Contacts of the strand formed by residues 620 - 628 (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 GLN 620 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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612C THR* 5.5 5.4 - - + -
613C GLU 3.4 7.0 - - - +
614C LYS* 4.0 17.7 - - - +
618C GLY 4.0 2.0 + - - -
619C GLN* 1.3 76.5 + - - +
621C ILE* 1.3 70.0 + - - +
622C TRP* 4.3 8.0 + - - +
623C GLU* 5.3 10.5 - - + +
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Residues in contact with ILE 621 (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* 2.5 24.9 + - + +
614C LYS* 4.4 2.2 - - - -
615C THR* 3.3 28.3 - - + +
619C GLN* 3.4 19.5 - - + +
620C GLN* 1.3 82.6 - - - +
622C TRP* 1.3 58.8 + - - +
646C ARG* 4.1 31.4 - - - +
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Residues in contact with TRP 622 (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* 4.0 21.5 - + + -
612C THR* 3.1 19.3 - - - +
613C GLU* 3.0 57.8 + - + +
620C GLN* 3.6 5.3 + - - +
621C ILE* 1.3 82.4 - - - +
623C GLU* 1.3 70.5 + - - +
624C MET* 3.4 36.1 - - + +
643C PRO* 4.6 1.8 - - + -
644C GLU 3.5 23.6 - - - -
645C TYR* 4.2 6.3 - + - -
646C ARG* 3.9 41.2 - - + +
656C VAL* 3.9 19.5 - - + -
675C TYR* 4.1 20.0 - + - -
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Residues in contact with GLU 623 (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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610C VAL* 3.7 25.1 - - + -
611C PHE 3.1 4.5 - - - +
612C THR* 4.6 7.9 - - + +
620C GLN* 5.3 11.3 - - + +
622C TRP* 1.3 82.0 - - - +
624C MET* 1.3 69.9 + - - +
659C TYR* 4.8 6.6 + - - -
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Residues in contact with MET 624 (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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610C VAL* 3.6 2.6 - - - -
611C PHE* 2.7 42.8 + - + +
622C TRP* 3.4 42.1 - - + +
623C GLU* 1.3 79.3 - - - +
625C GLU* 1.3 79.8 + - + +
643C PRO* 4.6 12.1 - - + -
644C GLU 4.8 4.5 - - - +
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Residues in contact with GLU 625 (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* 3.0 42.8 + - + +
609C VAL 3.6 13.5 - - - +
610C VAL* 4.5 9.9 - - + +
624C MET* 1.3 90.6 - - + +
626C ALA* 1.3 71.4 + - - +
627C THR* 4.1 3.3 + - - +
643C PRO* 4.7 3.5 - - - +
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Residues in contact with ALA 626 (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* 5.4 0.9 - - - +
609C VAL* 3.0 17.3 + - + +
611C PHE* 3.7 20.2 - - + -
624C MET 3.8 1.2 + - - -
625C GLU* 1.3 88.7 - - - +
627C THR* 1.3 62.7 + - - +
628C VAL* 3.5 7.9 + - - +
640C VAL* 3.7 22.0 - - + -
641C GLU* 3.4 20.0 - - - +
643C PRO* 4.0 7.6 - - + -
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Residues in contact with THR 627 (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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625C GLU 5.1 3.4 - - - +
626C ALA* 1.3 76.7 - - - +
628C VAL* 1.3 61.7 + - - +
629C ASP 3.7 1.7 + - - -
639C PHE 4.3 0.2 - - - +
641C GLU* 2.9 49.0 + - - +
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Residues in contact with VAL 628 (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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607C SER 3.9 21.1 - - - +
608C LYS* 4.9 16.9 + - + +
609C VAL* 3.8 20.9 - - + -
626C ALA 3.5 5.0 + - - +
627C THR* 1.3 71.0 - - - +
629C ASP* 1.3 53.4 + - - +
630C LYS* 2.6 28.2 + - + +
638C LEU* 4.6 17.0 - - + -
639C PHE 3.1 12.8 - - - +
640C VAL* 3.6 31.9 - - + +
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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