Contacts of the helix formed by residues 607 - 615 (chain A) in PDB entry 3QFS
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 TYR 607 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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597A ALA* 3.4 12.6 - - - +
599A SER* 3.7 10.1 - - - -
605A LYS* 3.5 27.5 - - + +
606A VAL* 1.3 79.7 - - - +
608A VAL* 1.3 68.0 + - - +
609A GLN* 3.2 31.9 - - - +
610A HIS* 2.7 36.6 + + - +
611A LEU* 3.5 4.0 + - - +
641A ASP* 5.7 0.2 - - - -
753A NAP 2.6 84.1 + + + -
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Residues in contact with VAL 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A VAL* 3.8 25.1 - - + -
536A PRO* 4.2 19.1 - - + -
566A TYR* 3.8 21.2 - - + +
567A TYR 3.5 34.1 - - - +
568A GLY* 4.0 5.1 - - - +
595A ASN 5.4 0.2 - - - +
597A ALA* 3.6 5.2 - - + +
607A TYR* 1.3 72.0 - - - +
609A GLN* 1.3 72.7 + - - +
611A LEU* 3.0 10.2 + - + +
612A LEU* 2.9 29.2 + - - +
638A MET* 4.8 0.2 - - + -
642A VAL* 4.1 7.0 - - + -
753A NAP 4.2 9.1 + - + +
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Residues in contact with GLN 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607A TYR* 3.4 19.1 - - + +
608A VAL* 1.3 81.4 - - - +
610A HIS* 1.3 71.2 + - + +
612A LEU* 3.6 14.7 - - + +
613A LYS* 3.0 25.1 + - - +
641A ASP* 3.5 24.4 - - + +
642A VAL* 4.1 7.8 - - + +
645A THR* 3.2 28.1 + - - +
753A NAP 3.1 40.6 + - - -
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Residues in contact with HIS 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605A LYS* 3.6 20.4 + - + -
606A VAL* 3.6 11.5 - - + -
607A TYR* 2.7 53.2 + + + +
609A GLN* 1.3 86.0 - - + +
611A LEU* 1.3 62.7 + - - +
613A LYS* 3.5 5.0 + - - +
614A GLN* 3.1 41.2 + - - +
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Residues in contact with LEU 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566A TYR* 4.0 14.6 - - + -
567A TYR 4.8 0.4 - - - +
595A ASN* 3.8 12.3 - - + +
596A VAL 3.5 44.0 - - - +
597A ALA* 3.6 9.0 - - + +
606A VAL* 4.7 13.5 - - + -
607A TYR 4.0 9.9 - - - +
608A VAL* 3.0 9.0 + - + +
610A HIS* 1.3 75.6 - - - +
612A LEU* 1.3 65.6 + - - +
614A GLN* 3.3 20.6 + - + +
615A ASP* 3.1 28.3 + - - +
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Residues in contact with LEU 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532A ILE* 4.8 0.7 - - + -
534A VAL* 4.1 10.8 - - + -
566A TYR* 3.6 35.2 - - + -
608A VAL 2.9 15.2 + - - +
609A GLN* 3.6 20.2 - - - +
610A HIS 3.3 0.2 - - - -
611A LEU* 1.3 78.4 - - - +
613A LYS* 1.3 62.1 + - - +
615A ASP 3.0 13.3 + - - -
616A ARG* 3.1 10.7 + - - -
619A LEU* 3.3 27.8 - - + +
642A VAL* 4.0 27.4 - - + -
645A THR* 4.0 13.5 - - + -
646A PHE* 4.1 20.2 - - + -
649A ILE* 3.7 4.8 - - + +
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Residues in contact with LYS 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609A GLN 3.0 17.2 + - - +
610A HIS* 3.8 6.1 - - - +
612A LEU* 1.3 77.4 - - - +
614A GLN* 1.3 57.8 + - + +
615A ASP 3.1 0.2 - - - -
616A ARG* 2.7 85.4 + - - +
645A THR* 4.2 11.4 - - + +
648A ASP* 4.3 24.2 + - + +
649A ILE* 4.0 22.0 - - + +
652A GLU* 3.8 8.6 + - - -
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Residues in contact with GLN 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A VAL* 6.0 1.0 - - - +
610A HIS* 3.1 34.5 + - - +
611A LEU* 3.7 19.3 - - + +
612A LEU 3.2 0.6 - - - -
613A LYS* 1.3 78.3 - - + +
615A ASP* 1.3 65.1 + - - +
616A ARG* 3.4 6.0 + - - +
617A GLU* 5.4 0.7 + - - +
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Residues in contact with ASP 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566A TYR* 2.7 37.4 + - - +
593A GLN* 3.9 6.8 + - - -
595A ASN* 3.6 12.8 + - - +
611A LEU* 3.1 13.6 + - - +
612A LEU 3.0 8.3 + - - +
614A GLN* 1.3 83.6 - - - +
616A ARG* 1.3 65.0 + - - +
617A GLU* 3.1 4.0 + - - -
618A HIS* 3.3 9.2 + - + +
619A LEU* 3.1 22.4 + - + +
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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