Contacts of the strand formed by residues 828 - 833 (chain A) in PDB entry 6M0X
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 TYR 828 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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824A ASP* 5.2 3.7 + - + -
826A THR* 3.4 46.7 - - + -
827A ILE* 1.3 72.9 - - - +
829A ALA* 1.3 61.2 + - - +
845A VAL* 3.7 20.9 - - + -
846A LEU 3.6 20.9 - - - -
847A GLY* 5.6 3.6 - - - -
939A ASP* 5.9 2.7 - - - -
956A LYS 4.1 0.2 - - - +
957A VAL* 3.4 10.2 - - - +
958A VAL* 3.0 43.4 + - + +
960A GLN* 3.7 41.1 - - + +
23B U 4.3 1.1 - - - -
7C T 4.0 1.0 + - - -
8C T 2.9 44.4 + - - -
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Residues in contact with ALA 829 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828A TYR* 1.3 77.3 - - - +
830A THR* 1.3 64.6 + - - +
831A ARG* 3.4 10.3 - - - +
845A VAL* 3.6 3.5 - - - +
846A LEU* 2.9 38.5 + - + +
936A LYS* 6.1 1.6 - - + +
956A LYS 4.3 3.4 - - - -
957A VAL* 4.9 2.2 - - - +
23B U 3.2 23.3 - - - +
24B U 3.2 27.8 - - - +
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Residues in contact with THR 830 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828A TYR 4.6 0.2 - - - +
829A ALA* 1.3 78.8 - - - +
831A ARG* 1.3 75.3 + - - +
832A GLN* 5.4 1.0 + - - -
843A THR* 3.9 20.7 - - + +
844A TYR 3.2 10.3 - - - -
845A VAL* 4.1 20.6 - - + -
846A LEU 4.4 0.4 - - - +
942A LEU* 4.5 3.8 - - + -
955A ASN* 3.0 23.2 + - - +
956A LYS* 2.8 40.0 + - + +
958A VAL* 4.4 18.6 - - + -
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Residues in contact with ARG 831 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829A ALA* 3.4 13.7 - - - +
830A THR* 1.3 93.1 + - - +
832A GLN* 1.3 68.2 + - - +
833A ALA* 3.8 0.6 + - - -
842A GLU 3.4 0.5 - - - +
843A THR* 3.4 2.3 - - - -
844A TYR* 2.8 35.1 + - - +
846A LEU* 3.8 24.3 - - + +
873A LEU* 4.9 0.2 - - + -
936A LYS* 4.5 7.5 - - - +
938A TYR* 4.1 21.3 - - + +
955A ASN* 3.2 28.2 + - - +
24B U 2.9 30.0 + - - -
25B U 5.7 1.2 + - - -
40B G 4.4 8.4 + - - -
41B C 2.7 43.5 + - - +
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Residues in contact with GLN 832 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830A THR* 5.4 1.0 + - - -
831A ARG* 1.3 76.0 - - - +
833A ALA* 1.3 63.1 + - - +
841A ASP* 3.8 24.4 + - - +
842A GLU* 3.1 16.3 + - - +
843A THR* 3.0 33.0 + - - +
938A TYR* 4.9 2.1 + - - -
955A ASN* 4.3 15.4 + - - +
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Residues in contact with ALA 833 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831A ARG 3.8 1.2 + - - -
832A GLN* 1.3 76.0 - - - +
834A LYS* 1.3 60.5 + - - +
835A VAL* 4.0 6.7 - - + -
841A ASP* 3.7 10.7 + - - -
842A GLU* 2.8 34.7 + - - +
844A TYR* 3.8 7.5 - - + -
876A ARG* 3.9 11.0 - - - +
938A TYR* 3.6 39.7 - - + +
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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