Contacts of the helix formed by residues 615 - 625 (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 ASP 615 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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566B TYR* 2.5 30.5 + - - +
593B GLN* 4.4 7.4 + - - +
595B ASN* 3.8 16.5 + - - -
611B LEU* 3.5 10.9 - - - +
612B LEU 3.2 7.3 + - - +
614B GLN* 1.3 87.0 - - - +
616B ARG* 1.3 66.7 + - - +
617B GLU 3.4 2.2 - - - -
618B HIS* 3.6 9.8 + - + +
619B LEU* 3.1 29.1 + - + +
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Residues in contact with ARG 616 (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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612B LEU 3.5 3.3 + - - -
613B LYS* 2.7 60.2 + - + +
614B GLN* 3.3 11.7 + - - +
615B ASP* 1.3 80.2 - - - +
617B GLU* 1.3 66.4 + - + +
619B LEU* 3.1 2.1 + - - +
620B TRP* 2.9 23.2 + - - +
649B ILE* 4.2 14.5 - - + +
652B GLU* 3.1 33.7 + - - -
653B LEU* 3.6 25.0 - - + +
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Residues in contact with GLU 617 (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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615B ASP 3.4 0.6 - - - -
616B ARG* 1.3 80.9 - - + +
618B HIS* 1.3 65.7 + - - +
620B TRP* 3.1 9.0 + - - +
621B LYS* 2.9 23.4 + - - +
653B LEU* 4.5 14.8 - - + +
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Residues in contact with HIS 618 (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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562B GLU* 2.9 40.2 + - - -
564B LEU* 4.2 14.6 - - + -
593B GLN* 4.7 12.6 + - - -
615B ASP* 3.6 12.3 + - + +
616B ARG 3.5 0.8 - - - -
617B GLU* 1.3 79.1 - - - +
619B LEU* 1.3 61.4 + - + +
621B LYS* 3.5 24.3 + - - +
622B LEU* 3.0 48.0 + - + +
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Residues in contact with LEU 619 (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* 3.6 33.7 - - + -
564B LEU* 4.2 22.7 - - + -
566B TYR* 4.0 5.6 - - + +
612B LEU* 3.4 47.8 - - + +
615B ASP* 3.1 25.7 + - + +
616B ARG 3.6 2.5 - - - +
618B HIS* 1.3 74.3 - - + +
620B TRP* 1.3 67.6 + - - +
622B LEU* 3.3 4.5 + - + +
623B ILE* 2.9 35.9 + - + +
646B PHE* 4.7 3.8 - - + -
649B ILE* 4.1 12.8 - - + -
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Residues in contact with TRP 620 (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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616B ARG 2.9 12.5 + - - +
617B GLU* 3.3 9.9 - - - +
619B LEU* 1.3 76.1 - - - +
621B LYS* 1.3 56.8 - - - +
623B ILE* 2.7 31.9 + - + +
624B GLU* 2.8 55.3 + - + +
649B ILE* 4.6 8.6 - - + +
650B VAL* 4.1 32.3 - - + -
653B LEU* 2.7 48.2 + - + -
654B GLY* 3.8 15.3 - - - -
656B MET* 4.8 2.7 - - + -
664B TYR* 4.0 34.1 - + - -
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Residues in contact with LYS 621 (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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562B GLU* 4.5 6.3 + - - -
617B GLU 2.9 13.4 + - - +
618B HIS* 3.7 34.8 - - - +
620B TRP* 1.3 78.3 - - + +
622B LEU* 1.3 65.9 + - - +
624B GLU* 3.4 7.7 + - - +
625B GLY* 3.1 24.1 + - - -
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Residues in contact with LEU 622 (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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530B PRO* 4.0 26.4 - - + +
532B ILE* 4.5 14.1 - - + -
562B GLU* 3.8 27.4 - - + +
564B LEU* 4.1 19.7 - - + -
618B HIS* 3.0 49.1 + - + +
619B LEU* 3.7 5.4 - - - +
621B LYS* 1.3 85.7 - - - +
623B ILE* 1.3 60.2 + - - +
625B GLY* 3.5 6.8 + - - -
626B GLY 3.5 0.9 + - - -
627B ALA* 3.0 33.3 + - + +
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Residues in contact with ILE 623 (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* 4.4 10.8 - - + -
619B LEU* 2.9 20.9 + - + +
620B TRP* 2.7 26.5 + - + +
622B LEU* 1.3 71.1 - - - +
624B GLU* 1.3 56.7 + - - +
625B GLY 2.9 4.5 - - - -
626B GLY 2.8 16.8 + - - -
627B ALA* 4.3 7.2 - - - +
629B ILE* 3.5 32.1 - - + -
646B PHE* 4.2 18.4 - - + -
649B ILE* 5.3 2.7 - - + -
650B VAL* 5.2 8.3 - - + -
664B TYR* 3.9 29.6 + - + +
665B ILE* 5.8 0.7 - - + -
668B LEU* 4.3 12.1 - - + -
673B ARG* 3.0 20.0 + - - +
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Residues in contact with GLU 624 (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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620B TRP* 2.8 61.5 + - + +
621B LYS* 3.8 8.1 - - - +
623B ILE* 1.3 75.7 - - - +
625B GLY* 1.3 57.5 + - - +
626B GLY 3.2 2.0 + - - -
664B TYR* 4.3 9.0 - - + +
673B ARG* 5.3 0.2 - - - -
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Residues in contact with GLY 625 (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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530B PRO* 4.9 9.1 - - - +
621B LYS 3.1 14.6 + - - -
622B LEU* 3.8 5.6 - - - -
623B ILE 2.9 1.4 - - - -
624B GLU* 1.3 78.8 - - - +
626B GLY* 1.3 59.7 + - - +
627B ALA 3.7 1.6 - - - -
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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