Contacts of the strand formed by residues 1061 - 1069 (chain B) in PDB entry 2OOQ
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 ILE1061 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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991A LYS* 3.5 33.9 - - + -
1031A GLY* 3.0 29.1 + - - +
1032A ASP* 4.7 6.4 - - - +
1052B THR* 3.8 31.6 - - + -
1053B VAL 3.6 5.6 - - - +
1054B GLN* 3.8 22.0 - - + +
1059B HIS 3.9 5.2 - - - +
1060B GLU* 1.3 79.4 - - - +
1062B ARG* 1.3 65.5 + - - +
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Residues in contact with ARG1062 (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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1056A LYS* 6.1 0.4 - - - +
997B ILE 4.3 0.6 + - - -
998B TRP* 2.8 71.7 + - + +
1001B ASN* 3.3 37.0 + - - +
1002B SER 5.5 6.3 - - - +
1052B THR* 3.2 7.9 - - - -
1053B VAL* 2.8 42.3 + - + +
1060B GLU* 2.8 41.3 + - + +
1061B ILE* 1.3 76.7 - - - +
1063B GLU* 1.3 63.0 + - - +
1064B LEU* 6.0 0.2 - - + -
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Residues in contact with GLU1063 (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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301B B3P 5.2 0.7 + - - -
1002B SER 5.3 0.2 - - - +
1003B ALA* 4.0 17.8 - - - +
1038B ILE* 4.0 12.8 - - + +
1050B THR* 3.7 28.3 - - + +
1051B PHE 3.4 4.9 - - - +
1052B THR* 4.7 2.5 - - + +
1061B ILE 4.3 0.2 + - - -
1062B ARG* 1.3 77.7 - - - +
1064B LEU* 1.3 63.0 + - - +
1065B ARG* 3.8 25.3 + - - +
1096B PRO* 5.7 0.7 - - - +
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Residues in contact with LEU1064 (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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994B TRP* 4.4 10.5 - - + -
997B ILE* 3.4 33.2 - - + -
1002B SER 3.7 14.4 - - - +
1003B ALA* 3.3 12.8 - - - +
1004B SER 5.2 0.2 - - - -
1005B ILE* 3.8 29.6 - - + -
1050B THR* 3.4 3.5 - - - +
1051B PHE* 2.8 49.3 + - + +
1053B VAL* 3.7 19.3 - - + -
1062B ARG* 6.0 0.4 - - + -
1063B GLU* 1.3 75.9 - - - +
1065B ARG* 1.3 80.6 + - - +
1066B LEU* 4.0 2.2 - - - +
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Residues in contact with ARG1065 (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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301B B3P 2.8 39.3 + - - -
1003B ALA 2.9 12.1 + - - +
1004B SER* 3.3 4.7 + - - +
1005B ILE 2.8 32.1 + - - +
1048B ILE* 4.2 12.6 - - + -
1049B ARG 3.4 4.7 - - - +
1050B THR* 3.8 16.1 - - + +
1063B GLU* 3.8 22.9 + - + +
1064B LEU* 1.3 80.1 - - - +
1066B LEU* 1.3 54.7 + - - +
1067B PHE* 3.6 29.8 - - + -
1094B LEU* 3.0 42.9 + - - +
1095B ASN* 5.0 0.2 - - - +
1096B PRO* 4.5 12.3 - - - +
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Residues in contact with LEU1066 (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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994B TRP* 6.3 0.7 - - + -
1005B ILE* 3.4 25.4 - - + +
1007B MET* 3.8 18.6 - - + -
1022B TYR* 3.4 28.3 - - + +
1023B TRP* 3.7 48.9 - - + -
1047B VAL 3.6 0.7 - - - +
1048B ILE* 3.4 3.4 - - - -
1049B ARG* 2.8 49.1 + - + +
1051B PHE* 3.8 19.3 - - + -
1064B LEU* 4.0 3.9 - - + +
1065B ARG* 1.3 70.7 - - - +
1067B PHE* 1.3 62.4 + - - +
1068B HIS* 3.5 3.1 + - + +
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Residues in contact with PHE1067 (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 SER* 3.5 30.5 - - - -
1005B ILE 2.7 20.1 + - - +
1006B VAL* 4.4 1.6 - - + -
1007B MET 2.9 25.7 + - - -
1047B VAL 3.9 3.1 - - - -
1048B ILE* 3.8 24.9 - - + +
1065B ARG* 3.6 31.4 - - + -
1066B LEU* 1.3 71.1 - - - +
1068B HIS* 1.3 60.3 + - - +
1087B PHE* 3.3 27.1 - + + -
1090B GLN* 3.8 23.6 - - + -
1091B VAL* 3.7 29.4 - - + -
1094B LEU* 3.9 24.9 - - + -
1095B ASN 4.7 0.9 - - - -
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Residues in contact with HIS1068 (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 MET* 3.5 35.1 - - + +
1009B THR 2.8 28.6 + - - -
1010B ASN* 4.3 8.7 + - - -
1011B LEU* 5.3 3.8 - - + -
1021B ARG* 6.3 0.2 - - - -
1023B TRP* 4.2 7.9 - + - -
1046B TYR* 3.2 4.3 - - - +
1047B VAL* 2.8 44.0 + - + +
1049B ARG* 3.1 36.8 + - - +
1066B LEU* 4.6 5.2 - - + +
1067B PHE* 1.3 70.3 - - - +
1069B PHE* 1.3 66.5 + - - +
1070B THR* 3.4 22.3 + - + +
1087B PHE* 3.8 3.3 - - - -
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Residues in contact with PHE1069 (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 MET 2.8 20.5 + - - +
1008B VAL* 4.0 21.0 - - + -
1009B THR* 3.7 14.7 + - - +
1045B GLU* 3.7 9.0 - - + -
1046B TYR* 3.9 4.5 - + + -
1068B HIS* 1.3 75.6 - - - +
1070B THR* 1.3 59.8 + - - +
1071B SER* 3.1 24.9 - - - -
1072B TRP* 3.5 36.9 + + + +
1078B PRO* 4.8 8.3 - - + -
1083B GLY* 3.8 8.1 - - - -
1084B LEU* 3.6 45.5 - - + -
1087B PHE* 3.6 35.9 - + + -
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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