Contacts of the helix formed by residues 435 - 455 (chain A) in PDB entry 3E7G
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 435 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A MET* 4.4 0.2 - - - -
375A GLY* 4.7 1.6 - - - +
423A LEU* 3.7 34.2 - - + +
434A MET* 1.3 79.5 - - - +
436A HIS* 1.3 64.7 + - - +
437A HIS* 2.8 35.0 + - - +
438A SER* 2.6 29.8 + - - -
439A ALA* 3.1 18.0 + - - +
406B LEU* 4.2 1.6 - - - +
407B ALA* 3.8 29.9 + - + +
409B LEU* 4.4 5.6 - - + -
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Residues in contact with HIS 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ILE* 5.3 0.2 - - - +
374A MET* 3.9 17.5 - - - +
375A GLY 5.3 0.4 - - - +
376A THR* 3.5 28.6 + - + +
419A ASN* 5.9 0.4 - - + -
423A LEU* 5.8 1.0 - - + +
434A MET 3.9 0.4 + - - -
435A ASP* 1.3 70.8 - - - +
437A HIS* 1.3 83.2 + + - +
439A ALA* 3.8 1.5 - - - +
440A ALA* 3.0 28.1 + - - +
466A PRO* 3.8 26.6 - - + +
468A MET* 4.0 26.3 - - + +
469A SER* 4.1 2.4 - - - -
473A THR* 4.3 6.9 - - + +
409B LEU* 3.7 22.7 - - + +
412B ASP* 2.9 28.8 + - - -
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Residues in contact with HIS 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A ASP* 2.8 15.4 + - - +
436A HIS* 1.3 95.6 + + - +
438A SER* 1.3 61.5 + - - +
440A ALA* 3.2 6.5 + - - +
441A GLU* 2.9 34.8 + - + +
469A SER* 4.6 1.3 - - - -
472A ILE* 3.9 27.4 + - + +
473A THR* 4.1 12.8 - - + +
474A PRO* 5.3 0.8 - - - +
406B LEU* 3.9 33.2 - - + -
409B LEU* 4.1 9.0 - - + -
411B LYS* 4.1 18.9 + - + +
412B ASP* 2.8 31.3 + - - -
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Residues in contact with SER 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A MET* 4.5 14.3 - - - +
435A ASP* 2.6 32.2 + - - -
437A HIS* 1.3 72.0 - - - +
439A ALA* 1.3 67.8 + - - +
441A GLU* 3.2 6.7 + - - +
442A SER* 2.9 25.3 + - - -
406B LEU* 4.0 19.4 - - - +
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Residues in contact with ALA 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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201A ILE* 4.1 17.3 - - + +
202A GLY* 6.4 0.2 - - - -
374A MET* 3.6 27.4 - - - -
434A MET* 3.9 20.8 - - + +
435A ASP 3.1 15.7 + - - +
436A HIS 3.8 1.3 - - - +
438A SER* 1.3 78.4 - - - +
440A ALA* 1.3 62.6 + - - +
442A SER* 3.0 10.5 + - - -
443A PHE* 3.0 22.9 + - - +
901A HEM 6.2 0.4 - - + -
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Residues in contact with ALA 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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201A ILE* 4.1 11.6 - - + +
436A HIS 3.0 19.0 + - - +
437A HIS 3.2 5.1 + - - +
439A ALA* 1.3 76.7 - - - +
441A GLU* 1.3 61.7 + - - +
443A PHE* 3.2 4.3 + - - +
444A MET* 3.1 24.8 + - - +
466A PRO* 5.2 1.1 - - + -
473A THR* 3.6 28.7 - - + -
474A PRO* 4.0 9.0 - - + -
475A VAL* 4.0 14.4 - - + +
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Residues in contact with GLU 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A HIS* 2.9 18.8 + - - +
438A SER* 3.7 5.9 - - - +
440A ALA* 1.3 75.0 - - - +
442A SER* 1.3 64.1 + - - +
444A MET* 3.1 14.3 + - - +
445A LYS* 3.3 16.2 + - - +
474A PRO* 4.4 17.3 - - + -
406B LEU* 3.7 30.2 - - - +
411B LYS* 5.0 6.1 + - - -
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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
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201A ILE 4.7 4.3 + - - -
202A GLY* 5.6 1.0 - - - -
204A ILE* 3.5 36.5 - - - +
434A MET* 4.4 11.3 - - - +
438A SER 2.9 14.5 + - - -
439A ALA* 3.0 13.5 + - - -
441A GLU* 1.3 76.5 - - - +
443A PHE* 1.3 66.8 + - - +
445A LYS* 3.1 11.8 + - - +
446A TYR* 3.0 19.3 + - - +
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Residues in contact with PHE 443 (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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200A CYS 3.9 7.9 - - - -
201A ILE* 3.5 35.4 - - + +
203A ARG* 3.5 32.1 - - + -
204A ILE* 5.6 0.9 - - - -
439A ALA 3.0 14.0 + - - +
440A ALA 3.5 8.5 - - - +
441A GLU 3.2 0.4 - - - -
442A SER* 1.3 79.5 + - - +
444A MET* 1.3 58.0 + - - +
446A TYR* 3.3 27.9 + + - +
447A MET* 2.8 46.5 + - + +
457A CYS* 4.4 8.5 - - - -
459A ALA* 4.4 2.0 - - + -
464A LEU* 3.6 22.0 - - + -
475A VAL* 3.7 19.3 - - + -
480A MET* 4.4 6.5 - - + -
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Residues in contact with MET 444 (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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89A ASN* 3.5 25.1 - - - +
96A PHE* 5.5 5.1 - - + -
440A ALA 3.1 13.1 + - - +
441A GLU* 3.1 9.9 + - - +
443A PHE* 1.3 80.8 - - - +
445A LYS* 1.3 61.1 + - + +
447A MET* 3.5 8.7 + - - +
448A GLN* 3.1 24.4 + - - +
474A PRO* 3.7 24.5 - - + +
475A VAL* 3.9 29.2 - - - -
478A GLN* 3.6 22.2 - - + +
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Residues in contact with LYS 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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204A ILE* 4.1 17.3 - - + +
441A GLU 3.3 11.6 + - - +
442A SER* 3.1 12.4 + - - +
444A MET* 1.3 77.9 - - + +
446A TYR* 1.3 64.3 + - - +
448A GLN* 3.2 12.3 + - - +
449A ASN* 3.0 34.6 + - - +
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Residues in contact with TYR 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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195A ARG* 3.0 28.1 + - - +
203A ARG* 3.6 43.5 + - + +
204A ILE* 3.8 25.1 - - + +
206A TRP* 3.6 15.7 - + - -
442A SER 3.0 12.6 + - - +
443A PHE* 3.5 29.8 - + - +
445A LYS* 1.3 77.3 - - - +
447A MET* 1.3 59.0 + - - +
449A ASN* 3.2 11.2 + - + +
450A GLU* 2.9 60.7 + - + +
454A ARG* 4.7 0.2 + - - -
457A CYS* 3.6 19.8 - - - -
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Residues in contact with MET 447 (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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87A ILE* 5.4 0.4 - - + -
96A PHE* 4.1 8.5 - - + -
443A PHE* 2.8 36.1 + - + +
444A MET* 3.8 10.1 - - + +
446A TYR* 1.3 80.7 - - - +
448A GLN* 1.3 62.2 + - - +
450A GLU* 3.3 1.4 + - - +
451A TYR* 3.1 58.8 + - + +
457A CYS* 4.1 17.3 - - - +
459A ALA* 4.2 14.4 - - + -
478A GLN* 3.7 30.5 - - + +
479A GLU 4.5 3.8 - - - +
480A MET* 4.0 27.8 - - + -
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Residues in contact with GLN 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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94A MET* 4.1 23.8 - - - +
96A PHE* 4.0 22.8 - - + -
444A MET 3.1 14.7 + - - +
445A LYS* 3.3 14.5 - - - +
447A MET* 1.3 77.6 - - - +
449A ASN* 1.3 64.2 + - - +
451A TYR* 3.2 4.3 + - - +
452A ARG* 3.1 60.3 + - + +
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Residues in contact with ASN 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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204A ILE* 5.3 5.9 - - - +
445A LYS* 3.0 29.9 + - - +
446A TYR* 3.6 10.7 - - + +
448A GLN* 1.3 80.8 + - - +
450A GLU* 1.3 61.1 + - - +
452A ARG* 3.1 15.6 + - - +
453A SER* 2.7 37.8 + - - +
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Residues in contact with GLU 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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195A ARG* 2.9 41.1 + - - -
206A TRP* 4.3 5.0 + - - -
446A TYR* 2.9 64.3 + - + +
447A MET 3.6 5.8 - - - +
448A GLN 3.2 0.2 - - - -
449A ASN* 1.3 79.7 - - - +
451A TYR* 1.3 57.7 + - - +
453A SER* 4.4 2.9 + - - +
454A ARG* 2.8 47.0 + - - +
455A GLY 3.4 0.7 + - - -
456A GLY 3.4 21.4 - - - +
457A CYS* 3.8 8.0 - - + -
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Residues in contact with TYR 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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87A ILE* 4.5 10.0 - - + +
96A PHE* 3.8 48.5 - + + -
97A GLN 3.7 13.9 - - - -
98A ASP* 2.8 44.7 + - + +
447A MET* 3.1 43.2 + - + +
448A GLN 3.8 4.5 - - - +
449A ASN 3.2 0.2 - - - -
450A GLU* 1.3 77.2 - - - +
452A ARG* 1.3 59.8 + - + +
455A GLY* 3.0 22.9 + - - -
456A GLY* 3.6 14.1 - - - +
457A CYS* 3.6 32.2 + - + -
480A MET* 5.9 0.2 - - - -
481A LEU* 5.1 5.2 + - - +
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Residues in contact with ARG 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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94A MET* 6.0 1.8 - - - +
448A GLN* 3.1 55.1 + - - +
449A ASN* 3.6 17.0 + - - +
451A TYR* 1.3 77.4 - - - +
453A SER* 1.3 61.6 + - - +
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Residues in contact with SER 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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195A ARG* 4.0 21.0 + - - -
449A ASN* 2.7 26.7 + - - +
450A GLU* 3.9 3.6 + - - -
452A ARG* 1.3 81.5 - - - +
454A ARG* 1.3 60.6 + - - +
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Residues in contact with ARG 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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99A THR* 4.6 1.9 + - - -
100A LEU* 3.7 37.7 + - + +
149A GLN* 5.9 1.2 - - - +
192A GLN* 4.1 11.9 + - - -
195A ARG* 3.7 42.0 + - - +
196A ASN* 2.9 30.7 + - - +
450A GLU* 2.8 41.8 + - - +
453A SER* 1.3 75.8 - - - +
455A GLY* 1.3 67.3 + - - +
456A GLY 3.2 7.9 + - - +
458A PRO* 4.0 15.2 - - - +
485A LEU* 3.8 12.1 - - - +
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Residues in contact with GLY 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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97A GLN 4.2 5.6 - - - -
98A ASP* 3.6 1.7 - - - -
99A THR* 3.0 20.2 + - - -
100A LEU 3.0 22.2 + - - -
451A TYR* 3.0 31.6 + - - -
453A SER 3.8 0.4 - - - -
454A ARG* 1.3 76.1 - - - +
456A GLY* 1.3 57.4 + - - +
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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
------------------------------------------------------------
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