Contacts of the strand formed by residues 608 - 614 (chain C) in PDB entry 1S9K
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 608 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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605C SER 5.6 3.4 - - - -
606C GLU 3.8 10.8 - - - +
607C SER* 1.3 81.9 + - - +
609C VAL* 1.3 64.4 + - - +
610C VAL* 4.1 2.2 - - + -
625C GLU* 3.0 32.1 + - + +
626C ALA 5.4 1.3 + - - +
628C VAL* 4.9 14.5 + - + +
630C LYS* 5.7 6.3 - - - +
660C VAL* 3.3 4.5 - - - +
661C ILE* 2.8 47.8 + - + +
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Residues in contact with VAL 609 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596C MET* 5.6 0.4 - - + -
598C LEU* 4.4 8.7 - - + -
607C SER 5.7 0.2 - - - -
608C LYS* 1.3 79.1 - - - +
610C VAL* 1.3 63.7 + - - +
611C PHE* 3.6 25.6 - - + -
625C GLU* 3.6 4.4 - - - +
626C ALA* 3.0 31.9 + - + -
628C VAL* 3.8 23.5 - - + +
638C LEU* 4.4 8.7 - - + -
640C VAL* 4.0 18.6 - - + -
658C PHE* 4.4 12.6 - - + -
659C TYR 3.3 7.9 - - - +
660C VAL* 4.2 20.0 - - + -
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Residues in contact with VAL 610 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608C LYS* 5.3 1.6 - - + -
609C VAL* 1.3 76.9 - - - +
611C PHE* 1.3 69.6 + - - +
612C THR* 4.6 0.4 - - + -
623C GLU* 3.7 29.8 - - + -
624C MET 3.8 7.0 - - - +
625C GLU* 4.5 9.2 - - + +
658C PHE* 2.8 26.7 - - - +
659C TYR* 2.8 60.1 + - + +
661C ILE* 4.0 14.6 - - + -
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Residues in contact with PHE 611 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596C MET* 4.6 12.6 - - + -
609C VAL* 3.6 23.1 - - + -
610C VAL* 1.3 80.6 - - - +
612C THR* 1.3 63.3 + - - +
622C TRP* 4.0 21.9 - + + -
623C GLU* 3.1 8.0 - - - -
624C MET* 2.7 43.0 + - + +
626C ALA* 3.7 10.5 - - + -
640C VAL* 4.6 1.8 - - + -
642C ILE* 4.7 8.3 - - + -
643C PRO* 3.6 35.7 - - + -
656C VAL* 5.0 2.2 - - + -
657C ASN 3.2 6.3 - - - -
658C PHE* 3.7 30.1 - + + -
673C PHE* 4.3 19.3 - + - -
675C TYR* 4.3 9.9 - + - -
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Residues in contact with THR 612 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611C PHE* 1.3 80.1 - - - +
613C GLU* 1.3 60.3 + - - +
614C LYS* 4.3 19.1 + - - +
620C GLN* 5.5 6.3 - - + -
622C TRP* 3.1 14.1 - - - +
623C GLU* 4.6 15.5 - - + +
656C VAL* 3.3 10.7 - - - +
657C ASN* 2.5 61.7 + - - +
658C PHE 4.4 0.2 + - - -
659C TYR* 4.3 26.0 - - + +
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Residues in contact with GLU 613 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612C THR* 1.3 72.4 - - - +
614C LYS* 1.3 68.8 + - - +
620C GLN* 3.4 5.4 - - - -
621C ILE* 2.5 38.4 + - + +
622C TRP* 3.0 38.9 + - + +
645C TYR* 2.8 18.2 + - + +
646C ARG* 2.7 31.0 + - - +
654C VAL* 3.7 9.6 - - - +
655C LYS 3.6 16.8 - - - +
656C VAL* 3.8 17.7 - - + +
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Residues in contact with LYS 614 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612C THR* 4.3 20.2 + - - +
613C GLU* 1.3 83.7 + - - +
615C THR* 1.3 67.2 + - - +
618C GLY* 3.4 30.3 - - - +
619C GLN 3.1 13.9 - - - +
620C GLN* 4.2 19.2 - - - +
621C ILE* 4.4 3.8 - - - +
655C LYS 5.3 3.3 + - - +
657C ASN* 4.7 13.2 + - - +
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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