Contacts of the strand formed by residues 1070 - 1079 (chain B) in PDB entry 1CJY
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 VAL1070 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1025B LEU 3.7 4.0 - - - +
1026B ARG* 3.9 18.6 - - + -
1061B ARG* 3.9 3.5 + - - -
1063B PHE* 3.4 21.7 - - - -
1066B ASP* 5.0 0.8 + - - -
1068B ASN 3.6 9.6 + - - +
1069B PRO* 1.3 77.4 - - - +
1071B TRP* 1.3 59.9 + - - +
1072B ASN* 3.8 28.3 - - - +
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Residues in contact with TRP1071 (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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1024B VAL* 3.6 24.0 - - + +
1025B LEU 2.8 8.1 + - - -
1026B ARG* 3.7 17.9 - - - -
1027B ALA* 3.6 27.1 - - + -
1044B PRO* 3.5 21.5 + - + -
1045B TYR* 4.0 4.5 - - - -
1046B VAL* 3.6 24.0 - - + -
1060B THR* 3.2 20.8 + - + -
1061B ARG* 3.1 51.5 + - - +
1063B PHE* 3.4 17.3 - + - -
1069B PRO* 3.4 31.6 - - + -
1070B VAL* 1.3 71.9 - - - +
1072B ASN* 1.3 72.2 + - - +
1073B GLU* 3.2 15.0 + - + +
1091B LEU* 4.5 5.2 - - + -
1130B MET* 4.2 5.2 - - + -
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Residues in contact with ASN1072 (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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1023B VAL* 4.6 8.1 - - + -
1024B VAL 2.9 11.6 + - - -
1025B LEU* 3.0 41.5 + - - +
1026B ARG* 5.4 2.0 - - - +
1070B VAL* 3.8 20.6 - - - +
1071B TRP* 1.3 78.5 - - - +
1073B GLU* 1.3 59.3 + - - +
1074B THR* 4.3 1.2 + - - -
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Residues in contact with GLU1073 (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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1023B VAL* 3.2 2.5 - - - -
1024B VAL 2.8 34.3 + - - -
1059B ARG 4.4 1.4 - - - +
1060B THR* 3.1 29.0 - - + -
1061B ARG* 2.8 48.5 + - - +
1071B TRP* 3.5 15.3 - - + +
1072B ASN* 1.3 77.9 - - - +
1074B THR* 1.3 62.0 + - - +
1075B PHE* 3.6 23.3 - - + -
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Residues in contact with THR1074 (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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1021B THR* 3.7 27.4 - - + -
1022B VAL 3.5 3.1 - - - -
1023B VAL* 3.2 21.6 - - + +
1072B ASN 5.1 1.0 + - - -
1073B GLU* 1.3 73.0 - - - +
1075B PHE* 1.3 77.6 + - - +
1076B GLU* 4.7 7.6 - - + +
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Residues in contact with PHE1075 (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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1021B THR* 3.5 4.0 - - - +
1022B VAL 2.9 38.0 + - - +
1024B VAL* 3.8 17.0 - - + -
1048B LEU* 3.6 18.4 - - + -
1058B LYS* 3.7 32.5 - - + +
1059B ARG 3.7 30.5 - - - -
1060B THR* 3.7 19.3 - - + -
1073B GLU* 3.6 33.2 - - + -
1074B THR* 1.3 77.4 - - - +
1076B GLU* 1.3 68.6 + - - +
1077B PHE* 3.9 13.2 - - + -
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Residues in contact with GLU1076 (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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1019B LYS* 3.3 34.4 + - + -
1020B PHE 3.4 6.3 - - - +
1021B THR* 3.4 20.6 + - - +
1058B LYS* 3.6 20.4 + - - +
1074B THR* 4.7 9.1 - - + +
1075B PHE* 1.3 81.7 - - - +
1077B PHE* 1.3 70.0 + - - +
1078B ILE* 5.3 3.6 - - + -
1378B VAL* 5.2 6.7 - - - +
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Residues in contact with PHE1077 (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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1018B HIS 3.4 0.7 - - - +
1019B LYS* 4.5 0.2 - - - +
1020B PHE* 2.9 50.5 + + + +
1022B VAL* 4.0 18.4 - - + -
1048B LEU* 4.1 21.3 - - + -
1050B ILE* 3.3 39.0 - - + -
1053B THR* 5.0 4.9 - - + +
1056B SER* 3.3 32.5 - - - -
1058B LYS* 4.0 22.9 - - + +
1075B PHE* 3.9 19.5 - - + -
1076B GLU* 1.3 78.3 - - - +
1078B ILE* 1.3 70.5 + - - +
1079B LEU* 3.8 10.2 + - + -
1087B LEU* 4.3 1.8 - - + -
1378B VAL* 6.2 1.6 - - - -
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Residues in contact with ILE1078 (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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1017B SER* 4.1 17.3 - - - +
1018B HIS 3.2 5.8 - - - +
1019B LYS* 4.2 24.2 - - + -
1053B THR* 2.7 35.2 - - - +
1076B GLU* 5.3 3.8 - - + -
1077B PHE* 1.3 84.4 - - - +
1079B LEU* 1.3 58.1 + - - +
1139B CYS* 4.6 6.1 - - - -
1373B PHE* 3.2 39.2 - - + +
1374B MET* 4.8 0.2 - - + -
1376B THR* 4.0 24.5 - - + -
1377B VAL 4.6 9.9 - - - +
1378B VAL* 4.1 21.9 - - + +
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Residues in contact with LEU1079 (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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1017B SER* 3.5 6.9 - - - -
1018B HIS* 2.8 45.0 + - + +
1020B PHE* 3.6 31.6 - - + -
1050B ILE* 3.9 23.8 - - + -
1052B THR 5.9 0.2 - - - -
1053B THR* 3.1 25.6 - - - +
1077B PHE* 4.1 4.7 - - + +
1078B ILE* 1.3 77.6 - - - +
1080B ASP* 1.3 57.0 + - - +
1081B PRO* 3.2 4.6 - - - +
1085B ASN* 3.0 35.2 - - + +
1109B VAL* 3.9 22.0 - - + -
1373B PHE* 4.3 4.9 - - - -
1374B MET* 4.4 0.4 - - - -
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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