Contacts of the strand formed by residues 1058 - 1064 (chain B) in PDB entry 3L9X
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 LEU1058 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001B MET 3.0 4.5 + - - +
1002B ILE* 3.4 21.3 - - + +
1003B LEU* 2.7 33.4 + - - +
1056B ALA* 4.2 0.4 - - - +
1057B ASP* 1.3 77.6 - - - +
1059B ILE* 1.3 69.4 + - - +
1060B VAL* 4.0 9.2 - - + -
1099B HIS* 3.7 12.6 - - + +
1101B LEU* 4.0 8.7 - - + -
1140B LEU* 3.5 30.5 - - + -
1167B LEU* 3.9 28.5 - - + -
1170B TRP* 3.8 35.9 - - + +
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Residues in contact with ILE1059 (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 LEU* 3.5 7.6 - - + +
1005B ILE* 4.3 6.7 - - + -
1053B LEU* 3.7 34.5 - - + -
1056B ALA* 4.2 12.6 - - + -
1058B LEU* 1.3 75.6 - - - +
1060B VAL* 1.3 64.4 + - - +
1061B TRP* 4.0 16.6 - - + +
1077B TRP* 4.8 0.7 - - + -
1082B PHE* 5.6 2.2 - - + -
1095B LEU* 4.1 7.0 - - + -
1098B LYS* 4.1 18.4 - - + -
1099B HIS 2.8 13.0 + - - +
1100B LEU* 3.3 19.7 - - + +
1101B LEU 2.8 26.2 + - - -
1137B LEU* 3.8 30.5 - - + -
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Residues in contact with VAL1060 (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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1002B ILE* 4.0 18.8 - - + -
1003B LEU 2.8 12.0 + - - +
1004B ILE* 4.1 11.0 - - + -
1005B ILE* 2.7 35.9 + - - +
1058B LEU* 4.0 21.8 - - + -
1059B ILE* 1.3 77.1 - - - +
1061B TRP* 1.3 66.3 + - - +
1062B GLN* 3.7 3.5 + - + +
1101B LEU* 3.3 19.1 - - + +
1103B ALA* 3.7 19.1 - - + -
1163B TYR* 3.4 21.1 - - - +
1167B LEU* 4.1 9.9 - - + -
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Residues in contact with TRP1061 (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* 3.6 17.9 - - + -
1059B ILE* 4.0 4.9 - - + +
1060B VAL* 1.3 79.1 - - - +
1062B GLN* 1.3 58.6 + - - +
1063B HIS* 4.1 2.0 + - - -
1074B LEU* 4.1 25.1 - - + -
1077B TRP* 3.4 22.0 - + - -
1078B ILE* 3.7 28.0 - - + -
1082B PHE* 3.8 32.3 - + - -
1100B LEU* 3.7 39.4 - - + +
1101B LEU 3.0 10.9 + - - +
1102B TRP* 3.6 13.8 - + + -
1103B ALA 2.9 26.6 + - - +
1128B LEU* 3.8 45.1 - - + -
1131B THR* 4.2 11.4 - - + -
1139B TRP* 5.4 0.9 - + - -
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Residues in contact with GLN1062 (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 ILE* 3.6 17.2 - - + +
1005B ILE 3.0 9.7 + - - +
1006B TYR* 3.3 11.9 - - + -
1007B ALA* 2.9 27.4 + - - +
1017B ASN* 2.9 48.0 + - - +
1020B MET* 3.7 13.4 - - + +
1021B LEU* 3.4 20.6 - - - +
1060B VAL* 3.7 0.6 + - + -
1061B TRP* 1.3 72.3 - - - +
1063B HIS* 1.3 63.9 + - - +
1074B LEU* 5.5 0.4 - - - +
1103B ALA* 3.2 14.8 - - + +
1163B TYR* 2.8 38.4 + - - +
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Residues in contact with HIS1063 (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 TYR* 4.9 0.2 - - - -
1007B ALA* 3.8 18.6 - - + +
1008B HIS 4.7 0.4 - - - +
1017B ASN* 3.8 9.1 - - - +
1061B TRP 4.3 1.3 - - - -
1062B GLN* 1.3 79.5 - - - +
1064B PRO* 1.4 95.3 + - + +
1069B SER 3.5 22.4 - - - -
1070B ILE* 3.5 15.4 - - + +
1071B PRO* 3.3 9.9 - - + +
1074B LEU* 3.8 21.1 - - + -
1102B TRP* 2.9 33.0 + + - -
1103B ALA 3.1 5.5 + - - +
1104B VAL* 3.3 23.1 - - + -
1105B THR 3.1 19.8 + - - -
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Residues in contact with PRO1064 (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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1007B ALA 4.3 0.9 - - - +
1008B HIS* 3.6 47.6 - - + +
1009B PRO* 4.2 2.7 - - + -
1017B ASN* 3.5 5.8 - - - +
1063B HIS* 1.4 105.0 + - + +
1065B MET* 1.3 60.0 + - - +
1066B GLN* 3.5 22.2 + - + +
1071B PRO* 4.0 3.8 - - - +
1105B THR* 3.3 13.0 - - - +
2400B FMN 3.5 30.3 - - - +
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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