Contacts of the strand formed by residues 654 - 661 (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 VAL 654 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613C GLU* 3.7 21.3 - - - +
645C TYR* 3.3 40.4 - - + +
650C ILE* 3.6 30.3 - - + -
652C THR 3.7 4.0 - - - +
653C PRO* 1.3 75.7 - - - +
655C LYS* 1.3 68.9 + - - +
656C VAL* 4.0 1.6 + - + +
674C THR* 3.0 19.8 + - - -
675C TYR* 3.1 21.6 + - + +
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Residues in contact with LYS 655 (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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613C GLU* 3.6 18.2 - - - +
614C LYS 5.3 2.6 + - - +
653C PRO* 5.6 1.8 - - + +
654C VAL* 1.3 77.4 - - - +
656C VAL* 1.3 61.9 + - - +
657C ASN* 5.3 0.4 - - - +
673C PHE 3.7 4.7 - - - +
674C THR* 4.5 12.1 - - - +
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Residues in contact with VAL 656 (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* 5.0 3.4 - - + -
612C THR 3.3 16.4 - - - +
613C GLU* 3.8 21.1 - - + +
622C TRP* 3.9 15.9 - - + -
645C TYR* 4.1 11.7 - - + -
654C VAL* 4.6 1.3 - - + -
655C LYS* 1.3 79.1 - - - +
657C ASN* 1.3 75.4 + - - +
672C HIS* 3.8 1.2 - - - +
673C PHE* 2.7 68.6 + - + +
674C THR* 4.1 1.3 - - - +
675C TYR* 3.9 15.5 - - + +
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Residues in contact with ASN 657 (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* 3.2 6.6 - - - +
612C THR* 2.5 57.2 + - - +
614C LYS* 4.7 16.5 + - - +
655C LYS 5.3 0.6 - - - +
656C VAL* 1.3 86.1 + - - +
658C PHE* 1.3 60.7 + - - +
659C TYR* 6.0 0.4 - - + -
670C PRO* 4.6 18.3 - - + +
671C GLN 3.0 10.5 + - - +
672C HIS* 3.8 24.0 + - - -
673C PHE 4.8 0.4 - - - +
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Residues in contact with PHE 658 (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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580C VAL* 4.8 0.9 - - + -
583C GLN* 3.3 32.1 - - - -
596C MET* 3.8 11.2 - - + -
598C LEU* 3.6 36.8 - - + -
609C VAL* 4.4 10.8 - - + -
610C VAL 2.8 16.6 - - - +
611C PHE* 3.7 30.5 - + + -
612C THR 4.6 0.2 - - - +
657C ASN* 1.3 76.0 - - - +
659C TYR* 1.3 66.8 + - - +
670C PRO* 5.0 0.2 - - - -
671C GLN* 2.8 57.4 + - + +
672C HIS 3.8 7.6 - - - -
673C PHE* 3.9 18.2 - - + -
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Residues in contact with TYR 659 (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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609C VAL* 3.3 6.0 - - - +
610C VAL* 2.8 76.8 + - + +
612C THR* 4.3 21.6 - - + +
623C GLU* 4.8 7.6 + - - -
657C ASN* 6.0 0.9 - - + -
658C PHE* 1.3 79.7 - - - +
660C VAL* 1.3 71.6 + - - +
661C ILE* 4.0 15.2 - - + +
667C ARG* 3.4 45.9 + - + -
668C SER* 3.4 24.0 - - - +
669C GLN 4.2 5.2 - - - +
670C PRO* 4.5 10.8 - - + -
671C GLN* 5.1 0.7 - - - -
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Residues in contact with VAL 660 (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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578C PRO* 3.8 8.9 - - + +
580C VAL* 3.7 30.1 - - + -
598C LEU* 3.8 17.5 - - + -
603C PHE* 4.6 9.6 - - + -
607C SER* 4.1 16.8 - - - +
608C LYS 3.3 11.4 - - - +
609C VAL* 4.2 3.4 - - + +
638C LEU* 3.6 26.7 - - + -
658C PHE* 5.5 0.2 - - + -
659C TYR* 1.3 75.3 - - - +
661C ILE* 1.3 62.5 + - - +
662C ASN* 4.2 3.6 - - - +
667C ARG* 3.3 1.7 - - - +
668C SER* 2.7 47.3 + - - +
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Residues in contact with ILE 661 (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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606C GLU 3.5 2.9 - - - +
607C SER* 3.5 0.9 - - - -
608C LYS* 2.8 54.9 + - + +
610C VAL* 4.0 19.3 - - + -
659C TYR* 4.0 9.0 - - + +
660C VAL* 1.3 74.8 - - - +
662C ASN* 1.3 68.4 + - - +
663C GLY 3.3 29.1 + - - +
664C LYS* 4.0 13.7 - - - +
666C LYS 3.3 6.7 - - - +
667C ARG* 4.0 25.6 - - + +
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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