Contacts of the helix formed by residues 578 - 588 (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 578 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293B ARG* 4.3 2.9 - - - -
295B LEU* 3.8 25.5 + - + +
305B HIS* 2.6 42.4 - + - -
462B ALA* 4.4 5.1 - - + +
475B CYS* 3.4 40.7 - - + +
540B VAL* 3.9 6.5 - - + -
544B ILE* 3.4 53.8 - - + -
576B TYR 3.4 0.2 + - - -
577B LEU* 1.3 78.9 - - + +
579B ARG* 1.3 64.8 + - - +
580B GLU 3.3 2.2 - - - -
581B GLU* 3.2 31.5 + - + +
582B LEU* 2.8 26.4 + - + +
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Residues in contact with ARG 579 (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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297B GLN* 4.2 21.4 + - - +
572B SER* 2.8 24.5 + - - -
573B ASP* 4.6 4.0 - - - +
576B TYR* 2.9 63.0 + - + +
577B LEU 3.0 0.2 + - - -
578B TYR* 1.3 74.9 - - - +
580B GLU* 1.3 91.3 + - - +
582B LEU* 4.0 1.6 - - - +
583B ALA* 3.0 31.7 + - + +
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Residues in contact with GLU 580 (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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297B GLN* 5.7 1.2 + - - -
578B TYR 3.3 0.4 - - - -
579B ARG* 1.3 120.7 + - - +
581B GLU* 1.3 72.8 + - - +
583B ALA* 3.5 6.3 + - - +
584B GLN* 3.3 21.8 + - - +
587B ARG* 5.6 0.5 + - - -
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Residues in contact with GLU 581 (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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293B ARG* 2.6 34.5 + - - -
544B ILE* 6.0 1.8 - - + -
578B TYR* 3.2 31.5 + - + +
580B GLU* 1.3 86.0 + - - +
582B LEU* 1.3 57.8 + - + +
584B GLN* 3.6 5.8 + - - +
585B PHE* 2.7 46.9 + - + -
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Residues in contact with LEU 582 (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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540B VAL* 4.7 7.2 - - + -
544B ILE* 3.7 18.6 - - + -
547B ILE* 3.5 31.0 - - + -
565B LEU* 4.1 8.7 - - + -
567B TYR* 5.1 5.4 - - + -
576B TYR* 4.5 9.4 - - + -
577B LEU 4.1 13.2 - - - +
578B TYR* 2.8 26.4 + - + +
579B ARG* 4.0 2.7 - - - +
581B GLU* 1.3 75.4 - - - +
583B ALA* 1.3 66.1 + - - +
585B PHE* 3.0 21.6 + - + +
586B HIS* 3.1 11.6 + - - +
591B LEU* 4.0 9.3 - - + +
594B LEU* 3.7 30.5 - - + -
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Residues in contact with ALA 583 (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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576B TYR* 6.0 0.7 - - - +
579B ARG* 3.0 19.2 + - + +
580B GLU* 3.8 8.1 - - - +
581B GLU 3.4 0.2 - - - -
582B LEU* 1.3 74.6 - - - +
584B GLN* 1.3 65.2 + - - +
586B HIS* 3.2 18.0 + - - +
587B ARG* 3.3 31.0 + - - +
594B LEU* 4.2 10.0 - - + +
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Residues in contact with GLN 584 (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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580B GLU 3.3 10.6 + - - +
581B GLU* 3.7 9.6 - - - +
583B ALA* 1.3 74.4 - - - +
585B PHE* 1.3 54.5 + - + +
586B HIS 2.7 16.3 + - - -
587B ARG* 2.5 51.7 + - - +
588B ASP* 3.1 37.3 + - - +
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Residues in contact with PHE 585 (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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544B ILE* 5.2 8.7 - - + -
547B ILE* 3.6 41.5 - - + -
548B GLN* 4.2 29.2 - - + -
551B ALA* 4.3 9.2 - - + -
581B GLU* 2.7 39.0 + - + -
582B LEU* 3.0 19.6 + - + +
584B GLN* 1.3 79.0 - - + +
586B HIS* 1.3 52.3 + - - +
588B ASP* 4.1 10.1 - - - -
589B GLY 3.7 0.3 + - - -
590B ALA* 3.1 23.3 + - + -
591B LEU* 2.7 34.6 + - + -
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Residues in contact with HIS 586 (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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582B LEU 3.1 8.7 + - - +
583B ALA* 3.2 14.6 - - - +
584B GLN 2.7 5.5 + - - -
585B PHE* 1.3 72.9 - - - +
587B ARG* 1.3 62.6 + - + +
589B GLY* 2.8 21.8 + - - -
591B LEU* 3.0 31.2 - - + +
592B THR 3.2 18.6 + - - -
593B GLN* 4.3 4.4 - - - -
594B LEU* 4.7 21.7 - - + +
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Residues in contact with ARG 587 (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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580B GLU 5.7 0.2 + - - -
583B ALA* 3.3 27.5 + - - +
584B GLN* 2.5 59.2 + - - +
586B HIS* 1.3 75.3 - - + +
588B ASP* 1.3 62.1 + - - +
589B GLY* 3.1 1.8 + - - -
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Residues in contact with ASP 588 (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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551B ALA* 6.0 1.4 - - + +
554B ARG* 2.9 21.0 + - - -
584B GLN* 3.1 42.7 + - - +
585B PHE* 4.3 9.3 - - - +
587B ARG* 1.3 79.2 - - - +
589B GLY* 1.3 55.5 + - - +
590B ALA* 3.1 14.0 + - + +
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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