Contacts of the strand formed by residues 1047 - 1057 (chain B) in PDB entry 5J67
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 VAL1047 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1014B LEU* 4.3 10.8 - - + -
1038B ASP* 3.8 15.0 - - - +
1039B VAL* 3.7 28.7 - - + -
1040B GLN* 3.0 25.4 + - + +
1045B THR* 5.5 0.9 - - + -
1046B LYS* 1.3 72.5 - - - +
1048B SER* 1.3 61.4 - - - +
1049B ASP 3.5 24.9 - - - +
1050B TYR* 3.7 24.7 - - + +
1120B ALA* 4.2 5.4 - - + -
1121B VAL 3.6 6.1 - - - +
1122B ASP* 4.1 1.3 - - - +
1123B THR* 4.8 0.9 - - - -
1262B ILE* 4.0 2.1 - - - -
1263B LEU* 3.1 24.5 + - + +
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Residues in contact with SER1048 (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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1046B LYS 3.6 2.2 + - - -
1047B VAL* 1.3 72.2 - - - +
1049B ASP* 1.3 62.3 + - - +
1074B ALA* 4.3 7.6 - - - +
1121B VAL* 2.7 28.4 + - - +
1122B ASP 3.0 18.2 + - - -
1123B THR* 4.0 3.8 - - - -
1260B TYR* 4.0 20.6 - - - +
1261B SER* 3.3 24.6 + - - +
1263B LEU* 3.6 16.4 - - - +
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Residues in contact with ASP1049 (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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1047B VAL* 3.5 8.3 - - - +
1048B SER* 1.3 84.9 - - - +
1050B TYR* 1.3 73.6 + - - +
1051B ILE* 3.5 10.0 - - - +
1072B SER* 2.5 26.5 + - - -
1073B PHE* 3.2 3.6 + - - +
1074B ALA* 2.9 33.4 + - - +
1075B ASP* 4.8 2.1 - - - +
1120B ALA* 3.5 0.3 - - - -
1121B VAL* 2.7 44.6 + - + -
1263B LEU* 4.1 6.2 - - - +
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Residues in contact with TYR1050 (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 PRO* 4.0 11.2 - - + -
1036B TRP* 3.4 49.4 - + + -
1038B ASP* 2.6 28.1 + - - -
1039B VAL* 3.1 17.3 + - + +
1047B VAL* 3.7 16.1 - - + +
1049B ASP* 1.3 76.8 + - - +
1051B ILE* 1.3 62.8 + - - +
1052B LEU* 4.0 1.4 + - - +
1071B LEU 3.7 0.7 - - - +
1073B PHE* 2.9 33.2 + - + +
1101B TYR* 3.7 27.6 - + - -
1118B LEU* 4.1 9.0 - - + -
1119B TYR 3.5 3.8 - - - -
1120B ALA* 3.6 28.5 - - + -
1263B LEU* 3.7 15.0 - - + +
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Residues in contact with ILE1051 (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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1049B ASP* 3.5 24.2 - - - +
1050B TYR* 1.3 73.7 - - - +
1052B LEU* 1.3 61.2 + - - +
1053B GLN* 4.3 7.4 - - + -
1070B PHE* 2.9 52.7 - - + -
1071B LEU 3.5 0.9 - - - -
1072B SER* 3.7 11.9 - - - -
1117B THR 3.8 0.5 - - - +
1118B LEU* 3.4 5.3 - - - +
1119B TYR* 2.8 80.2 + - + +
1121B VAL* 3.9 11.9 - - + -
1127B HIS* 5.8 0.2 - - + -
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Residues in contact with LEU1052 (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 LEU* 4.2 13.5 - - + -
1034B LEU* 4.7 4.3 - - + -
1036B TRP* 3.7 32.8 - - + -
1050B TYR 5.1 1.8 - - - +
1051B ILE* 1.3 75.1 - - - +
1053B GLN* 1.3 68.0 + - - +
1054B HIS* 5.0 0.2 - - + -
1069B GLU 3.8 0.3 - - - +
1071B LEU* 2.9 50.0 + - + +
1073B PHE* 6.4 0.7 - - + -
1077B LEU* 5.5 5.8 - - + -
1103B VAL* 3.7 15.0 - - + -
1105B PHE* 3.5 34.5 - - + -
1116B PHE* 5.0 2.9 - - + -
1117B THR 3.3 9.2 - - - +
1118B LEU* 4.0 11.2 - - + -
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Residues in contact with GLN1053 (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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1051B ILE* 4.3 12.8 - - + +
1052B LEU* 1.3 79.7 - - - +
1054B HIS* 1.3 63.8 + - - +
1067B THR* 4.4 12.5 - - - +
1068B GLY* 3.6 26.5 + - - +
1069B GLU 3.5 8.5 - - - +
1070B PHE* 4.6 16.8 - - - +
1116B PHE* 3.5 2.1 - - - +
1117B THR* 2.9 47.4 + - - +
1119B TYR* 4.2 19.6 + - + -
1130B LEU* 5.2 6.1 - - - +
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Residues in contact with HIS1054 (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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1052B LEU* 5.0 0.4 - - + -
1053B GLN* 1.3 78.5 - - - +
1055B LYS* 1.3 63.2 + - - +
1068B GLY* 3.3 16.9 - - - -
1069B GLU* 3.1 48.9 + - + +
1071B LEU* 4.5 10.8 - - + +
1105B PHE* 3.7 34.9 - + + -
1108B LEU* 4.7 12.6 - - + +
1114B TYR* 4.9 6.5 - + - -
1115B LYS 3.3 5.6 - - - -
1116B PHE* 3.4 29.8 - - + -
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Residues in contact with LYS1055 (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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1054B HIS* 1.3 76.3 - - - +
1056B LYS* 1.3 63.3 + - - +
1057B VAL* 3.9 26.2 - - + +
1064B ASP 4.1 6.3 + - - -
1065B LEU* 3.9 22.0 - - - +
1066B TYR* 3.0 56.2 - - + +
1068B GLY* 4.1 11.0 - - - +
1069B GLU* 5.7 0.2 - - - -
1114B TYR* 3.3 10.5 - - - -
1115B LYS* 2.8 61.8 + - + +
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Residues in contact with LYS1056 (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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1055B LYS* 1.3 79.4 - - - +
1057B VAL* 1.3 69.2 + - - +
1058B ASP* 4.9 10.2 - - - +
1066B TYR* 5.9 1.2 - - - -
1109B GLU* 3.4 36.6 + - - +
1110B PRO 5.3 1.6 + - - -
1111B ASP 5.4 0.6 + - - -
1112B GLY* 4.1 18.5 - - - -
1113B LEU 3.5 12.6 - - - +
1114B TYR* 3.6 34.9 - - + +
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Residues in contact with VAL1057 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1055B LYS* 3.9 33.7 - - + +
1056B LYS* 1.3 83.6 - - - +
1058B ASP* 1.3 72.4 + - - +
1063B THR* 5.8 0.4 - - - +
1113B LEU* 2.9 58.9 + - + +
1114B TYR 5.0 0.4 - - - -
1115B LYS* 4.2 18.2 - - + +
1134B THR* 5.9 1.8 - - + -
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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