Contacts of the strand formed by residues 1018 - 1026 (chain B) in PDB entry 4BQ9
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 ILE1018 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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985B PRO* 4.3 7.9 - - + -
1010B PRO* 5.1 2.9 - - + -
1011B PRO* 4.3 5.6 - - + -
1014B ALA* 3.7 36.6 - - + +
1016B GLY 3.3 1.5 + - - +
1017B LYS* 1.4 76.5 - - - +
1019B THR* 1.4 62.6 + - - +
1020B GLY 3.6 18.4 - - - +
1021B TYR* 3.7 19.3 - - + +
1043B GLY* 4.8 0.3 - - - -
1044B ASN* 3.6 49.8 + - + +
1065B ALA* 4.0 18.8 - - + -
1066B ARG 3.3 15.5 - - - +
1067B ASN* 4.6 1.1 - - + -
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Residues in contact with THR1019 (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 LYS* 3.4 20.4 + - + +
1018B ILE* 1.4 71.9 - - - +
1020B GLY* 1.3 55.5 + - - +
1042B VAL* 4.4 4.7 - - - +
1043B GLY* 2.9 22.4 + - - -
1066B ARG* 2.8 33.7 + - - -
1067B ASN* 3.4 11.3 - - - -
1068B SER* 4.0 16.9 - - - +
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Residues in contact with GLY1020 (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 ILE* 3.4 9.5 - - - +
1019B THR* 1.3 80.2 - - - +
1021B TYR* 1.3 60.8 + - - -
1041B VAL 3.1 14.1 - - - -
1042B VAL* 4.6 0.2 - - - -
1043B GLY 3.2 13.8 + - - -
1066B ARG* 2.8 39.8 + - - +
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Residues in contact with TYR1021 (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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989B PRO* 3.8 14.1 - - + -
1008B TRP* 3.4 30.3 - + + -
1010B PRO* 3.4 23.2 - - - +
1011B PRO* 4.0 6.3 - - + +
1018B ILE* 3.7 16.3 - - + +
1020B GLY* 1.3 71.6 - - - -
1022B ILE* 1.3 66.0 + - - +
1040B PRO* 4.5 0.3 - - - +
1041B VAL* 2.8 42.6 + - + +
1043B GLY 4.0 6.3 - - - -
1044B ASN* 2.9 25.9 + - - -
1045B ARG 3.3 27.1 - - - -
1046B LEU* 3.6 2.3 - - + +
1063B ILE* 3.8 10.8 - - + -
1064B GLN 3.1 10.5 - - - +
1065B ALA* 3.7 29.6 - - + +
1066B ARG* 4.6 1.1 + - - +
1071B MET* 5.3 0.2 - - - -
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Residues in contact with ILE1022 (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 TYR* 1.3 78.5 - - - +
1023B ILE* 1.3 66.9 + - - +
1024B TYR* 3.5 38.6 - - + +
1038B ILE* 3.5 29.4 - - + -
1039B GLU 3.8 5.4 - - - +
1040B PRO* 4.8 7.9 - - + -
1062B LYS 3.7 0.9 - - - +
1063B ILE* 3.3 3.7 - - - -
1064B GLN* 2.9 34.3 + - + +
1066B ARG* 4.2 15.9 - - - +
1071B MET* 3.5 33.7 - - + -
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Residues in contact with ILE1023 (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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1006B VAL* 4.6 9.9 - - + -
1008B TRP* 3.8 12.1 - - + -
1022B ILE* 1.3 78.4 - - - +
1024B TYR* 1.3 69.1 + - - +
1025B TYR* 4.9 0.7 - - + -
1037B VAL 3.5 1.3 - - - +
1038B ILE* 3.6 2.9 - - - -
1039B GLU* 2.8 43.0 + - + +
1041B VAL* 3.6 26.0 - - + -
1048B HIS* 3.6 29.2 - - + -
1050B ILE* 4.1 20.6 - - + -
1061B PHE* 4.3 11.9 - - + -
1062B LYS 3.4 7.6 - - - +
1063B ILE* 4.0 24.7 - - + -
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Residues in contact with TYR1024 (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 ILE* 3.5 25.9 - - + +
1023B ILE* 1.3 76.2 - - - +
1025B TYR* 1.3 62.4 + - - +
1033B ILE* 4.1 22.7 - - + -
1036B TRP* 3.5 25.0 - - + -
1037B VAL 3.3 4.7 - - - +
1038B ILE* 3.5 33.2 - - + -
1061B PHE* 3.3 6.9 - - - +
1062B LYS* 2.7 46.4 + - + +
1064B GLN* 2.6 38.0 + - + -
1074B MET* 3.7 26.8 - - + +
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Residues in contact with TYR1025 (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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1023B ILE* 4.9 0.7 - - + -
1024B TYR* 1.3 73.4 - - - +
1026B SER* 1.3 62.7 + - - +
1036B TRP* 3.5 3.7 - - - -
1037B VAL* 2.8 79.5 + - + +
1039B GLU* 3.6 33.6 + - + -
1050B ILE* 3.9 32.3 - - + +
1051B GLN 5.0 1.6 + - - -
1053B LEU* 3.8 19.9 - - + +
1059B TYR* 3.8 22.7 - + + -
1060B TYR 3.1 13.9 - - - +
1061B PHE* 3.4 18.6 - + + -
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Residues in contact with SER1026 (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 TYR* 1.3 79.2 - - - +
1027B THR* 1.3 68.6 + - - +
1028B ASP* 2.6 32.4 + - - +
1031B ALA* 3.8 8.5 - - - +
1035B ASP 5.3 2.1 + - - -
1036B TRP* 3.5 29.3 - - - -
1037B VAL* 5.5 1.3 - - - -
1059B TYR* 3.5 5.9 - - - -
1060B TYR* 2.8 33.1 + - - -
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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