Contacts of the strand formed by residues 1046 - 1052 (chain B) in PDB entry 2BOA
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 PRO1046 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1016A GLU* 4.0 8.3 - - + +
1019B TYR* 2.6 37.1 + - + -
1037B LYS* 3.9 12.3 - - - +
1039B GLY 3.7 6.1 - - - +
1040B HIS* 3.9 7.2 - - + -
1044B ASN 4.3 2.2 - - - +
1045B ARG* 1.3 91.2 - - + +
1047B MET* 1.3 55.4 + - - +
1048B TYR* 3.4 47.6 - - + +
1113B PRO* 4.4 1.7 - - - +
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Residues in contact with MET1047 (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 TYR* 4.2 2.0 - - - -
1037B LYS* 3.5 3.5 - - - +
1038B ILE* 2.9 44.6 + - + +
1039B GLY 2.8 30.1 + - - +
1040B HIS 3.6 10.3 - - - +
1041B SER 4.1 4.5 - - - +
1046B PRO* 1.3 71.9 - - - +
1048B TYR* 1.3 60.0 + - - +
1108B LEU* 4.1 27.6 - - + -
1110B VAL 4.7 0.7 - - - +
1111B ALA 3.7 19.1 - - - +
1113B PRO* 4.0 18.8 - - - -
1175B GLU* 3.7 43.1 - - - +
1178B SER* 4.2 5.4 - - - +
1179B VAL* 4.7 0.2 - - + -
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Residues in contact with TYR1048 (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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1016A GLU* 2.6 26.4 + - - -
1019B TYR* 3.6 38.3 + + + -
1022B MET* 3.6 15.9 - - + +
1035B ARG* 2.6 65.4 + - + -
1036B VAL 3.5 1.1 - - - -
1037B LYS* 3.7 36.8 - - + +
1046B PRO* 3.4 23.9 + - + +
1047B MET* 1.3 73.0 - - - +
1049B VAL* 1.3 61.4 + - - +
1108B LEU* 3.1 19.6 - - - +
1109B PRO* 4.1 3.6 - - - +
1110B VAL 5.4 0.5 + - - -
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Residues in contact with VAL1049 (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 MET* 3.7 4.7 - - - -
1034B ARG 3.5 0.3 - - - +
1035B ARG* 3.2 3.8 - - - -
1036B VAL* 2.7 40.3 + - + +
1038B ILE* 3.9 17.3 - - + -
1048B TYR* 1.3 79.2 - - - +
1050B LEU* 1.3 74.0 + - - +
1051B LYS* 4.0 0.8 + - + +
1063B TRP* 3.7 18.4 - - + -
1106B PHE* 3.9 22.2 - - + -
1107B LEU 3.3 17.9 - - - +
1108B LEU* 3.6 28.7 - - + -
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Residues in contact with LEU1050 (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 MET* 3.4 56.3 - - + +
1025B ILE* 4.3 6.7 - - + -
1026B ALA* 4.1 4.3 - - + +
1033B ALA* 4.1 19.3 - - + -
1034B ARG 3.4 21.5 - - - +
1035B ARG* 3.8 3.6 - - - +
1049B VAL* 1.3 74.1 - - - +
1051B LYS* 1.3 60.1 + - - +
1052B PHE* 3.8 18.6 + - + -
1083B ALA* 3.7 28.3 - - + -
1105B ILE 3.7 1.2 - - - +
1106B PHE* 3.4 3.3 - - - -
1107B LEU* 2.8 40.6 + - + +
1109B PRO* 5.4 0.9 - - + -
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Residues in contact with LYS1051 (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 LEU 3.6 1.0 - - - +
1033B ALA* 3.3 7.4 - - - +
1034B ARG* 2.8 79.6 + - + +
1036B VAL* 4.0 7.9 - - + -
1049B VAL 4.0 0.2 + - - -
1050B LEU* 1.3 72.4 - - - +
1052B PHE* 1.3 62.8 + - - +
1053B SER* 4.0 15.3 + - - -
1056B GLY* 4.9 11.1 + - - -
1057B VAL 5.5 3.1 + - - -
1058B ARG* 6.1 1.8 - - - +
1104B ASP* 3.8 14.3 + - - -
1105B ILE 3.6 2.7 - - - -
1106B PHE* 3.5 42.0 - - + -
1182B PHE* 5.6 2.6 - - + -
1186B HIS* 5.9 2.2 - - - -
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Residues in contact with PHE1052 (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 ILE* 4.4 3.4 - - + -
1032B LEU* 3.5 4.5 - - + +
1033B ALA* 3.7 28.3 - - + -
1050B LEU* 3.8 27.4 - - + -
1051B LYS* 1.3 71.2 - - - +
1053B SER* 1.3 60.6 + - - +
1083B ALA* 3.7 25.6 - - + -
1086B ILE* 3.7 38.1 - - + -
1087B VAL* 3.7 19.7 - - + -
1100B LEU* 3.6 23.2 - - + +
1104B ASP* 3.2 8.5 - - - +
1105B ILE* 2.7 50.4 + - + +
1107B LEU* 3.9 17.5 - - + -
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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