Contacts of the strand formed by residues 625 - 630 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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619F VAL* 3.9 3.5 - - - +
620F PHE 4.7 1.7 + - - -
621F THR* 2.8 31.2 + - + +
623F ALA* 3.3 21.8 - - - +
624F GLY* 1.3 77.3 - - - +
626F VAL* 1.3 59.7 + - - +
651F LYS* 4.9 16.0 + - + +
652F GLN 3.4 6.4 - - - +
653F GLN* 2.9 29.9 - - - +
3001F SO4 4.1 8.1 + - - +
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Residues in contact with VAL 626 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606F ARG 6.1 0.2 - - - +
617F ALA* 4.2 14.6 - - + +
618F PRO 3.8 20.6 - - - +
619F VAL* 4.1 10.8 - - + -
620F PHE* 5.4 2.2 - - + +
624F GLY 3.9 7.2 - - - +
625F ASP* 1.3 77.3 - - - +
627F GLN* 1.3 80.1 + - - +
628F PHE* 4.5 1.8 - - + -
650F HIS 4.0 0.2 - - - +
651F LYS* 3.7 1.5 - - - +
652F GLN* 3.0 38.1 + - + +
654F HIS* 4.0 7.0 - - + -
660F PRO* 3.8 28.3 - - + -
3001F SO4 3.5 12.9 + - - +
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Residues in contact with GLN 627 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597E ASP 4.6 5.1 + - - +
599E PRO* 3.9 32.2 - - - +
606F ARG* 4.9 7.3 + - - +
617F ALA* 5.2 0.5 - - - +
626F VAL* 1.3 85.2 - - - +
628F PHE* 1.3 64.4 + - - +
649F TRP* 3.7 19.7 - - + -
650F HIS 3.2 11.1 + - - +
651F LYS* 3.8 34.6 - - + +
3001F SO4 3.2 34.6 + - - +
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Residues in contact with PHE 628 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607F GLN* 3.4 14.8 - - + +
615F MET* 3.4 25.6 - - + -
617F ALA* 3.8 17.9 - - + -
626F VAL* 4.5 3.4 - - + -
627F GLN* 1.3 80.3 - - - +
629F TYR* 1.3 59.7 + - - +
630F LEU* 3.6 29.8 - - + -
644F LEU* 4.0 2.2 - - + -
648F ARG 4.2 0.2 - - - +
649F TRP* 3.4 10.0 - - - -
650F HIS* 2.8 51.7 + - + +
652F GLN* 3.4 31.6 - - + -
660F PRO* 3.4 27.6 - - + -
662F TYR* 3.8 15.0 - + - -
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Residues in contact with TYR 629 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649E TRP* 5.5 3.0 - + - -
591F MET* 5.0 0.2 - - + -
598F ASP* 2.4 35.0 + - - -
600F ALA* 3.6 19.9 - - + +
601F CYS* 3.9 11.0 - - - -
604F LEU* 4.0 23.1 - - + -
607F GLN* 2.8 32.7 + - - +
628F PHE* 1.3 74.2 - - - +
630F LEU* 1.3 84.4 + - - +
631F PRO* 3.5 6.7 - - + +
647F SER* 3.4 20.1 + - - -
648F ARG* 3.4 32.8 - - - -
649F TRP* 3.6 33.5 - + + +
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Residues in contact with LEU 630 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615F MET* 3.7 26.2 - - + -
628F PHE* 3.6 13.2 + - + -
629F TYR* 1.3 94.2 - - - +
631F PRO* 1.3 58.6 - - + +
635F TRP* 3.5 43.5 - - + +
644F LEU* 3.8 17.5 - - + -
645F ASP 4.9 0.2 - - - +
646F GLY* 4.0 7.2 - - - -
647F SER* 2.6 26.5 + - - -
648F ARG 3.0 12.9 + - - +
650F HIS* 3.2 31.6 - - + +
662F TYR* 4.6 3.6 - - + -
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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