Contacts of the strand formed by residues 1058 - 1064 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1001A MET 3.1 4.9 + - - +
1002A ILE* 3.4 12.9 - - + -
1003A LEU 2.7 31.9 + - - +
1056A ALA* 4.0 1.4 - - - +
1057A ASP* 1.3 79.6 - - - +
1059A ILE* 1.3 71.6 + - - +
1060A VAL* 4.1 9.6 - - + -
1099A HIS* 3.7 16.2 - - + +
1101A LEU* 4.0 9.4 - - + +
1140A LEU* 3.7 28.7 - - + -
1167A LEU* 4.0 26.7 - - + -
1170A TRP* 3.8 41.5 - - + +
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Residues in contact with ILE1059 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003A LEU* 3.3 5.2 - - + +
1005A ILE* 4.2 17.5 - - + -
1053A LEU* 3.7 37.0 - - + +
1056A ALA* 4.1 11.7 - - + -
1058A LEU* 1.3 78.6 - - - +
1060A VAL* 1.3 55.9 + - - +
1061A TRP* 4.4 7.4 - - + +
1077A TRP* 5.0 0.4 - - + -
1082A PHE* 6.0 2.2 - - + -
1095A LEU* 4.3 5.2 - - + -
1098A LYS* 4.1 23.3 - - + -
1099A HIS 2.9 8.9 + - - +
1100A LEU* 3.2 20.2 - - + +
1101A LEU 2.8 31.7 + - - -
1137A LEU* 4.0 27.1 - - + -
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Residues in contact with VAL1060 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002A ILE* 4.1 17.0 - - + -
1003A LEU 2.8 12.6 + - - +
1004A ILE* 3.7 11.2 - - + -
1005A ILE* 2.7 35.2 + - - +
1058A LEU* 4.1 22.7 - - + -
1059A ILE* 1.3 77.5 - - - +
1061A TRP* 1.3 66.6 + - - +
1062A GLN* 4.1 3.6 - - + +
1101A LEU* 3.2 18.6 - - + +
1103A ALA* 3.8 18.8 - - + -
1163A TYR* 3.5 20.0 - - - +
1167A LEU* 4.2 9.6 - - + -
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Residues in contact with TRP1061 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005A ILE* 3.6 17.7 - - + -
1059A ILE* 4.4 3.0 - - + +
1060A VAL* 1.3 77.7 - - - +
1062A GLN* 1.3 59.7 + - - +
1063A HIS* 4.2 2.2 - - - -
1074A LEU* 4.0 26.2 - - + +
1077A TRP* 3.5 22.0 - + - -
1078A ILE* 3.9 23.8 - - + -
1082A PHE* 3.8 26.7 - + - -
1100A LEU* 3.6 41.6 - - + +
1101A LEU 2.9 9.6 + - - +
1102A TRP* 3.6 14.3 - + + -
1103A ALA 2.9 23.6 + - - +
1128A LEU* 3.8 47.3 - - + -
1131A THR* 4.1 17.5 - - + -
1132A ALA 4.8 1.1 - - - -
1139A TRP* 5.0 1.8 - + - -
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Residues in contact with GLN1062 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004A ILE* 3.6 16.3 - - + +
1005A ILE 3.0 8.7 + - - +
1006A TYR* 3.4 8.4 - - + -
1007A ALA* 3.0 25.8 + - - +
1017A ASN* 3.0 46.1 + - - +
1020A MET* 3.7 23.4 - - + +
1021A LEU* 3.3 27.7 - - - +
1060A VAL* 3.7 3.1 - - + -
1061A TRP* 1.3 72.3 - - - +
1063A HIS* 1.3 61.9 + - - +
1074A LEU* 5.5 0.4 - - - +
1103A ALA* 3.1 12.1 - - + +
1163A TYR* 2.8 30.2 + - - +
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Residues in contact with HIS1063 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006A TYR* 4.9 0.2 - - - -
1007A ALA* 3.9 9.2 - - + +
1008A HIS 4.7 0.2 - - - +
1017A ASN* 3.8 9.7 - - - +
1061A TRP 4.2 5.6 - - - -
1062A GLN* 1.3 80.2 - - - +
1064A PRO* 1.3 88.4 + - + +
1069A SER 3.7 14.4 - - - -
1070A ILE* 3.5 22.7 - - + +
1071A PRO* 3.5 22.0 - - + +
1074A LEU* 3.8 20.4 - - + -
1102A TRP* 2.8 34.2 + + - -
1103A ALA 3.0 6.2 + - - -
1104A VAL* 3.3 21.4 - - + -
1105A THR 3.2 19.4 + - - -
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Residues in contact with PRO1064 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007A ALA 4.3 0.7 - - - +
1008A HIS* 3.6 45.8 - - + +
1009A PRO* 4.2 4.0 - - + -
1017A ASN* 3.6 6.2 - - - +
1063A HIS* 1.3 101.4 + - + +
1065A MET* 1.3 66.1 + - - +
1066A GLN* 3.5 24.3 + - + +
1071A PRO* 4.0 4.0 - - + +
1105A THR* 3.2 12.6 - - - +
2400A FMN 3.5 27.1 - - - +
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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