Contacts of the strand formed by residues 908 - 911 (chain K) in PDB entry 6D6Q
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 LYS 908 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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847K SER* 4.2 19.0 + - - +
848K GLU 3.4 6.7 - - - +
849K GLU* 3.6 35.6 + - + +
906K LYS* 5.0 5.5 - - - +
907K VAL* 1.3 74.4 - - - +
909K VAL* 1.3 66.1 + - - +
927K LEU* 3.8 0.3 - - - -
928K VAL* 2.8 51.4 + - + +
929K GLU* 4.7 9.7 - - - +
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Residues in contact with VAL 909 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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846K VAL 3.8 0.2 - - - -
847K SER* 2.6 32.1 + - - -
848K GLU 2.9 24.4 + - - +
850K ALA* 4.4 7.9 - - + -
862K VAL* 4.8 7.9 - - + -
864K ILE* 3.9 26.0 - - + -
907K VAL* 4.3 18.4 - - + +
908K LYS* 1.3 83.9 - - - +
910K LYS* 1.3 55.4 + - - +
911K ILE* 3.9 6.2 - - + +
925K MET* 4.0 25.8 - - + -
926K SER 3.1 13.7 - - - +
927K LEU* 4.5 5.4 - - + -
928K VAL* 4.8 0.4 - - - -
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Residues in contact with LYS 910 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846K VAL* 3.8 16.2 - - + +
847K SER* 3.5 30.5 + - - +
909K VAL* 1.3 73.1 - - - +
911K ILE* 1.3 62.1 + - - +
912K MET* 3.4 34.4 - - + +
924K ARG 3.6 2.1 - - - +
925K MET* 3.7 1.0 - - - -
926K SER* 2.9 39.2 + - - +
928K VAL* 3.5 37.1 - - + +
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Residues in contact with ILE 911 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840K PHE* 3.6 38.2 - - + +
844K GLY* 5.8 1.4 - - - -
845K ILE* 3.8 32.1 + - + +
846K VAL* 4.4 4.2 - - - +
847K SER 5.1 1.8 - - - +
848K GLU* 5.2 7.6 - - + +
864K ILE* 4.4 10.5 - - + -
867K TYR* 6.2 2.5 - - + -
869K LEU* 6.4 0.2 - - + -
909K VAL* 3.9 23.6 - - + +
910K LYS* 1.3 73.4 - - - +
912K MET* 1.3 63.5 + - - +
913K LEU* 4.2 4.3 + - - +
923K ILE* 3.4 31.6 - - + -
924K ARG 3.5 2.9 - - - -
925K MET* 3.7 23.1 - - + -
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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