Contacts of the strand formed by residues 1113 - 1122 (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 LEU1113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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793B ARG* 3.5 31.4 - - - +
1056B LYS* 3.5 6.0 - - - +
1057B VAL* 2.9 59.2 + - + +
1112B GLY* 1.3 70.8 - - - -
1114B TYR* 1.3 61.7 + - - +
1134B THR* 4.5 4.5 - - + -
1135B LEU 3.5 32.3 - - - +
1136B ARG* 3.8 26.2 - - + +
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Residues in contact with TYR1114 (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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1032B VAL* 6.4 0.2 - - + -
1054B HIS* 4.9 7.2 - + - -
1055B LYS 3.3 16.8 - - - -
1056B LYS* 3.6 26.4 - - + +
1057B VAL* 5.0 1.3 - - - -
1108B LEU* 3.7 27.7 - - + +
1109B GLU* 2.8 51.0 + - - +
1112B GLY* 3.5 20.0 - - - -
1113B LEU* 1.3 76.9 - - - +
1115B LYS* 1.3 59.1 + - - +
1116B PHE* 3.7 27.6 - + + -
1133B VAL 4.0 0.3 - - - +
1134B THR* 3.2 6.7 - - - -
1135B LEU* 2.8 35.9 + - + +
1137B THR* 3.8 18.6 - - + -
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Residues in contact with LYS1115 (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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1053B GLN 4.1 0.2 - - - +
1054B HIS* 3.3 4.3 - - - +
1055B LYS* 2.8 63.0 + - + +
1057B VAL* 4.2 10.3 - - + +
1065B LEU* 5.1 11.7 - - + +
1114B TYR* 1.3 73.8 - - - +
1116B PHE* 1.3 63.8 + - - +
1117B THR* 3.9 15.6 - - + +
1132B THR* 3.7 26.1 + - + +
1133B VAL 3.4 3.1 - - - -
1134B THR* 3.5 21.7 - - + +
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Residues in contact with PHE1116 (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* 3.7 20.1 - - + +
1032B VAL* 4.3 11.9 - - + -
1034B LEU* 3.6 17.3 - - + -
1052B LEU* 5.0 2.9 - - + -
1053B GLN 3.5 4.3 - - - +
1054B HIS* 3.4 27.1 - + + -
1105B PHE* 3.5 30.1 - + - -
1108B LEU* 4.1 20.0 - - + -
1114B TYR* 3.7 28.7 - + + -
1115B LYS* 1.3 74.6 - - - +
1117B THR* 1.3 62.9 + - - +
1132B THR* 3.4 2.4 - - - +
1133B VAL* 2.7 48.6 + - + +
1135B LEU* 4.1 27.1 - - + -
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Residues in contact with THR1117 (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* 4.5 2.0 - - - -
1051B ILE 3.8 0.2 - - - +
1052B LEU* 3.3 6.9 - - - +
1053B GLN* 2.9 57.4 + - - +
1115B LYS* 3.9 17.7 - - + -
1116B PHE* 1.3 79.9 - - - +
1118B LEU* 1.3 61.1 + - - +
1119B TYR* 5.7 0.8 - - - -
1130B LEU* 3.8 23.5 - - + +
1131B SER 3.2 6.3 - - - -
1132B THR* 3.6 26.0 - - + +
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Residues in contact with LEU1118 (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* 3.7 28.9 - - + +
1019B LEU* 4.1 20.4 - - + -
1036B TRP* 3.5 65.3 - - + -
1050B TYR* 4.1 11.4 - - + -
1051B ILE 3.4 13.9 - - - +
1052B LEU* 4.0 12.1 - - + -
1117B THR* 1.3 76.1 - - - +
1119B TYR* 1.3 66.5 + - - +
1129B GLU 4.3 0.5 - - - +
1130B LEU* 3.6 1.4 - - - -
1131B SER* 2.7 39.5 + - - +
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Residues in contact with TYR1119 (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* 4.1 6.3 - - - -
1050B TYR* 3.5 4.5 - - - -
1051B ILE* 2.8 83.6 + - + +
1053B GLN* 4.2 17.6 + - + -
1070B PHE* 4.4 6.8 - - - -
1117B THR 5.7 0.7 - - - -
1118B LEU* 1.3 78.4 - - - +
1120B ALA* 1.3 69.7 + - - +
1121B VAL* 3.8 1.1 - - + -
1127B HIS* 3.4 48.2 + + + -
1128B SER* 3.4 20.4 - - - +
1130B LEU* 4.2 22.4 - - + -
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Residues in contact with ALA1120 (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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1014B LEU* 4.1 7.9 - - + -
1017B PRO* 3.9 3.6 - - + +
1039B VAL* 3.9 17.7 - - + -
1047B VAL* 4.2 4.3 - - + -
1049B ASP 3.5 4.9 - - - -
1050B TYR* 3.6 25.4 - - + -
1119B TYR* 1.3 75.6 - - - +
1121B VAL* 1.3 65.9 + - - +
1122B ASP 4.3 0.4 - - - -
1127B HIS* 3.5 2.4 - - - -
1128B SER* 2.8 42.3 + - - +
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Residues in contact with VAL1121 (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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1014B LEU* 4.8 0.4 - - - -
1047B VAL* 3.6 3.2 - - - +
1048B SER* 2.7 42.7 + - - +
1049B ASP* 2.7 24.6 + - + +
1051B ILE* 3.9 17.7 - - + -
1119B TYR* 3.8 14.4 - - + -
1120B ALA* 1.3 80.9 - - - +
1122B ASP* 1.3 61.9 + - - +
1125B GLY* 4.2 11.4 - - - +
1126B ARG 3.3 11.4 - - - +
1127B HIS* 3.8 23.3 - - + +
1260B TYR* 5.3 4.0 - - + -
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Residues in contact with ASP1122 (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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1009B PRO 4.6 1.7 - - - +
1014B LEU* 4.1 9.6 - - + +
1045B THR* 3.4 19.9 - - + +
1046B LYS 3.2 14.4 - - - +
1047B VAL* 4.1 1.3 - - - +
1048B SER* 3.0 14.4 + - - +
1121B VAL* 1.3 76.8 - - - +
1123B THR* 1.3 64.2 + - - +
1124B ARG* 3.2 9.5 + - - +
1125B GLY* 2.8 23.4 + - - -
1126B ARG* 2.7 71.6 + - - +
1260B TYR* 3.8 1.4 - - - -
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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