Contacts of the strand formed by residues 1000 - 1009 (chain B) in PDB entry 4BQ7
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 LYS1000 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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997B LYS* 3.2 40.0 - - + +
998B GLU 3.1 9.8 - - - +
999B GLY* 1.4 82.4 - - - +
1001B PRO* 1.4 58.9 - - - +
1002B ARG 3.2 5.6 - - - -
1003B THR* 3.1 40.2 + - - +
1051B GLN* 5.7 3.0 + - - -
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Residues in contact with PRO1001 (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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996B SER* 3.7 11.8 + - - +
997B LYS 4.0 1.5 - - - +
999B GLY* 3.7 8.3 - - - +
1000B LYS* 1.4 85.1 - - - +
1002B ARG* 1.3 59.0 + - + +
1003B THR 3.3 4.2 + - - +
1004B ILE* 5.4 0.2 - - - +
1055B LEU* 3.3 31.1 - - + +
1082B THR* 4.3 7.4 - - - +
1083B PRO* 3.6 34.9 - - + +
1084B LYS 5.6 2.2 - - - +
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Residues in contact with ARG1002 (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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1000B LYS* 3.2 1.8 + - - +
1001B PRO* 1.3 77.2 - - + +
1003B THR* 1.3 58.5 + - - +
1004B ILE* 5.5 0.2 - - - -
1051B GLN 3.7 0.9 - - - -
1052B GLU* 3.3 54.6 + - - +
1053B LEU* 2.9 58.4 + - - +
1054B THR* 5.0 4.0 + - - +
1055B LEU* 3.8 26.0 - - + +
1082B THR* 5.8 0.4 - - - -
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Residues in contact with THR1003 (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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996B SER* 3.8 5.7 + - - -
997B LYS* 2.9 48.4 + - + +
1000B LYS* 3.1 24.1 + - - +
1001B PRO 4.2 0.7 - - - -
1002B ARG* 1.3 80.3 - - - +
1004B ILE* 1.3 74.6 + - - +
1049B GLN* 4.2 10.5 - - + +
1050B ILE 3.3 14.8 - - - +
1051B GLN* 3.8 24.2 + - + +
1052B GLU 4.7 0.3 + - - -
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Residues in contact with ILE1004 (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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994B VAL* 3.6 7.9 - - + -
995B VAL 3.2 8.5 - - - +
996B SER* 4.9 0.7 - - - +
1001B PRO 5.4 0.7 - - - +
1003B THR* 1.3 80.7 - - - +
1005B ILE* 1.3 61.0 + - - +
1006B VAL* 3.3 34.3 - - + -
1049B GLN* 3.4 4.5 - - - -
1050B ILE* 2.9 43.4 + - + +
1053B LEU* 3.6 30.7 - - + -
1059B TYR* 5.8 0.2 - - + -
1061B PHE* 3.6 22.0 - - + -
1080B PHE* 3.7 31.0 - - + -
1082B THR* 4.0 11.2 - - + -
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Residues in contact with ILE1005 (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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993B THR 3.8 0.7 - - - +
994B VAL* 3.4 4.5 - - - +
995B VAL* 2.8 47.5 + - + +
996B SER 4.9 0.2 - - - +
997B LYS* 3.8 38.8 - - + +
998B GLU 5.2 0.7 - - - +
1004B ILE* 1.3 77.2 - - - +
1006B VAL* 1.4 61.2 + - - +
1007B ASN* 3.4 11.2 - - - +
1047B THR* 3.4 25.4 - - - +
1048B HIS 3.4 6.7 - - - +
1049B GLN* 3.8 26.0 - - + +
187F TRP* 6.1 0.4 - - + -
309F LEU* 4.0 30.1 - - + -
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Residues in contact with VAL1006 (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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992B VAL* 4.3 10.1 - - + -
993B THR 3.5 8.3 - - - +
994B VAL* 4.4 6.3 - - + +
1004B ILE* 3.3 27.8 - - + -
1005B ILE* 1.4 71.3 - - - +
1007B ASN* 1.3 62.6 + - - +
1008B TRP* 3.3 5.1 - - + -
1023B ILE* 4.3 16.6 - - + -
1047B THR* 3.2 4.2 - - - -
1048B HIS 2.8 39.0 + - - +
1050B ILE* 4.2 10.5 - - + -
1061B PHE* 4.0 17.7 - - + -
1063B ILE* 3.7 30.7 - - + -
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Residues in contact with ASN1007 (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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991B ASP 3.5 1.4 - - - +
992B VAL* 3.6 0.5 - - - -
993B THR* 2.8 39.8 + - - +
995B VAL* 4.4 10.1 - - - +
1005B ILE* 3.4 13.1 - - - +
1006B VAL* 1.3 76.3 - - - +
1008B TRP* 1.3 64.5 + - - +
1046B LEU 3.4 3.8 - - - -
1047B THR* 2.6 32.2 + - - -
186F ALA* 2.7 35.3 + - + +
187F TRP* 4.1 21.8 - - - +
188F PRO* 4.0 9.7 - - - +
198F GLN* 4.0 2.5 - - - +
309F LEU* 4.4 0.6 - - - +
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Residues in contact with TRP1008 (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 13.9 - - + -
990B LYS 3.6 11.4 - - - +
991B ASP 4.0 0.7 - - - -
992B VAL* 4.3 5.6 - - + -
1006B VAL 3.3 23.6 - - - -
1007B ASN* 1.3 78.0 - - - +
1009B GLN* 1.3 79.5 + - - +
1021B TYR* 3.4 42.7 - + + -
1023B ILE* 3.9 20.4 - - + -
1041B VAL* 3.8 21.1 - - + -
1045B ARG 3.5 16.8 - - - -
1046B LEU* 3.0 41.4 + - + +
1047B THR* 3.7 15.9 - - - -
1048B HIS* 3.8 7.0 - - + -
1063B ILE* 3.7 29.6 - - + -
186F ALA* 3.6 5.4 - - - +
198F GLN* 3.4 12.3 + - - +
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Residues in contact with GLN1009 (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* 3.5 1.2 - - - +
990B LYS* 2.8 32.8 + - + +
991B ASP* 3.3 12.6 - - + +
1008B TRP* 1.3 90.3 - - - +
1010B PRO* 1.3 68.3 - - + +
1046B LEU* 4.2 0.2 - - - -
186F ALA* 4.1 1.3 - - + +
198F GLN* 3.9 9.0 + - - +
199F VAL* 3.2 13.9 + - - +
200F THR* 2.3 53.4 + - - +
215F LYS* 3.2 33.7 - - + +
217F THR* 2.9 26.7 + - - -
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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