Contacts of the helix formed by residues 438 - 449 (chain A) in PDB entry 2ZL6
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 438 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A LEU* 4.3 3.4 - - + -
241A LEU* 3.9 28.9 - - + -
242A SER 3.1 14.8 - - - +
250A ILE* 4.7 4.3 - - + -
421A PHE* 3.8 36.1 - - + -
435A CYS* 4.6 3.6 - - - -
437A LEU* 1.3 86.6 - - + +
439A GLN* 1.3 65.9 + - - +
440A GLU 4.3 0.9 - - - +
441A TYR* 3.0 49.0 + - + +
442A ILE* 3.4 5.5 + - - +
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Residues in contact with GLN 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A SER* 2.9 11.2 + - - +
243A ASN 3.8 15.3 - - - +
244A SER* 3.3 25.7 - - - +
268A GLY* 5.1 1.4 + - - -
280A THR* 5.2 0.5 - - - +
281A PRO* 3.0 29.0 + - - +
282A VAL 3.0 20.2 + - - +
283A SER 3.8 2.6 + - - +
284A LEU* 3.8 29.2 - - + +
287A VAL* 3.6 16.2 - - - +
437A LEU 3.5 1.4 + - - -
438A PRO* 1.3 72.0 - - - +
440A GLU* 1.3 63.9 + - - +
442A ILE* 2.9 36.6 + - - +
443A SER* 3.1 12.9 + - - +
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Residues in contact with GLU 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A PRO* 3.8 3.9 - - + +
236A LEU* 4.9 4.7 - - + -
241A LEU* 3.3 30.0 - - + +
242A SER* 2.8 30.9 + - - -
284A LEU* 5.1 2.4 - - - +
438A PRO 3.2 0.6 - - - -
439A GLN* 1.3 77.1 + - - +
441A TYR* 1.3 58.6 + - - +
443A SER* 4.0 7.5 - - - -
444A HIS* 3.0 28.2 + - - +
282B VAL 4.9 1.3 - - - +
283B SER* 2.6 37.9 + - - -
284B LEU* 4.0 3.3 + - - +
443B SER* 4.2 26.9 - - - +
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Residues in contact with TYR 441 (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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1A MG 2.6 25.3 - - - -
233A LEU* 4.1 34.3 - - + -
234A PRO* 3.6 24.7 - - + -
238A LEU* 3.6 7.1 - - + +
241A LEU* 3.6 26.0 - - + -
421A PHE* 5.3 3.1 - + - -
437A LEU* 4.2 22.4 - - + -
438A PRO* 3.0 36.1 + - + +
440A GLU* 1.3 75.9 - - - +
442A ILE* 1.3 54.3 + - - +
444A HIS* 3.3 1.0 + - - +
445A LEU* 2.8 44.7 + - + +
481A LEU* 5.3 4.0 - - + -
501A PHE* 3.3 29.2 + + - +
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Residues in contact with ILE 442 (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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244A SER* 4.5 2.2 - - - -
268A GLY* 3.8 25.6 - - - -
269A ARG 4.1 0.7 - - - +
270A CYS* 3.5 26.4 - - + +
276A LEU* 3.6 27.6 - - + -
280A THR* 3.8 3.6 - - + -
281A PRO 3.7 17.7 - - - +
282A VAL* 4.5 2.0 - - - +
437A LEU* 3.8 20.9 - - + -
438A PRO 3.5 13.7 - - - +
439A GLN* 2.9 26.5 + - - +
441A TYR* 1.3 73.2 - - - +
443A SER* 1.3 61.3 + - - +
445A LEU* 3.3 1.7 + - - +
446A ALA* 2.9 31.9 + - - +
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Residues in contact with SER 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A VAL* 2.7 29.0 + - - -
283A SER* 4.8 0.2 - - - -
439A GLN* 3.1 12.2 + - - +
440A GLU* 4.2 7.4 - - - -
442A ILE* 1.3 77.9 - - - +
444A HIS* 1.3 63.9 + - - +
446A ALA* 3.8 5.1 - - - -
447A SER* 2.9 26.5 + - - -
236B LEU* 3.8 13.5 - - - +
440B GLU* 4.0 24.7 - - - +
443B SER* 5.8 2.5 - - - -
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Residues in contact with HIS 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A THR* 2.9 49.7 + - - -
233A LEU 3.9 7.9 + - - -
234A PRO* 3.6 30.3 - - + +
440A GLU 3.0 20.1 + - - +
441A TYR 3.5 4.7 - - - +
443A SER* 1.3 78.2 - - - +
445A LEU* 1.3 60.8 + - - +
447A SER* 3.3 5.4 + - - -
448A GLU* 2.8 44.7 + - + +
444B HIS* 5.4 15.4 - + - -
447B SER* 4.5 10.6 + - - -
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Residues in contact with LEU 445 (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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231A PHE* 3.7 22.2 - - + -
232A THR 4.3 0.7 - - - +
233A LEU* 4.1 16.2 - - + -
270A CYS* 4.0 15.0 - - - +
271A THR 3.9 18.2 - - - +
272A LEU* 3.6 29.9 - - + +
273A ASP 4.3 0.5 - - - -
274A GLY* 3.3 10.5 + - - -
437A LEU* 4.1 25.6 - - + -
441A TYR* 2.8 28.8 + - + +
444A HIS* 1.3 75.0 - - - +
446A ALA* 1.3 58.8 + - - +
448A GLU* 3.9 14.3 - - - +
449A GLN 3.1 24.8 + - - -
450A ALA 4.8 0.3 + - - -
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Residues in contact with ALA 446 (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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270A CYS* 4.4 0.4 - - - -
274A GLY* 3.9 19.7 - - - +
276A LEU* 4.4 17.5 - - + -
282A VAL* 4.6 7.2 - - + -
442A ILE 2.9 19.3 + - - +
443A SER* 3.9 5.4 - - - +
445A LEU* 1.3 76.6 - - - +
447A SER* 1.3 57.9 + - - +
449A GLN* 2.9 28.9 + - - +
236B LEU* 3.8 17.2 - - + +
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Residues in contact with SER 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A SER 2.9 17.7 + - - -
444A HIS* 3.6 5.4 - - - -
446A ALA* 1.3 77.4 - - - +
448A GLU* 1.3 64.1 + - - +
449A GLN* 3.4 5.7 + - - +
233B LEU 4.5 0.3 + - - -
234B PRO* 3.5 8.4 - - - +
235B ASN* 2.8 55.3 + - - +
236B LEU* 3.7 10.9 - - - +
444B HIS* 4.4 11.1 - - - -
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Residues in contact with GLU 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A PHE* 3.5 22.7 - - - -
232A THR* 2.7 53.5 + - - +
272A LEU 5.9 0.2 - - - +
444A HIS* 2.8 28.4 + - + +
445A LEU* 3.3 11.1 + - - +
447A SER* 1.3 78.5 - - - +
449A GLN* 1.3 69.3 + - - +
450A ALA* 3.1 14.0 + - - +
451A PRO* 5.0 2.3 - - + +
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Residues in contact with GLN 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ASP 3.3 20.2 - - - +
274A GLY* 5.3 2.9 - - - +
445A LEU 3.1 7.7 + - - -
446A ALA* 2.9 25.9 + - - +
447A SER 3.7 1.7 + - - +
448A GLU* 1.3 77.3 - - - +
450A ALA* 1.3 66.5 + - - +
451A PRO* 3.2 7.6 - - - +
235B ASN* 3.6 39.0 + - - +
236B LEU* 5.3 0.4 - - - +
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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