Contacts of the helix formed by residues 607 - 614 (chain B) in PDB entry 3QFR
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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597B ALA* 3.6 7.2 - - - +
599B SER* 3.6 11.2 - - - -
605B LYS* 3.3 29.8 - - + +
606B VAL* 1.3 82.2 - - - +
608B VAL* 1.3 68.4 + - - +
609B GLN* 3.2 33.4 - - - +
610B HIS* 2.7 35.9 + + - +
611B LEU 3.4 2.4 + - - -
641B ASP* 5.6 0.4 - - - -
753B NAP 2.7 83.0 + + + -
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Residues in contact with VAL 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B VAL* 3.9 23.1 - - + -
536B PRO* 3.8 27.1 - - + -
566B TYR* 3.7 28.0 - - + +
567B TYR 3.6 24.7 - - - +
568B GLY* 4.6 1.8 - - - -
597B ALA* 3.8 6.9 - - - +
607B TYR* 1.3 70.4 - - - +
609B GLN* 1.3 73.1 + - - +
611B LEU* 2.6 31.4 + - + +
612B LEU* 2.9 13.7 + - + +
638B MET* 4.6 0.2 - - + -
642B VAL* 4.2 7.6 - - + -
753B NAP 4.2 5.1 + - + -
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Residues in contact with GLN 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607B TYR* 3.4 21.4 - - + +
608B VAL* 1.3 80.2 - - - +
610B HIS* 1.3 69.3 + - + +
612B LEU* 3.7 13.0 - - - -
613B LYS* 3.2 24.8 + - - +
641B ASP* 3.8 19.7 - - + +
642B VAL* 4.3 16.9 - - - +
645B THR* 3.2 30.0 + - - +
753B NAP 3.1 38.8 + - - -
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Residues in contact with HIS 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605B LYS* 3.6 21.4 + - + -
606B VAL* 3.8 5.1 - - + +
607B TYR* 2.7 49.5 + + + +
608B VAL 2.7 1.6 + - - -
609B GLN* 1.3 80.2 - - + +
611B LEU* 1.3 64.8 + - + +
612B LEU 3.1 4.5 - - - -
613B LYS* 3.5 7.2 + - + +
614B GLN* 3.3 38.4 + - - +
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Residues in contact with LEU 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566B TYR* 2.8 39.8 + - + -
567B TYR 5.1 0.4 - - - +
595B ASN* 4.3 15.1 + - + +
596B VAL 3.5 30.3 - - - +
597B ALA* 3.4 26.2 - - + +
606B VAL* 4.0 20.9 - - + -
607B TYR 3.4 0.6 + - - +
608B VAL* 2.6 17.2 + - + +
610B HIS* 1.3 78.7 - - + +
612B LEU* 1.3 53.5 + - - -
614B GLN* 4.1 22.4 - - - +
615B ASP* 3.5 12.5 - - - +
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Residues in contact with LEU 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532B ILE* 5.1 0.7 - - + -
534B VAL* 4.1 21.3 - - + -
566B TYR* 3.5 32.1 - - + -
608B VAL 2.9 11.3 + - - +
609B GLN* 3.9 20.2 - - + +
611B LEU* 1.3 76.7 - - - +
613B LYS* 1.3 67.8 + - - +
614B GLN 3.2 1.6 - - - -
615B ASP 3.2 10.3 + - - -
619B LEU* 3.4 37.8 - - + +
642B VAL* 4.1 20.0 - - + -
645B THR* 4.2 9.4 - - + -
646B PHE* 4.2 18.4 - - + -
649B ILE* 3.5 10.6 - - + +
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Residues in contact with LYS 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609B GLN 3.2 15.9 + - - +
610B HIS* 3.8 9.9 - - + +
612B LEU* 1.3 82.0 - - - +
614B GLN* 1.3 56.7 + - + +
616B ARG* 2.7 59.7 + - + +
645B THR* 4.0 15.4 - - + +
648B ASP* 3.9 27.7 + - + +
649B ILE* 4.6 5.4 - - + -
652B GLU* 3.7 18.2 + - - +
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Residues in contact with GLN 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610B HIS* 3.3 24.5 + - - +
611B LEU* 4.1 19.8 - - - +
612B LEU 3.2 0.4 - - - -
613B LYS* 1.3 78.9 - - + +
615B ASP* 1.3 67.3 + - - +
616B ARG* 3.3 13.3 + - - +
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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