Contacts of the strand formed by residues 1063 - 1068 (chain B) in PDB entry 1B0P
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 SER1063 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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978B LEU* 3.9 2.7 - - - +
984B VAL 3.1 5.7 + - - -
985B ASN* 3.7 14.1 - - - -
986B VAL* 2.9 33.0 + - - +
1035B VAL* 4.9 0.2 - - - -
1036B TYR* 3.3 15.5 - - - +
1056B ALA* 2.6 51.6 + - - -
1059B PHE* 4.0 1.0 - - - +
1062B PRO* 1.3 74.8 - - - +
1064B LEU* 1.3 60.8 - - - +
1065B VAL* 5.1 0.9 - - - -
1238B CA 3.4 3.8 - - - -
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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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974B LEU* 4.8 5.2 - - + -
978B LEU* 3.8 21.1 - - + -
986B VAL* 3.7 13.7 - - + -
988B VAL* 3.7 28.3 - - + -
1025B LEU* 4.2 17.5 - - + +
1029B VAL* 3.7 36.1 - - + -
1035B VAL* 4.8 0.9 - - + -
1036B TYR* 2.7 13.1 + - - +
1037B VAL* 3.3 11.6 - - + +
1038B ALA 2.9 26.9 + - - +
1063B SER* 1.3 72.3 - - - +
1065B VAL* 1.3 66.5 + - - +
1066B ILE* 4.2 17.9 - - + -
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Residues in contact with VAL1065 (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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958B TRP* 5.4 7.6 - - + -
986B VAL 2.9 13.3 + - - +
987B PHE* 3.5 28.0 - - + -
988B VAL* 3.0 26.9 + - - +
1036B TYR* 4.8 0.4 - - + -
1038B ALA* 3.4 7.0 - - + +
1040B VAL* 4.0 15.0 - - + -
1052B VAL* 3.4 35.0 - - + -
1053B LEU* 5.3 5.4 - - + +
1056B ALA* 3.9 22.7 - - + -
1063B SER* 5.1 0.9 - - - -
1064B LEU* 1.3 78.6 - - - +
1066B ILE* 1.3 62.6 + - - +
1067B ALA 4.1 0.2 - - - -
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Residues in contact with ILE1066 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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967B TYR* 4.0 15.3 - - - +
988B VAL* 3.6 17.3 - - + +
990B ASP* 3.9 23.1 - - + -
1025B LEU* 4.1 21.8 - - + -
1026B ALA* 4.0 29.8 - - + +
1037B VAL* 5.5 0.4 - - + -
1038B ALA 3.0 11.9 + - - +
1039B THR* 3.3 14.2 - - + -
1040B VAL* 3.0 24.7 + - - +
1064B LEU* 4.2 20.0 - - + -
1065B VAL* 1.3 75.7 - - - +
1067B ALA* 1.3 62.2 + - - +
1096B TRP* 4.0 11.1 - - + -
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Residues in contact with ALA1067 (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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820B TYR* 3.6 22.7 - - + -
987B PHE* 3.6 20.9 - - + -
988B VAL 2.9 9.5 + - - +
989B MET* 3.9 2.4 - - - -
990B ASP* 2.9 29.5 + - - +
1040B VAL* 3.4 24.2 - - + -
1065B VAL 4.1 0.2 - - - -
1066B ILE* 1.3 75.2 - - - +
1068B TYR* 1.3 61.0 + - - +
1069B ALA* 5.9 0.2 - - + -
1096B TRP* 3.8 3.8 - - - -
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Residues in contact with TYR1068 (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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820B TYR* 2.7 25.6 + - - -
990B ASP 4.0 5.8 - - - -
992B GLU* 4.1 11.4 - - + -
1040B VAL 3.1 9.3 + - - +
1041B SER* 4.0 13.2 - - - +
1067B ALA* 1.3 70.2 - - - +
1069B ALA* 1.3 60.8 + - - +
1070B THR* 4.1 20.9 - - + -
1074B GLN* 4.4 7.6 + - - -
1086B VAL* 4.3 7.9 - - + +
1087B MET* 3.8 26.6 - - + +
1090B ALA* 4.1 15.9 - - + -
1095B TYR* 3.8 20.6 - + - -
1096B TRP* 3.4 45.6 - + + +
1127B PHE* 3.5 14.0 - - - -
1131B GLN* 4.0 2.9 + - - -
1133B ARG* 2.9 25.6 + - - -
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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