Contacts of the helix formed by residues 435 - 449 (chain A) in PDB entry 4EEP
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
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Residue Dist Surf HB Arom Phob DC
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433A GLU 3.2 6.9 + - - +
434A THR* 1.3 70.2 - - - +
436A GLN* 1.3 59.2 + - - +
437A ALA* 3.0 24.3 + - - +
438A THR* 3.1 36.7 + - - +
439A VAL* 3.2 13.5 + - - +
456A LEU* 5.5 3.5 - - + +
457A ILE 5.2 3.8 - - - +
467A TRP* 6.5 1.6 - - + -
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Residues in contact with GLN 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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430A GLN* 5.0 2.7 + - - +
431A GLY 5.1 1.7 - - - +
434A THR* 3.2 25.5 + - - +
435A ASP* 1.3 71.5 + - - +
437A ALA* 1.3 59.6 + - - +
439A VAL* 3.6 27.9 - - - +
440A GLN* 2.9 28.4 + - - +
443A ARG* 5.6 1.9 + - - +
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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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435A ASP* 3.0 15.7 + - - +
436A GLN* 1.3 76.4 - - - +
438A THR* 1.3 58.2 + - - +
440A GLN* 3.4 16.9 + - - +
441A LYS* 3.1 38.7 + - - +
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Residues in contact with THR 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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435A ASP* 3.1 29.2 + - - +
437A ALA* 1.3 76.3 - - - +
439A VAL* 1.3 66.1 + - - +
441A LYS* 3.1 12.5 + - + +
442A ILE* 3.0 22.8 + - - +
454A VAL* 3.8 31.0 - - + -
455A GLN 3.6 23.7 + - - +
456A LEU* 3.9 14.6 - - + -
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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
----------------------------------------------------------
430A GLN* 3.8 18.2 - - - +
434A THR* 3.6 24.5 - - + -
435A ASP 3.2 13.8 + - - +
436A GLN* 3.4 28.2 + - - +
438A THR* 1.3 76.5 - - - +
440A GLN* 1.3 55.8 + - - +
442A ILE* 3.3 10.9 + - - +
443A ARG* 2.9 31.7 + - - +
456A LEU* 4.4 3.6 - - + -
1001A FMN 3.5 38.8 - - - +
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Residues in contact with GLN 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A GLN 2.9 14.5 + - - +
437A ALA* 3.4 18.9 + - - +
438A THR 3.2 0.2 - - - -
439A VAL* 1.3 77.0 - - - +
441A LYS* 1.3 57.3 + - + +
443A ARG* 3.3 32.6 + - - +
444A ASP* 2.9 50.4 + - - +
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Residues in contact with LYS 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A ALA* 3.1 26.0 + - - +
438A THR* 3.1 16.4 + - + +
440A GLN* 1.3 76.3 - - + +
442A ILE* 1.3 56.3 + - - +
444A ASP* 3.5 8.0 + - - +
445A ALA* 2.9 29.5 + - - +
450A ARG* 4.9 1.2 + - - -
452A ILE* 3.6 19.2 - - + +
454A VAL* 4.8 13.7 - - + -
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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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430A GLN* 5.5 0.2 - - - +
438A THR 3.0 19.0 + - - +
439A VAL* 3.3 8.0 + - - +
441A LYS* 1.3 72.9 - - - +
443A ARG* 1.3 59.0 + - - +
445A ALA* 3.2 6.4 + - - +
446A ILE* 2.9 49.0 + - + +
452A ILE* 4.7 5.6 - - + -
454A VAL* 3.9 21.1 - - + -
456A LEU* 3.9 27.6 - - + -
470A PHE* 3.9 31.4 - - + -
472A LEU* 4.7 4.3 - - + -
1001A FMN 3.8 28.5 - - + +
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Residues in contact with ARG 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A GLN* 5.6 2.0 + - - +
439A VAL* 2.9 25.1 + - - +
440A GLN* 3.4 45.0 + - - +
442A ILE* 1.3 74.2 - - - +
444A ASP* 1.3 65.3 + - - +
446A ILE* 3.4 8.3 + - - +
447A ARG* 2.9 29.1 + - + +
1001A FMN 2.9 44.5 + - - +
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Residues in contact with ASP 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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440A GLN* 2.9 36.3 + - - +
441A LYS* 3.8 7.2 - - - +
443A ARG* 1.3 82.3 + - - +
445A ALA* 1.3 59.2 + - - +
447A ARG* 3.2 38.5 + - - +
448A ASP* 2.9 34.8 + - - -
450A ARG* 4.2 8.7 - - - +
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Residues in contact with ALA 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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441A LYS 2.9 18.1 + - - +
442A ILE 3.2 4.2 + - - +
444A ASP* 1.3 75.6 - - - +
446A ILE* 1.3 58.7 + - - +
448A ASP 3.4 0.3 + - - -
449A GLN* 2.8 23.2 + - - -
450A ARG* 2.9 46.6 + - - +
452A ILE* 3.9 29.6 - - + -
472A LEU* 4.1 2.9 - - + +
485A PHE* 4.9 0.2 - - - -
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Residues in contact with ILE 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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396A PRO* 6.2 0.2 - - + -
401A ASN* 4.2 10.8 - - - +
442A ILE* 2.9 31.3 + - + +
443A ARG* 3.6 6.7 - - - +
445A ALA* 1.3 73.7 - - - +
447A ARG* 1.3 66.5 + - - +
449A GLN* 3.1 21.5 + - - +
472A LEU* 3.6 16.6 - - + -
485A PHE* 3.6 27.8 - - + -
1001A FMN 3.1 48.9 - - + +
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Residues in contact with ARG 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ARG* 2.9 15.9 + - + +
444A ASP* 3.2 41.9 + - - +
446A ILE* 1.3 77.6 - - - +
448A ASP* 1.3 93.7 + - - +
449A GLN* 3.5 10.6 + - - +
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Residues in contact with ASP 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ASP 2.9 17.4 + - - +
445A ALA 4.1 0.4 - - - +
447A ARG* 1.3 112.2 + - - +
449A GLN* 1.3 71.7 + - - +
450A ARG* 3.4 38.4 + - + +
476A ARG* 5.0 0.9 + - - -
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Residues in contact with GLN 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A ALA 2.8 9.6 + - - -
446A ILE 3.1 13.4 + - - +
447A ARG 4.3 8.7 + - - +
448A ASP* 1.3 81.1 - - - +
450A ARG* 1.3 56.7 + - - +
474A PRO* 3.4 24.7 - - + +
476A ARG* 2.6 47.6 + - - +
482A LEU* 3.7 36.1 - - + +
485A PHE* 4.1 4.0 - - + -
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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