Contacts of the strand formed by residues 996 - 1005 (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 ILE 996 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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991B VAL* 4.5 9.2 - - + -
992B SER 3.9 11.0 - - - +
993B ARG* 3.4 16.9 + - - +
994B GLU 3.0 4.1 - - - +
995B LYS* 1.3 90.8 - - + +
997B THR* 1.3 74.3 + - - +
998B LEU* 4.4 8.3 - - + -
1013B GLY* 6.2 0.2 - - - -
1014B ASN 3.6 6.1 - - - +
1015B ALA* 3.9 20.6 - - + -
1018B ILE* 4.6 4.3 - - + -
1027B VAL* 5.7 0.2 - - + -
1029B VAL* 4.3 20.2 - - + -
1066B VAL* 4.3 17.7 - - + -
1073B LEU* 4.2 20.6 - - + -
1075B VAL* 4.3 16.2 - - + -
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Residues in contact with THR 997 (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 GLU 4.8 6.3 - - - +
995B LYS 5.1 1.8 - - - +
996B ILE* 1.3 82.1 - - - +
998B LEU* 1.3 65.5 + - - +
999B LEU* 3.9 6.2 - - - +
1013B GLY* 3.0 4.2 - - - -
1014B ASN* 2.8 49.2 + - - +
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Residues in contact with LEU 998 (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* 4.4 9.0 - - + -
997B THR* 1.3 77.4 - - - +
999B LEU* 1.3 64.3 + - - +
1000B ARG 6.0 0.2 - - - -
1011B TYR* 3.9 37.5 - - + -
1012B GLU 3.7 4.0 - - - +
1013B GLY* 5.2 0.4 - - - -
1029B VAL* 3.4 38.6 - - + -
1031B THR* 5.7 3.1 - - + -
1073B LEU* 5.1 11.2 - - + -
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Residues in contact with LEU 999 (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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997B THR* 3.9 13.0 - - - +
998B LEU* 1.3 77.0 - - - +
1000B ARG* 1.3 66.5 + - + +
1012B GLU* 2.7 26.6 + - + +
1013B GLY* 3.8 10.5 - - - -
1014B ASN* 3.6 25.4 - - - +
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Residues in contact with ARG1000 (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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999B LEU* 1.3 83.3 + - + +
1001B GLU* 1.3 78.5 + - - +
1002B LEU* 4.7 6.0 - - + +
1011B TYR* 3.3 13.1 - - - +
1012B GLU* 3.0 50.8 + - + +
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Residues in contact with GLU1001 (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 ARG* 1.3 92.3 + - - +
1002B LEU* 1.3 63.5 + - - +
1003B GLY* 4.8 0.7 - - - +
1009B MET* 4.1 30.4 - - - +
1010B VAL 3.8 3.6 - - - -
1011B TYR* 3.7 30.4 + - + +
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Residues in contact with LEU1002 (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 ARG* 4.7 6.7 - - - +
1001B GLU* 1.3 75.4 - - - +
1003B GLY* 1.3 56.8 + - - +
1010B VAL* 2.7 26.1 + - + +
1011B TYR* 4.0 10.0 - - - +
1012B GLU* 3.7 36.6 - - + +
1028B ALA* 4.4 1.3 - - + -
1078B LEU* 3.5 30.1 - - + -
102F LEU* 5.8 1.4 - - - +
117F 112 3.8 26.4 + - + +
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Residues in contact with GLY1003 (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* 3.6 2.2 - - - +
1002B LEU* 1.3 83.7 - - - +
1004B GLN* 1.3 61.8 + - - -
1009B MET* 3.5 7.7 - - - +
1010B VAL* 2.9 31.0 + - - +
102F LEU* 5.3 9.9 - - - -
117F 112 4.0 13.9 + - - -
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Residues in contact with GLN1004 (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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1003B GLY* 1.3 71.9 - - - -
1005B GLY* 1.3 71.8 + - - +
1008B GLY 4.1 2.9 - - - +
1009B MET* 4.0 30.4 - - + +
102F LEU* 4.4 17.9 + - + +
103F PRO* 2.9 38.3 - - + +
117F 112 3.3 12.0 + - - +
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Residues in contact with GLY1005 (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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1003B GLY 3.8 2.4 + - - -
1004B GLN* 1.3 86.0 - - - +
1006B SER* 1.3 67.3 + - - -
1007B PHE 3.1 3.3 + - - -
1008B GLY 2.7 23.7 + - - +
1009B MET* 4.4 0.2 - - - +
1010B VAL* 4.9 0.4 - - - +
103F PRO* 3.8 4.2 - - - +
117F 112 3.4 30.0 - - - -
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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