Contacts of the strand formed by residues 1128 - 1139 (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 THR1128 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1027B ALA* 4.8 0.9 - - - +
1028B THR 2.9 13.9 + - - -
1029B LYS 2.7 22.9 - - - +
1030B VAL* 3.5 22.6 - - - +
1031B THR* 4.3 7.2 - - + +
1091B LEU* 4.2 10.5 - - + +
1122B PHE 3.9 0.2 - - - +
1123B ILE* 2.9 19.6 - - - +
1124B PHE* 2.9 48.3 + - + +
1125B ASN* 4.3 11.9 - - + +
1127B VAL* 1.3 75.5 - - - +
1129B GLU* 1.3 61.9 + - - +
1130B MET 4.3 0.2 - - - -
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Residues in contact with GLU1129 (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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1027B ALA* 2.9 5.3 - - - -
1028B THR* 2.7 48.9 + - - +
1121B PRO* 6.2 2.9 - - + -
1122B PHE 3.5 6.7 - - - +
1123B ILE* 4.6 5.8 - - + +
1127B VAL 3.8 3.2 + - - +
1128B THR* 1.3 74.7 - - - +
1130B MET* 1.3 62.1 + - - +
1131B VAL* 5.1 6.9 - - + +
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Residues in contact with MET1130 (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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1026B ARG 3.5 11.4 - - - +
1027B ALA* 4.1 4.3 - - + +
1046B VAL* 3.3 33.2 - - + -
1071B TRP* 4.2 7.6 - - + -
1089B ILE* 4.0 19.3 - - - -
1091B LEU* 3.5 34.1 - - + -
1120B VAL 3.8 0.5 - - - +
1121B PRO* 3.4 2.8 - - - +
1122B PHE* 2.7 43.4 + - + +
1124B PHE* 3.4 31.9 - - + -
1128B THR 4.2 0.2 + - - -
1129B GLU* 1.3 73.8 - - - +
1131B VAL* 1.3 66.3 + - - +
1132B LEU* 3.9 20.0 - - + -
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Residues in contact with VAL1131 (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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1025B LEU* 3.2 29.5 + - + +
1026B ARG* 3.0 37.6 + - + +
1119B GLU* 3.8 32.1 - - + +
1120B VAL 3.6 11.0 - - - +
1121B PRO* 4.8 9.9 - - + -
1129B GLU* 5.1 6.3 - - + +
1130B MET* 1.3 80.1 - - - +
1132B LEU* 1.3 76.9 + - - +
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Residues in contact with LEU1132 (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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1022B VAL* 4.2 16.8 - - + -
1023B VAL 3.4 6.3 - - - +
1024B VAL* 3.4 35.2 - - + -
1025B LEU* 4.7 1.3 - - - -
1048B LEU* 4.7 4.7 - - + -
1089B ILE* 3.8 42.2 - - + -
1118B LYS 3.9 0.3 - - - +
1119B GLU* 3.2 2.9 - - - -
1120B VAL* 2.7 41.1 + - - +
1122B PHE* 4.2 13.9 - - + -
1130B MET* 3.9 13.7 - - + -
1131B VAL* 1.3 94.9 - - - +
1133B GLU* 1.3 59.0 + - - +
1134B MET* 4.0 13.8 + - + -
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Residues in contact with GLU1133 (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 4.5 - - - +
1022B VAL* 3.5 1.6 - - - -
1023B VAL* 2.9 45.9 + - + +
1025B LEU* 4.5 8.4 - - + +
1117B LYS* 3.5 25.8 - - - +
1118B LYS 3.4 5.8 - - - +
1119B GLU* 4.0 18.6 - - + +
1132B LEU* 1.3 73.0 - - - +
1134B MET* 1.3 61.7 + - - +
1135B SER* 5.3 0.3 + - - -
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Residues in contact with MET1134 (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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1020B PHE* 4.0 13.0 - - + -
1021B THR 3.4 3.4 - - - -
1022B VAL* 4.0 19.3 - - - -
1087B LEU* 4.0 11.2 - - + -
1107B PHE* 3.2 52.9 - - + -
1112B MET* 3.7 23.6 - - + +
1117B LYS* 3.2 7.3 - - - +
1118B LYS* 2.8 34.5 + - + +
1120B VAL* 4.0 14.6 - - + -
1122B PHE* 4.1 17.0 - - + -
1132B LEU* 4.4 10.1 - - + +
1133B GLU* 1.3 79.7 - - - +
1135B SER* 1.3 63.7 + - - +
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Residues in contact with SER1135 (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 4.3 0.9 - - - -
1020B PHE* 3.2 10.9 - - - -
1021B THR* 2.9 48.4 + - - +
1112B MET* 4.1 2.7 - - - -
1116B GLU 3.5 8.5 - - - -
1117B LYS* 3.2 33.2 + - - +
1133B GLU 5.3 0.3 + - - -
1134B MET* 1.3 71.5 + - - +
1136B LEU* 1.3 62.1 + - - +
1137B GLU* 5.7 5.2 - - - -
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Residues in contact with LEU1136 (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* 3.9 32.8 - - + +
1019B LYS 3.6 7.0 - - - +
1020B PHE* 4.1 13.5 - - + -
1079B LEU* 5.0 0.2 - - + -
1109B VAL* 3.9 31.2 - - + +
1110B SER* 6.1 0.4 - - - -
1112B MET* 4.1 26.0 - - + +
1113B LYS 4.1 9.4 - - - +
1114B VAL* 3.9 29.6 - - + +
1115B GLY* 2.8 29.3 + - - -
1116B GLU 3.3 6.3 + - - -
1135B SER* 1.3 77.2 - - - +
1137B GLU* 1.3 69.1 + - - +
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Residues in contact with GLU1137 (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* 3.3 6.4 - - - +
1019B LYS* 2.6 46.3 + - + +
1114B VAL* 4.5 5.0 - - - +
1115B GLY* 3.1 30.0 + - - +
1116B GLU 5.0 0.7 - - - +
1135B SER* 5.7 4.9 - - - -
1136B LEU* 1.3 85.6 + - - +
1138B VAL* 1.3 66.9 + - - +
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Residues in contact with VAL1138 (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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1016B TYR* 4.0 13.2 - - + -
1017B SER 3.4 8.5 - - - +
1018B HIS* 3.8 11.4 - - + +
1019B LYS* 5.3 0.5 - - - +
1114B VAL* 3.8 30.5 - - + +
1137B GLU* 1.3 82.2 + - - +
1139B CYS* 1.3 68.8 + - - +
1140B SER* 3.5 24.9 + - - +
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Residues in contact with CYS1139 (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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1015B GLN 4.9 0.3 - - - +
1016B TYR* 3.5 8.0 - - - -
1017B SER* 2.5 49.5 + - - +
1019B LYS* 3.9 35.7 - - - -
1078B ILE* 4.6 5.4 - - - -
1138B VAL* 1.3 73.8 - - - +
1140B SER* 1.3 58.9 + - - +
1141B CYS 3.6 5.6 - - - +
1142B PRO* 5.7 0.5 - - - +
1376B THR* 4.3 25.4 - - + +
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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