Contacts of the helix formed by residues 431 - 444 (chain A) in PDB entry 4E2I
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 GLY 431 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A TRP* 5.2 3.4 - - - -
397A LEU* 3.9 11.7 - - - +
430A SER* 1.3 79.8 - - - +
432A LYS* 1.3 62.6 + - - +
433A THR 3.6 1.6 - - - -
434A THR* 3.2 20.4 + - - -
435A LEU* 2.9 26.2 + - - +
547A PHE* 3.3 15.6 - - - -
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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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424A PHE* 3.9 16.3 - - + +
426A GLY 3.1 29.4 - - - +
427A PRO 2.9 21.8 + - - -
428A ILE* 4.8 0.7 - - - +
429A ASP* 3.6 15.4 - - - +
430A SER* 2.9 22.8 + - - +
431A GLY* 1.3 72.6 - - - +
433A THR* 1.3 67.5 + - - +
434A THR 2.9 5.3 + - - -
435A LEU* 3.0 1.9 + - - +
436A ALA* 2.7 39.2 + - - +
474A ASP* 4.7 3.6 - - - -
527A THR* 4.9 7.2 - - + -
528A MET 3.9 4.0 - - - +
529A ASN* 3.3 20.9 - - - +
547A PHE* 3.4 26.6 - - + -
418F LYS* 4.8 4.8 - - - +
540F ARG* 6.2 0.4 - - - +
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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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431A GLY 3.6 0.2 - - - -
432A LYS* 1.3 87.8 + - - +
434A THR* 1.3 58.0 + - - +
435A LEU 3.5 0.2 - - - -
436A ALA* 4.6 0.2 - - - -
437A ALA* 3.1 24.3 - - - +
473A GLU* 3.1 34.3 + - - +
474A ASP* 4.4 9.7 + - - -
527A THR* 5.8 0.9 + - - -
418F LYS* 5.5 5.2 + - - -
499F ASP* 5.9 0.2 - - - -
502F ASP* 4.3 19.8 + - + +
504F SER* 3.5 28.9 - - - +
505F VAL* 5.1 2.7 - - + -
540F ARG* 4.8 4.3 + - - -
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Residues in contact with THR 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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393A TRP* 3.9 14.1 - - + -
394A LEU* 4.8 2.5 - - + -
397A LEU* 5.3 0.9 - - + -
431A GLY* 3.4 21.0 - - - -
432A LYS 2.9 0.8 - - - -
433A THR* 1.3 80.9 - - - +
435A LEU* 1.3 60.5 + - - +
437A ALA 4.1 0.2 - - - -
438A ALA* 3.5 7.1 + - - +
569A ILE* 3.2 50.9 - - + +
570A GLN* 3.5 25.9 - - + +
504F SER* 5.5 1.1 - - - -
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Residues in contact with LEU 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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394A LEU* 5.5 5.2 - - + -
397A LEU* 4.4 6.7 - - + -
398A LEU* 4.1 3.4 - - + -
401A MET* 3.8 34.3 - - + -
404A VAL* 6.4 1.1 - - + -
405A VAL* 5.5 0.9 - - + -
424A PHE* 3.5 29.4 - - + -
431A GLY 2.9 15.9 + - - +
434A THR* 1.3 75.0 - - - +
436A ALA* 1.3 62.8 + - - +
437A ALA 2.9 6.3 + - - -
438A ALA* 3.1 3.1 + - + +
439A LEU* 2.9 51.1 + - + +
545A ILE* 5.6 1.8 - - + -
547A PHE* 3.6 15.5 - - + -
569A ILE 5.4 0.7 - - - -
575A LEU* 4.3 20.0 - - + -
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Residues in contact with ALA 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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424A PHE* 3.8 14.4 - - + -
432A LYS 2.7 19.6 + - - +
433A THR* 4.6 0.4 - - - -
435A LEU* 1.3 73.7 - - - +
437A ALA* 1.3 58.7 + - - +
439A LEU* 4.3 7.0 - - - +
440A LEU* 3.7 14.0 + - - +
471A VAL* 3.7 23.2 - - + +
473A GLU* 3.8 12.6 - - - +
525A ILE* 4.6 6.9 - - + +
527A THR* 3.7 27.8 - - + -
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Residues in contact with ALA 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 21.6 + - - +
434A THR 4.1 3.8 - - - +
435A LEU 2.9 0.6 - - - -
436A ALA* 1.3 80.0 - - - +
438A ALA* 1.3 66.9 + - - +
439A LEU 3.2 0.2 - - - -
440A LEU* 3.0 21.0 + - - +
441A GLU* 3.4 5.9 + - - +
570A GLN* 4.3 9.8 - - + +
504F SER* 3.1 31.9 - - - +
505F VAL* 4.0 11.7 - - + -
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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
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394A LEU* 5.8 0.9 - - + -
434A THR 3.5 12.1 + - - +
435A LEU* 3.1 5.5 + - - +
437A ALA* 1.3 77.9 - - - +
439A LEU* 1.3 57.9 + - - +
441A GLU* 3.1 3.6 + - - +
442A LEU* 2.9 24.3 + - - +
569A ILE 4.4 3.8 - - - +
570A GLN* 3.6 21.9 + - - -
571A SER 3.5 19.5 - - - +
572A GLY* 3.4 9.5 - - - +
575A LEU* 3.5 22.9 - - + -
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Residues in contact with LEU 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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405A VAL* 4.4 14.6 - - + -
408A PHE* 4.4 27.4 - - + -
424A PHE* 3.6 20.4 - - + -
435A LEU* 2.9 34.4 + - + +
436A ALA 4.4 3.4 - - - +
438A ALA* 1.3 76.3 - - - +
440A LEU* 1.3 64.0 + - - +
442A LEU* 3.6 13.5 - - + +
443A CYS* 3.0 28.9 + - - +
469A LEU* 4.7 2.7 - - - +
525A ILE* 3.5 28.7 - - + -
575A LEU* 3.5 20.8 - - + +
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Residues in contact with LEU 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 ALA 3.7 11.7 + - - +
437A ALA* 3.0 14.4 + - - +
439A LEU* 1.3 79.1 - - - +
441A GLU* 1.3 55.7 - - - +
444A GLY* 2.8 29.6 + - - -
445A GLY 3.4 32.5 + - - +
446A LYS* 3.5 8.7 - - - +
447A ALA* 3.8 28.9 - - + +
469A LEU* 3.5 24.7 - - + -
471A VAL* 3.5 13.2 - - + -
505F VAL* 4.8 11.9 - - + -
506F LYS* 5.0 11.2 - - + +
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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
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364A ARG* 2.8 48.9 + - - +
368A LEU* 3.7 6.9 - - + +
371A ARG* 3.4 24.0 + - - +
437A ALA 3.4 5.1 + - - +
438A ALA* 3.1 8.7 + - - +
440A LEU* 1.3 78.3 - - + +
442A LEU* 1.3 61.2 + - - +
443A CYS 3.3 0.7 - - - -
570A GLN 5.0 1.2 - - - +
571A SER* 3.6 12.0 + - - -
572A GLY* 2.8 30.2 + - - +
573A ILE* 4.1 3.1 + - - +
506F LYS* 5.2 9.7 + - - -
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Residues in contact with LEU 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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364A ARG* 3.5 6.8 - - - +
365A PHE* 3.9 13.9 - - + -
368A LEU* 3.5 27.6 - - + +
405A VAL* 3.7 24.5 - - + -
409A LEU* 4.4 11.2 - - + -
438A ALA 2.9 16.8 + - - +
439A LEU* 3.2 11.4 + - + +
441A GLU* 1.3 78.7 - - - +
443A CYS* 1.3 61.4 + - - +
572A GLY* 3.6 20.6 - - - +
575A LEU* 3.6 26.9 - - + -
576A LEU* 3.8 11.7 - - + +
579A LEU* 3.8 22.9 - - + -
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Residues in contact with CYS 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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360A MET 5.4 0.2 - - - +
361A LEU* 3.7 26.4 - - + +
364A ARG* 3.2 20.1 - - - +
408A PHE* 4.0 13.9 - - - -
409A LEU* 3.5 31.4 - - - -
412A MET* 5.2 0.4 - - - -
439A LEU* 3.0 14.7 + - - +
442A LEU* 1.3 82.9 - - - +
444A GLY* 1.3 59.5 + - - +
468A PHE* 3.8 10.6 - - + +
469A LEU* 3.5 29.6 - - + -
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Residues in contact with GLY 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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364A ARG* 4.2 17.3 - - - -
440A LEU 2.8 22.3 + - - -
441A GLU 4.1 0.4 + - - -
442A LEU 3.8 0.4 - - - -
443A CYS* 1.3 76.3 - - - +
445A GLY* 1.3 58.2 + - - -
468A PHE* 3.4 23.8 - - - +
469A LEU* 3.4 13.8 - - - +
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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