Contacts of the helix formed by residues 433 - 446 (chain A) in PDB entry 4OG6
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 HIS 433 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361A TYR* 3.5 25.7 + - - -
365A PHE* 4.0 11.7 - + - -
431A VAL 4.1 4.3 - - - -
432A LEU* 1.3 76.7 - - - +
434A VAL* 1.4 66.2 + - - +
435A GLY* 3.1 33.5 + - - -
436A TRP* 2.9 36.3 + + - +
437A ALA 3.4 2.6 + - - -
579A LEU* 4.8 0.9 - - - +
580A THR* 3.6 14.9 - - - +
603A PG4 3.8 41.8 - - - -
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Residues in contact with VAL 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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433A HIS* 1.4 76.5 - - - +
435A GLY* 1.3 59.7 + - - +
437A ALA* 2.9 23.0 + - + +
438A THR* 3.4 12.4 + - - +
576A LYS* 4.1 29.4 - - + +
580A THR* 3.7 15.1 - - + +
582A GLN* 5.3 10.1 - - - +
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Residues in contact with GLY 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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365A PHE* 5.1 4.0 - - - -
369A ASN* 4.2 2.7 - - - +
433A HIS* 3.0 22.9 + - - -
434A VAL* 1.3 84.5 - - - +
436A TRP* 1.3 58.2 + - - +
438A THR* 4.3 6.7 + - - -
439A PHE* 3.5 24.8 - - - -
603A PG4 6.4 0.2 - - - -
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Residues in contact with TRP 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A TYR* 3.1 37.7 + + - -
364A PHE* 4.0 11.0 - - + -
365A PHE* 3.6 40.1 - + - -
368A ALA* 3.6 26.5 - - + -
369A ASN* 3.6 19.5 - - - +
417A TYR* 4.6 10.6 + + + -
420A ILE* 4.1 25.8 - - + -
431A VAL* 3.4 14.5 + - + -
432A LEU* 3.6 22.9 - - + -
433A HIS* 2.9 39.5 + + - +
435A GLY* 1.3 74.8 - - - +
437A ALA* 1.3 65.5 + - - +
438A THR 3.3 0.9 - - - -
439A PHE* 3.3 4.6 + - - +
440A LEU* 3.0 22.3 + - - +
579A LEU* 4.1 5.1 - - + +
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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 HIS 3.4 2.4 + - - +
434A VAL* 2.9 20.9 + - + +
436A TRP* 1.3 80.3 - - - +
438A THR* 1.3 61.2 + - - +
440A LEU* 3.2 3.1 + - - +
441A VAL* 3.0 28.8 + - + +
575A ILE* 5.3 1.3 - - + +
576A LYS* 3.6 37.9 - - + +
579A LEU* 3.7 18.6 - - + +
580A THR* 4.6 2.7 - - + -
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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
----------------------------------------------------------
434A VAL* 3.4 13.1 + - - +
435A GLY* 4.6 7.2 - - - -
436A TRP 3.3 0.4 - - - -
437A ALA* 1.3 77.0 - - - +
439A PHE* 1.3 73.1 + - + +
441A VAL* 3.4 6.4 + - - +
442A GLN* 3.1 23.3 + - + +
576A LYS* 4.5 16.6 + - - +
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Residues in contact with PHE 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A PHE* 5.9 1.8 - + - -
368A ALA 4.0 9.6 - - - +
369A ASN* 3.3 57.2 - - + +
373A PRO* 3.8 11.9 - - + -
417A TYR* 4.2 2.7 - - - +
435A GLY 3.5 16.8 - - - -
436A TRP 3.3 1.6 + - - +
437A ALA 3.2 0.2 - - - -
438A THR* 1.3 83.9 - - + +
440A LEU* 1.3 59.7 + - - +
442A GLN* 3.2 26.1 + - - +
443A SER* 2.8 34.0 + - - -
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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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413A LEU* 5.5 1.1 - - + -
414A LEU* 5.9 0.4 - - + -
417A TYR* 3.6 47.4 + - + +
436A TRP 3.0 14.4 + - - +
437A ALA* 3.5 8.3 - - - +
439A PHE* 1.3 75.2 - - - +
441A VAL* 1.3 57.5 + - - +
443A SER* 3.2 2.7 + - - -
444A LEU* 2.8 60.0 + - + +
558A MET* 5.5 3.4 - - + -
561A MET* 4.0 15.5 - - - -
575A ILE* 3.7 23.1 - - + -
579A LEU* 3.9 28.5 - - + -
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Residues in contact with VAL 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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437A ALA 3.0 20.7 + - - +
438A THR* 3.7 6.3 - - - +
440A LEU* 1.3 76.6 - - - +
442A GLN* 1.3 64.4 + - - +
444A LEU* 3.5 8.8 + - - +
445A GLY* 3.1 19.8 + - - -
570A ILE* 4.3 12.7 - - + +
572A SER* 3.8 39.0 - - - +
575A ILE* 3.7 31.9 - - + -
576A LYS* 4.8 3.1 - - + -
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Residues in contact with GLN 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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373A PRO* 3.9 16.2 - - - +
438A THR* 3.1 17.9 + - + +
439A PHE* 3.6 28.4 - - - +
441A VAL* 1.3 80.4 - - - +
443A SER* 1.3 63.4 + - - +
445A GLY* 3.3 9.9 + - - -
446A ARG* 3.3 40.9 + - - +
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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
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368A ALA 4.9 1.9 + - - -
372A ILE* 4.1 9.7 - - - +
373A PRO* 4.2 15.1 - - - +
376A LEU* 3.8 23.8 - - - +
413A LEU* 4.1 18.6 - - - -
417A TYR* 4.9 3.6 + - - -
439A PHE 2.8 19.4 + - - -
440A LEU* 3.8 4.9 - - - -
442A GLN* 1.3 75.0 + - - +
444A LEU* 1.3 65.9 + - - +
446A ARG* 3.2 20.5 + - - +
447A PHE* 3.5 11.1 - - - -
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Residues in contact with LEU 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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410A PHE* 3.6 30.1 - - + -
413A LEU* 4.4 6.5 - - + -
414A LEU* 3.9 18.4 - - + -
440A LEU* 2.8 50.8 + - + +
441A VAL* 3.8 7.2 - - - +
443A SER* 1.3 72.7 - - - +
445A GLY* 1.3 61.8 + - - +
446A ARG 3.1 0.2 - - - -
447A PHE* 3.1 21.1 + - - +
452A ARG* 3.4 12.9 + - - -
565A LEU* 4.0 12.1 - - + -
570A ILE* 4.4 19.3 - - + -
575A ILE* 3.9 27.6 - - + -
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Residues in contact with GLY 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 VAL 3.1 13.1 + - - -
442A GLN 3.3 5.6 + - - -
443A SER 3.2 0.4 - - - -
444A LEU* 1.3 77.6 - - - +
446A ARG* 1.3 62.2 + - - +
447A PHE 3.1 8.9 + - - +
448A GLU* 4.6 6.8 - - - +
452A ARG* 4.9 2.2 + - - -
570A ILE* 4.4 12.6 - - - -
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Residues in contact with ARG 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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373A PRO 4.8 2.2 + - - -
376A LEU* 3.8 29.6 + - + +
377A LYS* 3.6 37.3 + - - +
380A ALA* 3.9 20.1 - - - +
383A LEU* 5.6 1.2 - - - +
404A LEU* 3.6 37.0 - - + +
442A GLN* 3.3 40.0 + - - +
443A SER* 3.4 12.8 - - - +
444A LEU 3.1 0.8 - - - -
445A GLY* 1.3 77.3 - - - +
447A PHE* 1.3 60.4 + - + +
448A GLU* 4.0 2.1 + - - +
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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