Contacts of the strand formed by residues 842 - 848 (chain B) in PDB entry 4DQL
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 GLN 842 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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668B VAL* 3.8 28.8 - - - +
686B GLU* 2.9 37.2 - - + +
687B ILE 3.4 19.3 - - - +
688B GLU* 4.6 4.2 - - - +
689B LEU* 4.6 0.4 - - - +
695B TYR* 2.9 20.9 + - - -
834B SER* 3.9 2.9 + - - -
839B ASP* 3.1 31.7 + - + +
840B GLU 3.6 0.2 - - - -
841B LYS* 1.3 81.4 - - - +
843B ALA* 1.3 60.2 + - - +
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Residues in contact with ALA 843 (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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685B LEU 3.9 0.2 - - - +
686B GLU* 3.5 5.2 - - - -
687B ILE* 2.9 39.2 + - + +
689B LEU* 4.5 14.0 - - + +
695B TYR* 3.9 17.5 - - + -
701B LEU* 5.6 4.3 - - + -
832B ILE* 4.0 22.9 - - + -
834B SER* 3.5 5.4 - - - -
842B GLN* 1.3 75.3 - - - +
844B SER* 1.3 60.0 + - - +
845B ILE* 5.6 1.3 - - + -
882B ILE* 5.6 0.9 - - + -
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Residues in contact with SER 844 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684B HIS* 3.6 17.9 - - - -
685B LEU 3.0 13.0 - - - -
686B GLU* 3.7 12.3 - - - -
832B ILE* 3.3 4.9 - - - +
833B SER* 2.7 52.2 + - - -
834B SER* 3.1 10.7 + - - -
843B ALA* 1.3 75.9 - - - +
845B ILE* 1.3 68.6 + - - +
912B ARG* 3.0 17.5 + - - -
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Residues in contact with ILE 845 (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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683B ARG 3.7 0.6 - - - +
684B HIS* 3.5 6.2 + - - -
685B LEU* 3.0 46.4 + - + +
687B ILE* 5.2 4.5 - - + -
701B LEU* 3.9 38.6 - - + -
703B VAL* 4.5 0.2 - - + -
830B TYR* 3.8 28.7 - - + +
831B SER 4.3 8.5 - - - +
832B ILE* 4.5 3.1 - - + -
833B SER* 3.5 4.0 + - - -
843B ALA* 5.6 0.9 - - + -
844B SER* 1.3 80.6 - - - +
846B THR* 1.3 65.0 + - - +
847B VAL* 3.7 21.8 - - + -
869B LEU* 4.2 25.4 - - + -
878B ILE* 5.6 0.2 - - + -
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Residues in contact with THR 846 (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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673B LEU* 4.0 2.5 - - + -
682B THR* 4.0 18.4 - - + -
683B ARG 3.3 4.0 - - - -
830B TYR* 4.6 0.2 - - - -
831B SER 4.6 3.4 + - - -
833B SER* 2.9 19.9 + - - -
845B ILE* 1.3 72.5 - - - +
847B VAL* 1.3 60.7 + - - +
848B SER 3.9 0.4 + - - -
906B THR* 4.3 10.8 - - + -
908B VAL* 5.2 0.4 - - + -
909B ALA* 4.0 15.0 - - + +
945B LEU* 4.0 12.8 - - + -
946B TYR* 2.7 38.3 + - + +
1101B FAD 2.9 26.2 + - - +
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Residues in contact with VAL 847 (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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682B THR* 3.2 5.0 - - - -
683B ARG* 2.7 45.5 + - + +
685B LEU* 3.8 14.4 - - + -
830B TYR* 3.9 21.3 - - + -
845B ILE* 3.7 30.3 - - + -
846B THR* 1.3 78.1 - - - +
848B SER* 1.3 61.9 + - - +
849B VAL* 3.6 4.4 + - + +
866B SER* 3.7 39.3 - - - +
869B LEU* 4.0 9.9 - - + -
1101B FAD 3.6 2.9 - - - -
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Residues in contact with SER 848 (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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680B ARG* 5.5 1.7 + - - -
681B SER 4.0 5.5 + - - -
682B THR* 4.3 4.2 + - - -
846B THR 3.9 1.0 + - - -
847B VAL* 1.3 71.4 - - - +
849B VAL* 1.3 65.3 + - - +
850B VAL* 3.5 8.6 + - - +
866B SER* 3.2 18.5 - - - -
906B THR* 3.7 25.4 - - - +
1101B FAD 3.0 17.5 + - - +
1102B NAP 3.8 23.3 + - - -
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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