Contacts of the helix formed by residues 434 - 447 (chain T) in PDB entry 1BGX
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 GLU 434 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375T LEU* 3.5 27.4 - - + +
378T TYR* 3.8 20.7 - - - -
379T LEU* 4.6 14.6 - - + -
429T LEU 2.9 24.6 + - - +
430T TYR* 4.2 11.4 - - + -
433T VAL* 1.3 75.3 - - + +
435T ARG* 1.3 63.6 + - - +
437T LEU* 3.3 10.3 + - - +
438T SER* 3.3 5.2 + - - -
566T GLN* 2.9 44.1 + - - +
726T ARG* 4.1 9.6 + - - +
762T LYS* 3.4 28.3 + - - +
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Residues in contact with ARG 435 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369T PRO 4.4 10.7 - - - +
370T GLY* 3.5 27.0 - - - +
371T ASP* 3.1 35.1 + - - +
375T LEU* 4.8 4.0 - - + -
417T TRP* 5.5 6.1 - - - -
430T TYR* 3.2 43.9 + - + +
431T ARG* 3.4 42.4 - - - +
434T GLU* 1.3 76.0 - - - +
436T PRO* 1.3 71.8 - - + +
437T LEU 3.3 0.7 + - - -
438T SER* 3.4 19.7 + - - -
439T ALA* 4.1 2.8 + - - +
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Residues in contact with PRO 436 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431T ARG 3.4 24.0 - - - +
432T GLU* 3.5 22.9 - - - +
433T VAL 3.5 9.0 - - - +
435T ARG* 1.3 93.8 - - + +
437T LEU* 1.3 58.4 + - - -
439T ALA* 3.6 14.5 + - + +
440T VAL* 3.4 16.3 - - - +
766T VAL* 4.0 21.3 - - + +
769T PHE* 5.7 0.5 - - - -
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Residues in contact with LEU 437 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433T VAL* 3.2 18.1 + - + +
434T GLU* 3.3 8.5 + - - +
435T ARG 3.2 0.6 - - - -
436T PRO* 1.3 75.0 - - - +
438T SER* 1.3 61.1 + - - +
439T ALA 3.1 2.0 - - - -
440T VAL* 3.0 22.3 + - + +
441T LEU* 3.1 18.7 + - + +
566T GLN* 3.5 27.4 - - + +
574T LEU* 4.2 6.3 - - + -
762T LYS* 3.7 52.7 - - + +
765T MET* 3.9 36.3 - - + -
766T VAL* 4.4 3.4 - - + -
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Residues in contact with SER 438 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353T ALA* 6.3 0.2 - - - -
354T LYS* 3.6 22.9 - - - +
369T PRO* 3.8 23.0 - - - +
370T GLY 5.8 1.1 - - - -
375T LEU* 3.9 10.9 - - - +
434T GLU 3.3 8.2 + - - -
435T ARG* 3.4 11.8 + - - -
436T PRO 3.3 0.6 - - - -
437T LEU* 1.3 79.4 - - - +
439T ALA* 1.3 58.0 + - - +
440T VAL 3.3 0.2 - - - -
441T LEU* 4.1 1.6 - - - +
442T ALA* 3.4 23.0 + - - +
566T GLN* 3.2 21.3 + - - -
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Residues in contact with ALA 439 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368T PRO* 5.7 3.1 - - + -
369T PRO* 4.1 20.8 - - + +
435T ARG 4.1 2.6 + - - +
436T PRO* 3.6 15.1 + - + +
437T LEU 3.1 0.4 - - - -
438T SER* 1.3 77.2 - - - +
440T VAL* 1.3 61.6 + - - +
442T ALA* 4.0 3.4 + - - +
443T HIS* 2.9 33.2 + - + -
769T PHE* 3.6 15.6 - - + -
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Residues in contact with VAL 440 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436T PRO 3.4 18.8 - - - +
437T LEU* 3.0 16.1 + - + +
439T ALA* 1.3 75.8 - - - +
441T LEU* 1.3 63.1 + - - +
442T ALA 3.2 1.3 - - - -
443T HIS* 3.3 13.7 + - - +
444T MET* 3.4 17.8 + - + +
765T MET* 3.7 33.2 - - + +
766T VAL* 4.7 1.8 - - - -
769T PHE* 3.9 33.3 - - + -
779T MET* 3.7 32.7 - - + +
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Residues in contact with LEU 441 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354T LYS* 4.2 20.4 + - + +
437T LEU* 3.1 17.8 + - + +
438T SER* 4.9 1.3 - - - -
440T VAL* 1.3 75.8 - - - +
442T ALA* 1.3 61.0 + - - +
444T MET* 3.6 28.3 + - + +
445T GLU* 3.5 23.4 + - - +
564T PHE* 3.7 35.1 + - + +
566T GLN* 3.5 37.2 - - + +
574T LEU* 3.9 31.4 - - + -
765T MET* 4.3 5.6 - - + -
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Residues in contact with ALA 442 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354T LYS* 4.3 6.2 - - + +
357T SER* 4.3 19.5 - - - -
358T VAL* 3.8 24.5 - - + +
361T LEU* 3.8 7.0 - - + +
369T PRO* 4.9 1.3 - - + -
438T SER 3.4 19.0 + - - +
439T ALA* 4.1 8.3 - - - +
440T VAL 3.2 0.6 - - - -
441T LEU* 1.3 79.5 - - - +
443T HIS* 1.3 61.7 + - + +
446T ALA* 3.3 27.0 + - - +
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Residues in contact with HIS 443 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361T LEU* 3.9 32.1 - - + +
367T LEU 6.0 2.0 - - - -
439T ALA* 2.9 24.8 + - + +
440T VAL 3.3 8.6 + - - +
441T LEU 3.3 0.4 - - - -
442T ALA* 1.3 81.0 - - + +
444T MET* 1.3 59.7 + - + +
445T GLU 3.3 0.7 - - - -
446T ALA* 3.9 4.0 - - + -
447T THR* 3.0 38.5 + - - +
769T PHE* 3.6 27.4 - + + -
773T GLU* 5.3 9.8 + - - -
779T MET 4.9 2.3 - - - +
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Residues in contact with MET 444 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440T VAL 3.4 13.6 + - - +
441T LEU* 3.6 35.4 + - + +
442T ALA 3.5 0.2 - - - -
443T HIS* 1.3 77.6 - - + +
445T GLU* 1.3 58.2 + - - +
447T THR* 5.3 0.7 - - - -
448T GLY* 3.3 23.5 + - - +
449T VAL* 5.9 0.3 - - - +
562T THR* 4.7 5.9 + - - +
564T PHE* 3.9 24.8 - - + -
765T MET* 3.8 14.8 - - + -
779T MET* 3.5 44.9 - - + +
780T LEU* 3.1 35.6 - - - +
781T LEU* 4.3 2.2 - - - +
782T GLN* 4.8 6.5 - - + -
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Residues in contact with GLU 445 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316T PRO* 3.5 31.2 - - - +
317T MET* 3.6 6.1 - - + +
354T LYS* 3.0 30.2 + - - +
358T VAL* 3.5 23.3 - - + +
441T LEU 3.5 12.2 + - - +
442T ALA 4.2 1.1 - - - +
444T MET* 1.3 80.3 - - - +
446T ALA* 1.3 58.3 + - - +
447T THR 3.5 0.2 - - - -
561T HIS* 2.9 35.4 + - + +
562T THR 3.4 28.0 + - - +
563T ARG* 3.5 22.8 - - + +
564T PHE 4.0 1.7 + - - +
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Residues in contact with ALA 446 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317T MET* 3.4 27.2 - - + +
358T VAL* 4.0 9.6 - - + +
361T LEU* 3.9 32.5 - - + -
362T ARG* 6.0 0.5 - - - -
442T ALA 3.3 18.5 + - - +
443T HIS* 4.1 3.6 - - + +
444T MET 3.5 0.2 - - - -
445T GLU* 1.3 80.3 - - - +
447T THR* 1.3 62.7 + - - +
557T THR* 4.6 6.1 - - - +
561T HIS* 3.5 3.3 - - - -
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Residues in contact with THR 447 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443T HIS* 3.0 21.8 + - - +
444T MET* 5.0 0.7 - - - -
446T ALA* 1.3 78.6 - - - +
448T GLY* 1.3 66.6 + - - +
557T THR* 4.7 4.8 + - - +
559T ARG* 3.4 18.9 - - - +
561T HIS* 3.3 14.2 - - - -
778T ARG* 3.8 45.4 + - - +
779T MET 5.8 1.1 - - - -
780T LEU* 5.4 2.2 - - - -
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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