Contacts of the helix formed by residues 459 - 465 (chain C) in PDB entry 2QLF
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 ILE 459 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441C LEU* 5.0 3.8 - - + -
446C GLU 5.3 0.2 - - - +
448C ASN* 2.9 35.4 + - - +
449C VAL 4.0 5.2 - - - +
450C ILE* 3.0 36.3 - - + -
457C THR 3.6 0.2 + - - -
458C PRO* 1.3 73.0 - - - +
460C LYS* 1.3 63.4 + - - +
462C LEU* 3.0 5.5 + - - +
463C THR* 3.0 33.4 + - + -
483C ILE* 3.9 27.1 - - + -
485C ALA* 6.5 0.2 - - + -
487C ARG* 5.7 2.2 - - + +
521D PHE* 4.6 4.3 - - + -
523D TYR* 3.8 36.3 - - + +
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Residues in contact with LYS 460 (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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190A GLU* 3.3 33.9 + - - -
227B PRO 4.2 13.8 + - - -
228B GLY* 5.2 1.0 - - - -
229B TYR* 4.6 2.2 - - - -
448C ASN 4.7 0.4 + - - -
458C PRO* 3.2 6.2 - - + +
459C ILE* 1.3 79.5 - - - +
461C ASP* 1.3 62.8 + - - +
463C THR* 3.2 7.5 + - - +
464C ALA* 2.8 39.2 + - + +
516D GLU* 4.5 14.4 - - - -
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Residues in contact with ASP 461 (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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420C GLN* 3.6 15.6 - - - +
458C PRO* 3.1 38.9 + - + +
459C ILE 3.3 0.6 - - - -
460C LYS* 1.3 80.5 - - - +
462C LEU* 1.3 64.4 + - - +
464C ALA* 3.8 11.5 + - - +
465C HIS* 3.3 21.5 + - - -
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Residues in contact with LEU 462 (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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419C MET* 4.0 27.6 - - + +
420C GLN* 2.9 33.7 - - - +
423C LEU* 3.6 32.7 - - + +
441C LEU* 4.0 21.1 - - + -
450C ILE* 3.4 32.5 - - + -
457C THR* 4.4 6.7 - - + -
458C PRO 3.4 4.9 + - - +
459C ILE* 3.0 9.9 + - + +
461C ASP* 1.3 79.6 - - - +
463C THR* 1.3 62.5 + - + +
465C HIS* 3.0 24.8 - - - +
466C PHE* 4.0 2.4 - - - -
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Residues in contact with THR 463 (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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441C LEU* 6.0 0.7 - - + -
459C ILE* 3.0 22.5 + - + +
460C LYS* 3.2 10.0 + - - +
462C LEU* 1.3 74.3 - - + +
464C ALA* 1.3 64.3 + - - +
465C HIS 2.8 7.1 + - - -
466C PHE* 2.8 17.8 + - - -
481C PHE* 3.4 36.8 - - + -
519D PHE* 3.7 13.4 - - - -
521D PHE* 3.3 40.5 - - + -
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Residues in contact with ALA 464 (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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460C LYS* 2.8 30.2 + - + +
461C ASP* 4.1 9.9 - - - +
462C LEU 3.5 0.6 - - - -
463C THR* 1.3 72.2 + - - +
465C HIS* 1.3 62.5 + - - +
466C PHE 2.9 2.3 + - - -
467C ARG* 3.0 36.3 + - - +
470C ARG* 3.6 29.9 - - - +
519D PHE* 5.3 0.4 - - - -
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Residues in contact with HIS 465 (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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420C GLN* 3.2 31.7 + - + -
423C LEU* 4.1 4.5 - - + -
424C LYS* 3.6 45.2 - - + +
427C SER* 3.1 29.3 + - - +
461C ASP 3.3 10.8 + - - -
462C LEU* 3.0 23.8 - - - -
463C THR 2.8 1.4 + - - -
464C ALA* 1.3 76.3 - - - +
466C PHE* 1.3 72.5 + - + +
467C ARG 3.5 0.2 - - - -
470C ARG* 3.7 17.2 - - - +
471C CYS* 3.7 6.2 - - - +
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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