Contacts of the strand formed by residues 1082 - 1086 (chain B) in PDB entry 3M5M
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 LEU1082 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1053B TRP* 3.6 42.8 - - + -
1054B THR 3.5 13.5 - - - +
1056B TYR* 3.8 1.2 - - - +
1075B TYR* 5.7 1.1 - - + +
1076B THR 3.7 0.3 + - - -
1077B ASN* 2.8 36.6 + - + +
1080B LYS* 4.0 21.8 - - + +
1081B ASP* 1.3 77.7 - - - +
1083B VAL* 1.3 66.9 + - - +
1153B ILE* 5.0 3.1 - - + -
1170B ILE* 4.1 18.8 - - + -
1175B LEU* 3.8 30.3 - - + -
1178B THR* 4.1 22.2 - - + +
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Residues in contact with VAL1083 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1053B TRP* 3.4 12.7 - - - -
1054B THR* 2.9 60.0 + - + +
1055B VAL 4.3 0.4 - - - +
1056B TYR* 3.6 23.8 - - + -
1059B ALA* 4.0 7.2 - - + -
1060B GLY 3.5 14.4 - - - +
1073B GLN* 3.5 35.7 - - - +
1075B TYR 3.3 5.8 - - - -
1076B THR* 4.2 3.4 - - + -
1082B LEU* 1.3 80.0 - - - +
1084B GLY* 1.3 59.0 - - - +
1085B TRP* 4.3 6.1 - - + -
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Residues in contact with GLY1084 (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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1051B VAL* 4.0 6.7 - - - -
1052B LEU 3.2 10.5 - - - -
1053B TRP* 4.0 13.7 - - - -
1073B GLN* 3.5 3.9 - - - -
1074B MET* 2.8 29.8 + - - -
1075B TYR* 2.9 18.0 + - - +
1083B VAL* 1.3 77.3 - - - +
1085B TRP* 1.3 59.1 - - - -
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Residues in contact with TRP1085 (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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992B VAL* 3.9 27.4 - - + -
1036B VAL* 5.9 0.4 - - + -
1045B ALA* 4.9 2.9 - - + -
1051B VAL* 3.4 7.4 - - - -
1052B LEU* 2.7 61.3 + - + +
1054B THR* 3.5 34.3 - - + -
1059B ALA* 3.8 8.1 - - + -
1062B ARG 3.1 28.3 + - - -
1064B ILE* 3.5 43.8 - - + +
1071B VAL* 3.3 26.2 + - + -
1072B THR 3.8 1.3 - - - -
1073B GLN* 3.3 31.4 - - + +
1074B MET* 4.2 6.3 - - - +
1083B VAL* 4.3 2.5 - - + -
1084B GLY* 1.3 75.4 - - - -
1086B GLN* 1.3 67.4 + - - +
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Residues in contact with GLN1086 (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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1050B GLY 4.0 9.6 - - - +
1051B VAL* 4.6 0.2 - - - +
1064B ILE* 5.7 1.2 - - - +
1071B VAL* 4.8 14.3 - - + +
1072B THR 5.4 0.2 + - - -
1074B MET* 3.4 35.8 - - + +
1085B TRP* 1.3 78.2 - - - +
1087B ALA* 1.3 74.6 + - - +
1088B PRO* 3.5 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