Contacts of the helix formed by residues 436 - 451 (chain A) in PDB entry 6A69
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 PRO 436 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A GLN* 4.1 22.2 + - + +
366A LEU* 4.2 20.0 - - + -
367A THR* 4.1 26.7 - - + +
370A ALA* 5.2 5.6 - - + -
434A GLY* 4.2 2.2 - - - -
435A LEU* 1.4 91.2 - - + +
437A LEU* 1.3 62.7 + - + +
438A ALA 3.0 0.2 - - - -
439A VAL* 3.0 24.2 + - + +
440A THR* 3.3 10.8 + - - -
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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
----------------------------------------------------------
174A ASP* 6.0 2.7 - - - +
177A LYS* 3.4 25.1 - - - +
434A GLY* 3.9 28.9 - - - +
435A LEU 3.1 0.6 - - - -
436A PRO* 1.3 81.9 - - + +
438A ALA* 1.3 55.6 + - - +
439A VAL 3.3 0.2 - - - -
440A THR* 3.6 10.0 - - - +
441A ILE* 2.8 37.6 + - + +
899A SER* 6.0 0.4 - - - -
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Residues in contact with ALA 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A LEU* 5.4 0.4 - - + -
434A GLY 4.6 2.6 + - - -
435A LEU* 3.1 18.5 + - + +
436A PRO 3.0 0.6 - - - -
437A LEU* 1.3 74.0 - - - +
439A VAL* 1.3 66.4 + - + +
441A ILE* 3.9 4.6 - - - +
442A SER* 3.0 28.9 + - - -
852A ILE* 5.1 12.1 - - + -
855A PHE* 3.8 35.4 - - + -
899A SER* 5.0 9.8 - - - -
903A ALA* 4.8 4.8 - - + +
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Residues in contact with VAL 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A LEU* 3.7 12.6 - - + -
363A GLN* 3.4 25.8 - - + +
366A LEU* 3.7 25.4 - - + -
436A PRO 3.0 9.9 + - - +
438A ALA* 1.3 74.8 - - - +
440A THR* 1.3 60.0 + - - +
442A SER* 3.0 6.8 + - - -
443A LEU* 2.9 47.0 + - + +
464A GLU* 5.8 4.3 - - + -
848A VAL* 5.3 3.6 - - + -
852A ILE* 3.7 28.5 - - + -
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Residues in contact with THR 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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177A LYS* 3.6 29.4 - - - +
181A PHE* 4.2 21.8 - - + -
363A GLN* 3.8 12.8 + - - -
436A PRO 3.3 9.1 + - - -
437A LEU* 3.3 11.4 + - + +
438A ALA 3.2 0.6 - - - -
439A VAL* 1.3 81.4 - - - +
441A ILE* 1.3 61.3 + - - +
443A LEU* 3.9 4.2 - - + +
444A ALA* 3.0 23.7 + - - +
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Residues in contact with ILE 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ASN* 3.8 28.5 - - - +
177A LYS* 3.7 35.4 - - + +
437A LEU* 2.8 27.7 + - + +
438A ALA* 3.9 4.5 - - - +
440A THR* 1.3 70.9 - - - +
442A SER* 1.3 66.6 + - - +
444A ALA* 3.1 14.5 + - - +
445A TYR* 3.1 41.5 + - + +
899A SER* 4.6 26.7 - - - +
900A LEU* 4.6 7.6 - - + -
903A ALA* 4.8 2.9 - - + -
904A THR* 5.2 0.4 - - - +
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Residues in contact with SER 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A ALA 3.0 19.3 + - - -
439A VAL* 3.0 9.4 + - - -
441A ILE* 1.3 79.1 - - - +
443A LEU* 1.3 60.1 + - - +
445A TYR* 4.1 3.7 - - - +
446A SER* 3.0 31.1 + - - -
848A VAL* 4.2 17.1 - - - +
851A SER* 4.3 10.5 - - - -
852A ILE* 4.8 4.1 - - - +
903A ALA* 3.6 31.1 - - - +
904A THR* 5.7 0.4 - - - +
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Residues in contact with LEU 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A PHE* 5.0 4.7 - - + -
439A VAL* 2.9 29.1 + - + +
440A THR* 3.9 4.7 - - + +
442A SER* 1.3 84.0 + - - +
444A ALA* 1.3 56.2 + - - +
446A SER* 3.5 5.5 + - - -
447A VAL* 2.9 40.4 + - + +
460A LEU* 3.7 46.0 - - + +
463A CYS* 3.8 33.4 - - + -
464A GLU* 4.7 13.5 - - + -
848A VAL* 4.7 8.1 - - + -
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Residues in contact with ALA 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LYS* 4.8 12.6 - - + +
180A GLN* 4.7 16.0 - - + +
181A PHE* 3.6 31.7 - - + -
440A THR 3.0 14.3 + - - +
441A ILE* 3.1 11.0 + - + +
443A LEU* 1.3 73.8 - - - +
445A TYR* 1.3 70.2 + - + +
447A VAL* 3.0 13.9 + - - +
448A LYS* 3.1 13.7 + - - +
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Residues in contact with TYR 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ASN* 5.0 2.3 + - - -
176A SER* 4.7 11.1 - - - -
177A LYS* 5.3 2.5 + - - -
180A GLN* 3.1 42.8 + - + -
441A ILE* 3.1 40.8 + - + +
442A SER* 4.2 2.9 - - - +
444A ALA* 1.3 80.6 - - + +
446A SER* 1.3 62.6 + - - +
448A LYS* 3.5 6.7 + - + +
449A LYS* 3.1 31.2 + - - +
900A LEU* 3.9 28.1 - - + +
904A THR* 3.2 39.3 - - + +
1008A ILE* 6.1 6.3 - - + -
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Residues in contact with SER 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A SER 3.0 20.2 + - - -
443A LEU* 3.5 8.3 - - - -
445A TYR* 1.3 74.7 - - - +
447A VAL* 1.3 59.4 + - - +
449A LYS* 3.4 1.4 + - - +
450A MET* 2.8 43.6 + - - +
463A CYS* 4.4 1.8 - - - -
844A TRP* 3.2 35.1 - - - -
848A VAL* 4.3 13.1 - - - +
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Residues in contact with VAL 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A GLN 5.8 0.7 - - - +
181A PHE* 5.0 4.9 - - + -
184A LEU* 3.7 40.4 - - + -
443A LEU* 2.9 38.7 + - + +
444A ALA* 3.0 10.5 + - - +
446A SER* 1.3 72.3 - - - +
448A LYS* 1.3 65.8 + - + +
450A MET* 3.1 19.0 + - - +
451A MET* 3.1 16.4 + - + +
457A VAL* 4.5 20.2 - - + +
460A LEU* 4.1 14.1 - - + -
463A CYS* 5.6 2.0 - - - -
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Residues in contact with LYS 448 (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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179A LYS* 6.2 1.8 - - - +
180A GLN* 3.8 37.9 - - + +
183A GLY* 5.6 11.9 - - - -
184A LEU* 6.3 0.7 - - - +
444A ALA 3.1 9.2 + - - +
445A TYR* 4.0 8.1 - - + +
446A SER 3.4 0.2 - - - -
447A VAL* 1.3 82.0 - - + +
449A LYS* 1.3 63.6 + - + +
451A MET* 3.7 24.8 - - + +
452A LYS* 4.4 4.0 + - - +
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Residues in contact with LYS 449 (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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445A TYR* 3.1 22.1 + - - +
446A SER* 5.7 0.2 - - - +
448A LYS* 1.3 78.9 - - + +
450A MET* 1.3 65.2 + - - +
452A LYS* 3.7 25.9 + - - +
453A ASP* 4.1 9.9 + - - +
844A TRP* 4.3 25.6 - - + -
904A THR* 4.3 22.5 - - - +
905A GLU 4.7 0.6 - - - -
906A PRO* 3.7 34.1 - - - +
1005A ASN 5.5 2.4 + - - -
1006A ASN* 5.0 1.6 + - - +
1008A ILE* 5.6 3.0 - - - +
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Residues in contact with MET 450 (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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446A SER* 2.8 28.4 + - - +
447A VAL* 3.1 8.0 + - + +
449A LYS* 1.3 77.0 - - - +
451A MET* 1.3 55.6 + - - +
453A ASP* 2.7 36.2 + - + +
455A ASN* 3.4 29.1 + - + +
457A VAL* 3.6 30.3 - - + -
463A CYS* 3.7 31.6 - - + +
828A ILE* 6.4 0.4 - - + -
841A ALA* 5.4 4.9 - - + +
844A TRP* 3.7 47.3 - - + -
845A GLY 5.4 0.4 - - - +
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Residues in contact with MET 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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183A GLY 4.4 4.3 - - - +
184A LEU* 3.7 48.0 - - + +
187A ARG* 3.5 43.9 + - + +
188A ILE 5.8 0.2 - - - +
447A VAL* 3.1 14.3 + - + +
448A LYS* 3.7 18.6 - - + +
449A LYS 3.3 0.6 - - - -
450A MET* 1.3 78.2 - - - +
452A LYS* 1.3 58.6 + - - +
453A ASP 3.6 0.2 + - - -
454A ASN* 4.0 7.6 + - - -
455A ASN 3.7 12.6 + - - -
456A LEU* 5.2 16.8 - - + +
831A THR* 6.0 1.0 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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