Contacts of the helix formed by residues 450 - 461 (chain A) in PDB entry 4XZC
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 VAL 450 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A ASP* 4.5 0.7 - - - +
176A ARG* 3.5 28.0 - - - +
435A PHE* 4.8 0.7 - - + -
438A GLN* 3.5 26.2 - - - +
444A LEU* 4.0 24.9 - - + -
447A MET* 3.8 12.3 - - + -
449A ILE* 1.3 75.6 - - - +
451A ALA* 1.3 65.1 + - - +
452A SER* 3.9 9.2 - - - +
453A GLU* 3.0 43.8 + - + +
454A HIS* 3.1 12.5 + - - +
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Residues in contact with ALA 451 (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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63A TYR* 3.1 28.0 - - + +
67A MET* 5.1 3.8 - - + -
438A GLN* 3.3 13.0 - - - +
449A ILE* 3.9 8.1 + - - +
450A VAL* 1.3 69.9 - - - +
452A SER* 1.3 57.2 + - - +
454A HIS* 3.3 8.4 + - - +
455A LEU* 3.0 34.0 + - + +
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Residues in contact with SER 452 (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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63A TYR* 4.4 0.8 + - - -
169A MET* 3.2 19.2 - - - +
431A ILE* 3.3 23.6 - - - +
434A LEU* 4.5 7.9 - - - -
435A PHE* 3.2 28.0 - - - -
438A GLN* 2.7 24.1 + - - -
450A VAL* 3.9 1.7 - - - +
451A ALA* 1.3 78.1 - - - +
453A GLU* 1.3 57.1 + - - +
455A LEU* 3.8 9.8 - - - +
456A LEU 3.1 21.5 + - - -
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Residues in contact with GLU 453 (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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169A MET* 3.8 22.3 - - + +
172A ASP* 2.7 38.0 - - - +
173A MET* 3.7 31.4 - - + +
176A ARG* 3.4 12.3 + - - -
435A PHE* 4.0 16.6 - - + -
444A LEU* 5.6 0.3 - - - +
450A VAL* 3.0 38.3 + - + +
452A SER* 1.3 76.3 + - - +
454A HIS* 1.3 59.6 + - - +
456A LEU* 3.4 0.5 + - - +
457A HIS* 2.9 30.6 + - - +
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Residues in contact with HIS 454 (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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301A GLN 4.9 11.4 + - - -
303A ALA 4.7 11.5 + - - -
374A LEU* 5.7 7.0 - - + -
412A LYS* 4.5 12.0 - - - -
449A ILE* 4.7 13.9 - - + -
450A VAL 3.1 11.4 + - - +
451A ALA* 3.6 11.4 + - - +
453A GLU* 1.3 78.7 - - - +
455A LEU* 1.3 61.4 + - - +
457A HIS* 3.6 12.1 + + + +
458A GLN* 3.3 57.5 + - + +
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Residues in contact with LEU 455 (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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67A MET* 4.6 12.3 - - + -
411A SER* 3.9 29.4 - - - +
412A LYS* 4.6 6.3 - - + -
414A LEU* 4.2 28.5 - - + -
415A LEU* 4.0 15.3 - - + +
431A ILE* 4.4 6.2 - - + +
434A LEU* 4.6 16.6 - - + -
451A ALA* 3.0 25.1 + - + +
452A SER* 3.8 9.4 - - - +
453A GLU 3.2 0.4 - - - -
454A HIS* 1.3 77.0 - - + +
456A LEU* 1.3 59.8 + - - +
458A GLN* 2.9 34.3 + - - +
459A SER* 3.0 12.6 + - - -
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Residues in contact with LEU 456 (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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156A TYR* 4.3 26.5 - - + +
166A VAL* 4.4 19.7 - - + -
169A MET* 3.8 28.0 - - + -
170A LEU* 5.5 0.4 - - + -
173A MET* 3.5 28.3 - - + -
428A ALA* 5.5 4.0 - - + -
431A ILE* 3.8 26.3 - - + +
452A SER 3.1 15.3 + - - +
453A GLU 3.7 2.5 - - - +
455A LEU* 1.3 74.1 - - - +
457A HIS* 1.3 67.1 + - - +
459A SER* 3.1 1.5 + - - -
460A LEU* 2.9 32.1 + - + +
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Residues in contact with HIS 457 (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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173A MET* 4.7 7.6 - - - -
177A ARG* 5.7 4.0 + - - -
301A GLN* 3.2 42.7 + - + +
453A GLU 2.9 18.5 + - - +
454A HIS* 3.7 14.2 + + + +
456A LEU* 1.3 76.6 - - - +
458A GLN* 1.3 65.8 + - - +
460A LEU* 3.3 13.1 + - + +
461A VAL* 3.0 46.1 + - + +
477A ALA* 3.4 21.6 + - + +
478A THR* 4.7 16.9 + - + +
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Residues in contact with GLN 458 (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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412A LYS* 3.2 30.9 - - - +
415A LEU* 3.9 12.0 - - + +
454A HIS* 3.3 38.6 + - + +
455A LEU* 2.9 22.2 + - - +
457A HIS* 1.3 80.5 - - - +
459A SER* 1.3 66.6 + - - +
461A VAL* 3.5 7.1 + - - +
462A GLY 3.4 3.8 + - - -
463A LYS* 3.0 64.7 + - + +
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Residues in contact with SER 459 (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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156A TYR* 2.7 30.2 + - - -
415A LEU* 4.3 3.5 - - - +
419A ILE* 3.2 18.7 - - - +
427A CYS* 4.0 15.8 - - - -
431A ILE* 4.5 2.0 - - - -
455A LEU 3.0 11.2 + - - -
456A LEU* 3.5 12.8 - - - -
458A GLN* 1.3 77.6 - - - +
460A LEU* 1.3 56.7 + - - +
462A GLY* 2.9 12.0 + - - -
463A LYS 4.2 6.4 + - - -
464A ARG* 2.7 26.9 + - - +
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Residues in contact with LEU 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A VAL* 4.1 11.9 - - - +
153A GLN* 4.9 8.8 + - - +
156A TYR* 3.4 42.6 - - + -
170A LEU* 3.9 21.3 - - + -
173A MET* 4.6 2.9 - - + -
456A LEU* 2.9 29.5 + - + +
457A HIS* 3.4 15.9 - - + +
459A SER* 1.3 76.0 - - - +
461A VAL* 1.3 57.4 + - - +
462A GLY* 3.1 5.2 + - - -
477A ALA* 3.4 34.3 - - + +
480A VAL* 3.5 19.2 - - + +
482A ILE* 4.9 3.1 - - + -
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Residues in contact with VAL 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A LEU* 4.6 0.2 - - - +
150A HIS* 3.0 23.6 + - - -
152A VAL* 4.1 18.4 - - + -
301A GLN* 5.3 3.4 - - - +
304A GLN* 5.6 4.5 - - - +
457A HIS* 3.0 28.6 + - + +
458A GLN* 3.9 8.7 - - - +
459A SER 3.3 0.4 - - - -
460A LEU* 1.3 75.7 - - - +
462A GLY* 1.3 56.3 + - - +
463A LYS* 4.8 3.8 - - + +
470A ALA* 4.0 28.0 - - + +
473A VAL* 3.7 18.2 - - + +
477A ALA* 3.7 24.0 - - + +
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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