Contacts of the helix formed by residues 433 - 448 (chain A) in PDB entry 4BWM
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 VAL 433 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A TRP* 4.0 25.6 - - + -
429A LEU* 2.9 21.2 + - + +
432A GLU* 1.3 84.8 - - - +
434A GLU* 1.3 68.2 + - - +
435A ARG 3.5 0.9 - - - -
436A PRO* 3.6 2.4 - - - +
437A LEU* 2.9 33.7 + - + +
724A PHE* 5.3 2.0 - - + -
726A ARG* 4.6 4.5 - - - +
759A ASP* 5.0 4.3 - - - +
762A LYS* 3.7 40.2 - - + -
763A LEU* 4.0 22.7 - - + +
766A VAL* 3.7 4.0 - - - +
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Residues in contact with GLU 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A LEU* 3.7 23.6 - - + +
378A TYR* 4.6 4.2 - - + -
379A LEU* 4.2 21.8 - - + -
429A LEU 2.8 20.8 + - - +
430A TYR* 4.2 7.0 - - + +
433A VAL* 1.3 77.3 - - + +
435A ARG* 1.3 63.2 + - - +
437A LEU* 3.3 4.5 + - - +
438A SER 3.0 10.6 + - - -
566A GLN* 2.7 54.8 + - - +
726A ARG* 2.5 42.6 + - - +
762A LYS* 3.2 15.2 + - - -
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Residues in contact with ARG 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A PRO 4.8 4.3 - - - +
370A GLY* 3.6 31.4 - - - +
371A ASP* 2.8 31.1 + - - +
375A LEU* 4.1 8.7 - - + +
417A TRP* 5.8 1.6 - - - -
430A TYR* 2.9 47.1 + - + +
431A ARG* 3.9 34.5 + - - +
434A GLU* 1.3 72.7 - - - +
436A PRO* 1.3 65.4 - - + +
438A SER* 2.6 24.3 + - - +
439A ALA* 3.8 2.1 + - - +
1838A FMT 3.3 25.3 + - - -
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Residues in contact with PRO 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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431A ARG 3.2 29.4 - - - +
432A GLU* 3.5 19.5 - - - +
433A VAL 3.6 6.7 - - - +
435A ARG* 1.3 91.9 - - + +
437A LEU* 1.3 61.8 + - - +
439A ALA* 3.1 17.5 + - + +
440A VAL* 3.4 13.3 + - + +
766A VAL* 3.9 19.3 - - + -
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Residues in contact with LEU 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A VAL* 2.9 22.0 + - + +
434A GLU* 3.6 5.6 - - - +
435A ARG 3.2 0.2 - - - -
436A PRO* 1.3 76.4 - - - +
438A SER* 1.3 58.6 + - - +
440A VAL* 3.0 9.7 + - + +
441A LEU* 2.8 35.8 + - + +
566A GLN* 3.7 15.9 - - - +
574A LEU* 4.1 12.3 - - + -
762A LYS* 3.6 46.2 - - + +
765A MET* 4.1 42.0 - - + -
766A VAL* 3.7 8.9 - - + +
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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
----------------------------------------------------------
354A LYS* 3.4 21.9 - - - +
369A PRO* 3.4 23.9 + - - +
370A GLY 4.7 1.4 + - - -
372A ASP* 6.4 0.4 - - - -
375A LEU* 4.4 9.7 - - - +
434A GLU 3.0 10.1 + - - -
435A ARG* 2.6 24.3 + - - +
437A LEU* 1.3 76.5 - - - +
439A ALA* 1.3 56.1 + - - +
441A LEU* 3.5 3.0 + - - -
442A ALA* 3.0 22.9 + - - +
566A GLN* 3.3 22.9 + - - -
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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
----------------------------------------------------------
361A LEU* 5.7 0.2 - - - +
368A PRO* 5.4 5.2 - - + -
369A PRO* 3.7 26.5 - - + +
435A ARG 4.8 2.0 - - - +
436A PRO* 3.1 12.3 + - + +
438A SER* 1.3 77.6 + - - +
440A VAL* 1.3 66.4 + - + +
442A ALA* 3.4 3.3 + - - +
443A HIS* 3.1 22.3 + - - +
769A PHE* 4.8 9.1 - - + -
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Residues in contact with VAL 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A PRO 3.6 13.5 - - - +
437A LEU* 3.0 15.1 + - + +
439A ALA* 1.3 77.7 - - + +
441A LEU* 1.3 57.6 + - - +
443A HIS* 3.2 8.4 + - - +
444A MET* 3.0 34.3 + - + +
765A MET* 4.3 17.3 - - + +
766A VAL* 4.4 8.5 - - + +
769A PHE* 3.7 38.4 - - + -
779A MET* 3.5 32.1 - - - -
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Residues in contact with LEU 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A LYS* 4.4 12.8 - - + -
437A LEU* 2.8 23.0 + - + +
438A SER 3.9 4.0 - - - +
440A VAL* 1.3 75.7 - - - +
442A ALA* 1.3 57.3 + - - +
444A MET* 3.3 23.4 + - - +
445A GLU* 2.9 32.7 + - - +
564A PHE* 4.1 30.0 - - + +
566A GLN* 3.7 47.3 - - + +
574A LEU* 4.0 17.7 - - + -
765A MET* 4.1 14.6 - - + -
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Residues in contact with ALA 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A LYS* 3.8 11.4 - - + +
357A SER* 3.8 28.0 - - - +
358A VAL* 3.7 17.1 - - + +
361A LEU* 3.6 7.5 - - + +
369A PRO* 4.8 0.4 - - + -
438A SER 3.0 17.4 + - - +
439A ALA* 3.6 8.5 - - - +
440A VAL 3.2 0.2 - - - -
441A LEU* 1.3 76.1 - - - +
443A HIS* 1.3 57.9 + - - +
446A ALA* 2.9 33.6 + - - +
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Residues in contact with HIS 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A LEU* 4.0 12.5 - - + +
439A ALA 3.1 13.8 + - - +
440A VAL 3.4 7.2 - - - +
442A ALA* 1.3 77.0 - - - +
444A MET* 1.3 58.3 + - + +
446A ALA* 4.2 0.2 - - - +
447A THR* 2.7 54.2 + - - -
769A PHE* 3.4 36.0 - + + -
773A GLU* 4.4 9.0 + - + -
777A ALA 4.8 3.4 - - - -
778A ARG* 3.6 20.5 - - + +
779A MET* 3.1 46.7 + - + -
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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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440A VAL* 3.0 22.1 + - + +
441A LEU* 3.7 18.4 - - + +
442A ALA 3.3 0.2 - - - -
443A HIS* 1.3 75.7 - - + +
445A GLU* 1.3 63.3 + - - +
447A THR* 4.0 0.9 - - - -
448A GLY* 3.1 22.2 + - - +
564A PHE* 4.0 20.1 - - + -
765A MET* 3.5 31.6 - - + -
779A MET* 3.2 36.7 - - + +
780A LEU* 3.6 26.3 - - - +
781A LEU* 3.7 24.2 - - - +
782A GLN* 3.7 6.5 - - + +
787A LEU* 4.9 0.2 - - + -
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Residues in contact with GLU 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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316A PRO* 3.4 30.0 - - - +
317A MET* 3.9 4.6 + - + +
354A LYS* 2.9 29.3 + - - -
358A VAL* 4.0 18.2 - - + -
441A LEU 2.9 16.1 + - - +
442A ALA 4.0 2.7 - - - +
444A MET* 1.3 78.6 - - - +
446A ALA* 1.3 57.1 + - - +
448A GLY 3.7 0.7 + - - -
561A HIS* 2.8 37.3 + - + +
562A THR 3.3 22.0 - - - +
563A ARG* 3.6 22.4 + - - +
564A PHE* 3.3 15.2 + - + +
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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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317A MET* 3.7 18.2 - - - +
358A VAL* 4.0 13.2 - - + +
361A LEU* 3.6 33.9 - - + -
362A ARG* 4.8 1.7 - - - +
442A ALA 2.9 18.3 + - - +
443A HIS 4.2 0.2 - - - +
445A GLU* 1.3 75.1 - - - +
447A THR* 1.3 60.8 + - - +
557A THR* 5.2 1.2 - - - +
561A HIS* 3.0 19.4 - - - -
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Residues in contact with THR 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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443A HIS* 2.7 43.3 + - - -
444A MET* 4.0 2.5 - - - -
446A ALA* 1.3 80.1 - - - +
448A GLY* 1.3 57.0 + - - +
557A THR* 5.8 0.2 - - - -
559A ARG* 2.9 30.1 + - - +
561A HIS* 3.8 3.6 - - - -
778A ARG* 3.7 28.0 - - + +
780A LEU* 3.6 26.2 - - + -
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Residues in contact with GLY 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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444A MET 3.1 16.5 + - - -
445A GLU 3.7 1.3 + - - -
446A ALA 3.4 1.4 - - - -
447A THR* 1.3 79.5 - - - +
449A VAL* 1.3 59.0 + - - -
559A ARG* 2.8 19.8 + - - -
560A LEU 3.0 15.5 - - - -
561A HIS* 3.6 13.9 - - - -
562A THR 5.3 0.9 - - - -
780A LEU* 3.3 15.9 - - - +
781A LEU* 6.0 0.7 - - - -
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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