Contacts of the helix formed by residues 470 - 483 (chain A) in PDB entry 2QLU
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 SER 470 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A HIS* 6.0 0.4 - - - -
386A MET* 3.7 6.1 - - - -
468A ARG 4.1 0.4 + - - -
469A LEU* 1.3 77.1 - - - +
471A ALA* 1.4 64.1 + - - +
472A GLY* 3.6 3.6 + - - -
473A CYS* 3.1 30.6 + - - +
474A VAL* 3.1 13.0 + - - +
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Residues in contact with ALA 471 (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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295A SER* 3.8 9.2 - - - +
298A LEU* 3.7 15.0 - - + -
299A SER* 3.0 38.4 - - - +
302A HIS* 4.2 8.0 + - + +
386A MET* 3.6 25.9 - - + -
470A SER* 1.4 73.1 - - - +
472A GLY* 1.3 56.2 + - - +
474A VAL* 3.3 5.0 + - - +
475A GLU* 2.9 27.5 + - - +
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Residues in contact with GLY 472 (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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299A SER* 3.5 21.8 + - - -
470A SER* 3.2 5.4 + - - -
471A ALA* 1.3 79.2 - - - +
473A CYS* 1.3 55.8 + - - +
475A GLU* 3.5 8.0 + - - +
476A GLU* 3.2 27.6 + - - +
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Residues in contact with CYS 473 (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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469A LEU* 4.1 22.9 - - - -
470A SER* 3.1 25.6 + - - +
472A GLY* 1.3 77.7 - - - +
474A VAL* 1.3 56.9 + - - +
476A GLU* 3.9 8.9 - - - +
477A ARG* 2.9 46.4 + - - +
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Residues in contact with VAL 474 (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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295A SER* 3.9 17.3 - - - +
386A MET* 3.9 7.0 - - + -
389A MET* 4.8 3.6 - - - -
393A LEU* 4.2 23.3 - - + -
456A THR* 4.1 7.0 - - + -
460A CYS* 3.6 28.5 - - - -
469A LEU* 3.9 15.9 - - + -
470A SER 3.1 13.0 + - - +
471A ALA* 3.3 9.6 + - - +
473A CYS* 1.3 72.7 - - - +
475A GLU* 1.3 64.3 + - - +
477A ARG* 3.4 5.5 + - - +
478A VAL* 2.9 39.9 + - + +
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Residues in contact with GLU 475 (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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292A GLU* 3.7 31.2 - - + +
295A SER* 3.3 14.5 + - - +
296A ARG* 3.5 43.7 + - + +
299A SER* 4.4 10.0 + - - -
471A ALA 2.9 19.0 + - - +
472A GLY* 3.8 7.1 - - - +
473A CYS 3.5 0.2 - - - -
474A VAL* 1.3 71.1 - - - +
476A GLU* 1.3 57.9 + - - +
478A VAL* 3.3 3.1 + - - +
479A SER* 3.1 27.9 + - - -
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Residues in contact with GLU 476 (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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472A GLY 3.2 15.1 + - - +
473A CYS* 3.9 7.0 - - - +
475A GLU* 1.3 75.9 - - - +
477A ARG* 1.3 69.6 + - - +
478A VAL 3.3 0.2 + - - -
479A SER* 3.3 9.1 + - - -
480A LEU* 3.2 38.1 + - + +
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Residues in contact with ARG 477 (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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455A VAL* 4.6 5.3 - - - +
456A THR* 3.3 37.4 + - + +
459A GLU* 2.5 33.5 + - - -
469A LEU* 3.7 26.0 - - - +
473A CYS* 2.9 35.3 + - - +
474A VAL* 3.6 6.5 - - - +
476A GLU* 1.3 74.4 - - - +
478A VAL* 1.3 63.2 + - + +
480A LEU* 3.1 12.6 + - + +
481A ILE* 3.0 32.2 + - + +
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Residues in contact with VAL 478 (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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288A CYS* 3.6 34.4 - - + +
291A ALA* 3.9 16.8 - - + +
292A GLU* 3.6 19.7 - - + +
393A LEU* 5.2 0.9 - - + -
453A LEU* 3.5 28.9 - - + -
456A THR* 5.7 1.1 - - + -
474A VAL* 2.9 36.6 + - + +
475A GLU 3.3 3.6 + - - +
477A ARG* 1.3 71.0 - - + +
479A SER* 1.3 64.7 + - - +
481A ILE* 3.1 8.1 + - - +
482A ARG* 3.0 23.9 + - - +
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Residues in contact with SER 479 (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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292A GLU* 3.4 25.0 + - - -
475A GLU* 3.1 13.5 + - - -
476A GLU* 3.5 13.7 - - - -
478A VAL* 1.3 77.4 - - - +
480A LEU* 1.3 57.9 + - - -
482A ARG* 3.6 13.4 + - - +
483A ARG* 3.4 29.3 + - - +
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Residues in contact with LEU 480 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452A GLN* 5.1 1.2 - - - +
476A GLU* 3.2 37.4 + - + +
477A ARG* 3.1 13.8 + - + +
479A SER* 1.3 77.6 - - - +
481A ILE* 1.3 63.3 + - + +
483A ARG* 3.8 19.9 - - + +
484A SER* 3.6 16.3 + - - -
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Residues in contact with ILE 481 (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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284A TRP* 3.7 21.7 - - + -
288A CYS* 5.5 0.7 - - - -
449A GLY* 3.6 26.9 - - - +
452A GLN* 3.7 40.4 - - + +
453A LEU* 3.9 28.7 - - + +
456A THR* 4.4 8.1 - - - +
477A ARG* 3.0 28.4 + - + +
478A VAL* 3.1 4.2 + - - +
480A LEU* 1.3 75.8 - - + +
482A ARG* 1.3 68.8 + - - +
483A ARG 3.0 1.6 - - - -
484A SER* 3.1 22.5 + - - +
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Residues in contact with ARG 482 (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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284A TRP* 4.4 10.8 + - - +
285A ASN* 4.7 14.6 + - - +
288A CYS* 3.0 56.9 + - + -
289A HIS* 4.3 10.3 + - - +
292A GLU* 3.3 32.1 + - - +
478A VAL 3.0 10.5 + - - +
479A SER* 3.6 17.7 + - - +
481A ILE* 1.3 79.2 - - - +
483A ARG* 1.3 60.2 + - + +
484A SER 3.6 8.0 - - - +
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Residues in contact with ARG 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A SER* 3.4 20.6 + - - +
480A LEU* 4.0 19.9 - - + +
482A ARG* 1.3 80.4 - - + +
484A SER* 1.3 61.8 + - - +
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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