - +
1103C LEU* 3.5 25.1 - - + +
1139C TYR* 3.2 30.1 + - - -
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Residues in contact with MET1028 (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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1027C ARG* 1.3 74.0 - - - +
1029C LEU* 1.3 68.8 + - - +
1098C PHE* 3.4 55.5 - - + +
1099C CYS 3.2 26.0 - - - +
1100C ARG* 3.7 39.3 - - - +
1150C GLU* 4.3 6.3 - - + -
1151C TYR* 4.0 15.7 - - + -
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Residues in contact with LEU1029 (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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1027C ARG* 3.9 18.4 - - + -
1028C MET* 1.3 81.5 - - - +
1030C PHE* 1.3 63.1 + - - +
1061C PHE* 3.7 25.5 - - + -
1062C ALA 3.9 7.6 - - - +
1063C GLU* 3.6 32.5 - - + +
1098C PHE* 3.8 7.4 - - - -
1099C CYS* 2.8 34.4 + - - +
1101C VAL* 4.0 24.9 - - + -
1103C LEU* 4.6 2.5 - - + -
1139C TYR* 3.6 35.7 - - + -
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Residues in contact with PHE1030 (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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968C VAL 5.5 0.4 - - - -
971C GLU* 3.9 10.1 - - + -
972C MET* 3.7 47.6 - - + -
975C THR* 3.7 18.2 - - - -
1029C LEU* 1.3 73.9 - - - +
1031C HIS* 1.3 59.5 + - - +
1061C PHE* 3.2 8.9 - - - +
1062C ALA 2.9 45.5 + - - +
1063C GLU* 3.8 7.9 - - - -
1065C SER* 3.7 17.5 - - - -
1068C SER* 3.1 22.9 + - - +
1096C LEU* 4.3 13.0 - - + -
1097C LEU 3.3 10.8 - - - +
1098C PHE* 3.5 37.9 - + + -
1153C ILE* 4.2 2.5 - - + -
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Residues in contact with HIS1031 (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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1030C PHE* 1.3 76.2 - - - +
1032C GLY* 1.3 59.0 + - - +
1033C SER* 3.5 22.5 + - - -
1036C VAL* 5.3 1.3 - - + +
1039C ILE* 3.8 19.4 - - + +
1044C PHE* 3.7 16.3 - + - -
1048C HIS* 4.5 11.2 + - - +
1059C ILE* 3.9 20.2 - - + -
1060C TYR 2.8 28.3 + - - -
1061C PHE* 3.7 18.0 - - + -
1068C SER* 4.0 3.4 - - - -
1096C LEU* 3.8 2.0 - - - -
1097C LEU* 2.9 35.7 + - + +
1099C CYS* 4.0 11.2 - - - -
2165C 32X 3.5 16.7 + + - -
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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