Contacts of the strand formed by residues 625 - 629 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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616C ARG* 3.6 25.4 - - + -
617C PHE 3.5 7.9 - - - +
618C THR* 4.1 5.4 - - - -
623C GLY 4.2 4.0 - - - -
624C LYS* 1.3 78.8 - - - +
626C LEU* 1.3 70.7 + - - +
627C ASP* 4.0 2.8 - - - +
637C ILE* 3.5 3.3 - - - -
638C SER 2.9 28.0 + - - +
640C CYS* 2.5 53.6 - - + -
647C GLN* 4.4 6.6 + - + +
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Residues in contact with LEU 626 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537C ILE* 5.0 0.4 - - + -
546C ILE* 4.0 22.0 - - + -
579C LEU* 5.1 7.6 - - + -
595C VAL* 4.0 20.0 - - + -
608C TRP* 3.9 22.0 - - + -
617C PHE* 3.0 46.4 + - + +
618C THR* 4.8 0.4 - - - +
624C LYS 4.3 0.2 + - - -
625C CYS* 1.3 69.7 - - - +
627C ASP* 1.3 58.3 + - - +
635C VAL* 3.7 27.1 - - + -
636C PHE 3.7 4.7 - - - +
637C ILE* 3.8 5.5 - - + +
647C GLN* 2.9 28.9 - - - +
649C TRP* 3.2 16.8 + - + +
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Residues in contact with ASP 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 CYS 4.0 0.2 - - - +
626C LEU* 1.3 76.0 - - - +
628C ARG* 1.3 63.6 + - - +
635C VAL* 3.6 3.8 - - - +
636C PHE* 2.6 53.6 + - + +
638C SER* 3.4 21.3 + - - +
644C LYS* 3.4 21.5 + - - -
646C THR* 2.4 36.8 + - - -
647C GLN* 2.5 34.6 + - + +
649C TRP* 3.7 4.2 - - - -
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Residues in contact with ARG 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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539C GLY* 2.9 38.1 - - - -
540C PHE 3.6 1.0 + - - +
542C THR* 4.1 9.9 + - - +
544C TYR* 5.6 1.0 - - - +
559C LEU* 3.5 27.9 - - + +
627C ASP* 1.3 83.1 + - - +
629C SER* 1.3 58.4 + - - +
630C GLU* 4.1 15.3 + - - -
634C GLN 2.9 18.6 - - - +
635C VAL* 4.1 3.1 - - + -
636C PHE* 3.9 11.2 - - - -
645C THR 4.1 1.6 + - - -
646C THR* 2.6 82.1 + - - +
647C GLN 3.0 10.9 - - - +
648C LYS 3.5 14.3 + - - +
649C TRP* 3.4 27.1 - - + -
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Residues in contact with SER 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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559C LEU* 3.8 4.2 - - - +
628C ARG* 1.3 75.5 - - - +
630C GLU* 1.3 60.2 + - - +
631C VAL 3.2 16.9 + - - -
632C LEU* 2.5 37.2 + - - +
633C HIS* 3.5 1.6 - - - -
634C GLN* 2.9 20.4 + - - -
636C PHE* 3.8 14.6 - - - -
646C THR* 4.9 0.2 - - - -
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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