Contacts of the strand formed by residues 1008 - 1016 (chain B) in PDB entry 1RQQ
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 GLY1008 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1004B GLN* 3.8 4.0 - - - +
1005B GLY* 2.7 35.3 + - - +
1007B PHE* 1.3 82.4 - - - +
1009B MET* 1.3 56.4 + - - +
1010B VAL* 5.5 1.1 - - - -
1031B THR 2.9 20.9 - - - -
1033B ASN* 4.0 8.5 - - - -
117F 112 5.8 0.4 - - - -
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Residues in contact with MET1009 (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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1001B GLU* 4.1 30.3 - - + +
1003B GLY* 3.5 24.7 - - - +
1004B GLN* 4.0 29.2 - - + +
1008B GLY* 1.3 74.3 - - - +
1010B VAL* 1.3 63.9 + - - +
1011B TYR* 3.3 46.3 - - + +
1029B VAL 3.6 0.2 - - - +
1031B THR* 3.0 34.5 + - - +
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Residues in contact with VAL1010 (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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1001B GLU* 3.7 2.3 - - - -
1002B LEU* 2.7 37.1 + - + -
1003B GLY 2.9 16.8 + - - +
1005B GLY* 5.0 1.1 - - - +
1008B GLY 5.5 0.2 - - - -
1009B MET* 1.3 75.9 - - - +
1011B TYR* 1.3 63.5 + - - +
1028B ALA* 4.6 5.8 - - + -
1029B VAL 3.4 8.7 - - - +
1030B LYS* 3.9 21.5 - - + -
117F 112 3.2 74.7 - - + +
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Residues in contact with TYR1011 (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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998B LEU* 3.9 29.2 - - + -
1000B ARG 3.3 18.2 - - - +
1001B GLU* 3.7 29.6 + - + -
1002B LEU* 4.0 6.9 - - - +
1009B MET* 3.3 41.8 - - + +
1010B VAL* 1.3 75.3 - - - +
1012B GLU* 1.3 63.2 + - - +
1028B ALA* 3.3 4.3 - - - -
1029B VAL* 2.7 55.4 + - + +
1031B THR* 3.6 21.6 + - + -
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Residues in contact with GLU1012 (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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998B LEU* 3.6 3.6 - - - -
999B LEU* 2.7 29.2 + - + +
1000B ARG* 3.0 38.1 + - + +
1002B LEU* 3.7 26.8 - - + +
1011B TYR* 1.3 75.8 - - - +
1013B GLY* 1.3 65.6 + - - +
1026B ARG* 3.0 32.2 + - - +
1027B VAL 3.4 11.9 - - - +
1029B VAL* 4.6 1.6 - - - -
1078B LEU* 3.6 18.0 - - + +
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Residues in contact with GLY1013 (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 ILE* 6.2 0.4 - - - -
997B THR 3.0 15.3 - - - -
998B LEU* 4.1 2.9 - - - -
999B LEU* 3.7 9.9 - - - -
1012B GLU* 1.3 78.6 - - - +
1014B ASN* 1.3 65.4 + - - +
1026B ARG* 3.4 7.4 - - - +
1027B VAL* 2.9 36.1 + - - +
1029B VAL* 4.9 2.2 - - - +
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Residues in contact with ASN1014 (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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995B LYS 3.6 0.8 - - - +
996B ILE* 3.6 6.8 - - - +
997B THR* 2.8 43.2 + - - +
999B LEU* 3.6 19.8 - - + +
1013B GLY* 1.3 77.6 - - - +
1015B ALA* 1.3 61.1 + - - +
1016B ARG 4.3 0.2 - - - -
1024B GLU* 3.8 26.2 - - + +
1025B THR 3.5 14.5 - - - +
1026B ARG* 4.0 8.4 - - - +
1027B VAL* 4.6 1.8 - - - -
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Residues in contact with ALA1015 (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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995B LYS 3.3 4.3 - - - -
996B ILE* 3.9 11.4 - - + -
1014B ASN* 1.3 77.0 - - - +
1016B ARG* 1.3 62.7 + - - +
1017B ASP 3.7 0.5 + - - -
1018B ILE* 3.3 39.4 - - + +
1024B GLU* 3.2 4.1 - - - -
1025B THR 2.8 38.9 + - - +
1027B VAL* 4.2 12.1 - - + -
1075B VAL* 4.9 1.6 - - + -
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Residues in contact with ARG1016 (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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995B LYS* 2.9 44.3 + - + +
1014B ASN 4.3 0.2 - - - -
1015B ALA* 1.3 70.2 - - - +
1017B ASP* 1.3 72.7 + - + +
1018B ILE* 3.3 3.3 + - - +
1023B ALA 3.1 10.1 - - - +
1024B GLU* 4.2 4.3 - - + +
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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