Contacts of the strand formed by residues 625 - 630 (chain C) in PDB entry 1XSK
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 ASP 625 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619C VAL* 4.0 2.9 - - - +
620C PHE 4.9 0.9 + - - -
621C THR* 2.8 35.1 + - + +
623C ALA* 3.3 23.2 - - - +
624C GLY* 1.3 77.3 - - - +
626C VAL* 1.3 62.2 + - - +
651C LYS* 4.0 24.0 + - - +
652C GLN 3.4 6.6 - - - +
653C GLN* 2.9 29.6 - - - +
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Residues in contact with VAL 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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617C ALA* 4.3 13.5 - - + +
618C PRO 3.9 20.6 - - - +
619C VAL* 4.1 11.2 - - + -
620C PHE* 5.5 1.3 - - + +
624C GLY 4.0 2.9 - - - +
625C ASP* 1.3 76.1 - - - +
627C GLN* 1.3 76.7 + - - +
628C PHE* 4.5 2.0 - - + -
650C HIS 3.9 0.2 - - - +
651C LYS* 3.4 4.1 - - - +
652C GLN* 2.8 47.3 + - + +
654C HIS* 3.9 24.5 - - + -
660C PRO* 3.9 17.0 - - + -
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Residues in contact with GLN 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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597B ASP 4.5 4.9 + - - +
599B PRO* 3.9 31.4 - - + +
606C ARG* 4.9 14.4 + - - +
607C GLN* 4.9 0.3 - - - +
617C ALA* 5.3 0.7 - - - +
626C VAL* 1.3 86.4 - - - +
628C PHE* 1.3 62.9 + - - +
649C TRP* 3.8 19.4 - - + +
650C HIS 3.1 9.3 + - - +
651C LYS* 3.7 37.5 - - + +
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Residues in contact with PHE 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 GLN* 3.5 14.8 - - + +
615C MET* 3.3 27.1 - - + -
617C ALA* 3.8 17.5 - - + -
626C VAL* 4.5 2.5 - - + -
627C GLN* 1.3 80.2 - - - +
629C TYR* 1.3 58.4 + - - +
630C LEU* 3.9 17.3 - - + -
644C LEU* 3.9 4.0 - - + -
649C TRP* 3.4 9.2 - - - -
650C HIS* 2.8 64.6 + + + +
652C GLN* 3.8 22.4 - - + -
660C PRO* 3.6 23.1 - - + -
662C TYR* 3.8 24.9 - + - -
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Residues in contact with TYR 629 (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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649B TRP* 5.7 1.7 - + - -
591C MET* 5.1 0.2 - - + -
598C ASP* 2.6 31.5 + - - -
600C ALA* 3.5 21.3 - - + +
601C CYS* 3.8 13.5 - - - -
604C LEU* 3.8 28.5 - - + -
607C GLN* 2.9 28.7 + - - +
628C PHE* 1.3 74.1 - - - +
630C LEU* 1.3 72.7 + - - +
631C PRO* 3.5 18.0 - - + +
647C SER* 3.5 19.8 + - - -
648C ARG* 3.4 35.4 - - - -
649C TRP* 3.7 32.6 - + + -
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Residues in contact with LEU 630 (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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615C MET* 3.6 38.4 - - + -
628C PHE* 3.9 5.6 + - + -
629C TYR* 1.3 82.3 - - - +
631C PRO* 1.3 58.6 - - + +
635C TRP* 3.6 49.1 - - + +
644C LEU* 3.9 21.5 - - + +
646C GLY* 4.1 6.5 - - - -
647C SER* 2.5 27.9 + - - -
648C ARG 3.0 20.7 + - - +
650C HIS* 3.8 24.2 - - + +
662C TYR* 4.5 5.4 - - + -
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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