Contacts of the strand formed by residues 625 - 629 (chain F) in PDB entry 6IWQ
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 CYS 625 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616F ARG* 3.5 35.2 - - + -
617F PHE 3.6 7.0 - - - +
618F THR* 4.7 2.5 - - - -
619F HIS 5.2 0.2 - - - -
624F LYS* 1.3 73.9 - - - +
626F LEU* 1.3 67.0 + - - +
637F ILE* 3.2 8.1 - - - -
638F SER* 2.9 27.2 + - - +
640F CYS* 2.1 46.2 - - - -
647F GLN* 3.7 26.7 - - + +
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Residues in contact with LEU 626 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537F ILE* 4.9 1.6 - - + -
546F ILE* 4.0 23.1 - - + -
579F LEU* 5.3 6.5 - - + -
595F VAL* 4.1 15.3 - - + -
608F TRP* 4.1 14.1 - - + -
617F PHE* 3.0 46.7 + - + +
625F CYS* 1.3 73.9 - - - +
627F ASP* 1.3 57.7 + - - +
635F VAL* 3.9 20.6 - - + -
636F PHE 3.6 15.3 - - - +
637F ILE* 4.2 6.2 - - + +
647F GLN* 3.3 28.4 + - - +
649F TRP* 3.3 22.8 + - + +
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Residues in contact with ASP 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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625F CYS 3.5 0.4 + - - +
626F LEU* 1.3 74.9 - - - +
628F ARG* 1.3 95.4 + - - +
635F VAL* 3.6 5.2 - - - +
636F PHE* 2.7 60.8 + - + +
638F SER* 3.1 26.3 + - - +
644F LYS* 3.8 12.8 + - - -
646F THR* 2.6 33.0 + - - +
647F GLN* 4.0 3.6 - - - +
649F TRP* 4.2 2.6 - - - -
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Residues in contact with ARG 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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539F GLY* 3.3 20.3 - - - -
540F PHE 3.9 3.6 + - - +
542F THR* 3.8 15.5 + - - +
544F TYR* 5.4 1.1 - - - -
559F LEU* 4.0 24.7 - - + -
627F ASP* 1.3 103.9 + - - +
629F SER* 1.3 60.2 + - - +
630F GLU* 3.0 31.3 + - - +
634F GLN 3.1 14.6 - - - +
635F VAL* 4.4 3.1 - - + -
636F PHE* 3.6 8.2 - - - -
645F THR* 3.0 25.1 + - - -
646F THR* 3.3 34.3 + - - +
648F LYS 3.2 22.6 + - - -
649F TRP* 3.5 29.3 - - + -
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Residues in contact with SER 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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559F LEU* 4.1 2.1 - - - +
628F ARG* 1.3 75.7 - - - +
630F GLU* 1.3 64.9 + - - +
631F VAL 2.6 31.7 + - - -
632F LEU* 2.9 29.3 + - - +
633F HIS* 3.6 0.5 - - - -
634F GLN* 2.9 18.4 + - - +
636F PHE* 3.6 12.0 - - - -
646F THR* 5.4 1.3 - - - -
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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