Contacts of the helix formed by residues 430 - 440 (chain A) in PDB entry 3QXY
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 430 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424A LEU* 6.5 0.7 - - - -
429A THR* 1.3 80.1 + - - +
431A LEU* 1.3 65.1 + - - +
432A LYS* 3.7 17.4 - - + +
433A THR* 2.8 35.5 + - - -
434A ASP 3.8 2.1 + - - -
462A LYS* 3.3 12.4 + - - +
466A HIS* 5.7 3.6 - - + +
476A EDO 3.9 13.4 + - - +
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Residues in contact with LEU 431 (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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424A LEU* 5.9 0.8 - - - +
430A ASP* 1.3 75.1 - - - +
432A LYS* 1.3 60.6 + - + +
434A ASP* 3.1 3.3 + - + -
435A GLN* 2.8 32.3 + - + +
459A TYR* 3.8 33.0 - - + -
462A LYS* 3.8 30.2 - - + +
463A MET* 3.8 24.2 - - + -
466A HIS* 3.6 51.7 + - + +
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Residues in contact with LYS 432 (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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430A ASP* 3.3 17.0 + - - +
431A LEU* 1.3 79.7 - - + +
433A THR* 1.3 63.1 + - - +
435A GLN* 3.5 7.8 + - + +
436A GLY* 3.0 19.9 + - - -
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Residues in contact with THR 433 (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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429A THR* 3.9 26.5 - - + +
430A ASP* 2.8 27.4 + - - -
431A LEU 3.2 0.2 - - - -
432A LYS* 1.3 75.5 - - - +
434A ASP* 1.3 65.1 + - - +
436A GLY* 3.2 2.8 + - - -
437A LEU* 3.1 31.1 + - + +
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Residues in contact with ASP 434 (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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429A THR* 4.1 5.7 + - - -
430A ASP 3.8 0.8 + - - -
431A LEU 3.1 7.9 + - - +
433A THR* 1.3 79.1 - - - +
435A GLN* 1.3 65.4 + - - +
437A LEU* 3.2 12.4 + - - +
438A LEU* 3.0 23.4 + - - +
455A LEU* 3.3 24.1 - - + +
458A ARG* 3.0 40.6 + - - +
459A TYR* 4.3 14.8 + - + -
462A LYS* 2.7 32.7 + - + +
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Residues in contact with GLN 435 (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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431A LEU* 2.8 25.4 + - + +
432A LYS* 3.8 9.0 - - + +
434A ASP* 1.3 72.4 - - - +
436A GLY* 1.3 58.5 + - - +
438A LEU* 3.3 5.3 + - - +
439A SER* 2.8 64.4 + - - +
459A TYR* 2.7 41.3 + - + -
463A MET* 4.2 8.1 - - - +
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Residues in contact with GLY 436 (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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432A LYS 3.0 14.6 + - - -
433A THR 3.2 4.7 + - - -
434A ASP 3.2 0.2 - - - -
435A GLN* 1.3 78.9 - - - +
437A LEU* 1.3 61.2 + - - +
438A LEU 3.3 0.3 + - - -
439A SER* 4.3 4.3 - - - -
440A ASN* 3.6 22.9 + - - +
443A VAL* 5.0 1.4 - - - +
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Residues in contact with LEU 437 (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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433A THR* 3.1 19.9 + - + +
434A ASP* 3.2 27.1 + - - +
436A GLY* 1.3 75.9 - - - +
438A LEU* 1.3 58.6 + - - +
440A ASN 3.6 4.8 - - - +
443A VAL* 3.9 23.1 - - + -
444A TYR* 3.3 29.6 + - - +
447A LEU* 4.6 21.1 - - + -
455A LEU* 3.8 18.8 - - + -
458A ARG* 4.4 6.7 - - - +
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Residues in contact with LEU 438 (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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303A TYR* 4.7 11.4 - - + -
434A ASP 3.0 16.5 + - - +
435A GLN* 3.9 8.3 - - - +
437A LEU* 1.3 78.6 - - - +
439A SER* 1.3 65.9 + - - +
440A ASN 3.3 5.0 + - - -
441A LYS* 4.1 19.4 + - + +
444A TYR* 3.6 33.1 - - + +
455A LEU* 4.4 6.5 - - + -
456A GLN* 3.8 15.3 - - - +
459A TYR* 3.5 46.2 - - + +
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Residues in contact with SER 439 (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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435A GLN* 2.8 44.5 + - - +
436A GLY* 3.6 4.7 + - - -
438A LEU* 1.3 77.2 - - - +
440A ASN* 1.3 59.5 + - - +
441A LYS* 3.4 13.6 + - - +
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Residues in contact with ASN 440 (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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436A GLY 3.6 11.3 + - - +
437A LEU 3.6 4.7 - - - +
438A LEU 3.3 1.8 - - - -
439A SER* 1.3 76.7 - - - +
441A LYS* 1.3 57.1 + - - +
442A GLU* 3.2 14.6 + - - +
443A VAL* 3.1 28.7 + - + +
444A TYR 2.9 22.9 + - - -
481A EDO 3.3 41.0 + - - -
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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