Contacts of the helix formed by residues 427 - 445 (chain A) in PDB entry 3OMA
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 427 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387A PHE* 3.0 36.0 - - - -
391A PHE* 4.8 6.3 - - - -
422A TYR 3.2 5.9 + - - -
423A VAL* 3.1 14.4 + - - -
425A SER 3.5 1.2 - - - -
426A LEU* 1.3 79.9 - - - +
428A ALA* 1.3 65.7 + - - +
429A VAL 3.3 0.4 - - - -
430A PHE* 3.1 3.6 + - - +
431A GLY 3.0 10.0 + - - -
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Residues in contact with ALA 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A HEA 5.0 0.2 - - + -
111A VAL* 5.3 4.5 - - + -
115A LEU* 4.3 10.2 - - + +
290A ILE* 3.6 32.8 - - + +
291A VAL* 4.8 6.0 - - + +
294A ALA* 4.2 15.7 - - + +
387A PHE* 4.3 0.8 - - - -
423A VAL 3.1 8.5 + - - +
424A MET* 3.1 14.0 + - + +
427A GLY* 1.3 73.2 - - - +
429A VAL* 1.3 59.1 + - + +
431A GLY* 3.1 4.5 + - - -
432A ILE* 2.9 30.3 + - - +
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Residues in contact with VAL 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A HEA 3.9 59.7 - - + -
111A VAL* 4.3 12.6 - - + -
424A MET 3.0 14.5 + - - +
425A SER* 3.4 19.7 - - - +
428A ALA* 1.3 72.5 - - - +
430A PHE* 1.3 63.3 + - + +
432A ILE* 3.1 8.1 + - + +
433A PHE* 2.9 53.1 + - + -
460A MET* 5.4 0.4 - - - -
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Residues in contact with PHE 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A TRP* 3.4 64.5 - + - +
386A GLY* 3.9 4.3 - - - -
387A PHE* 3.8 15.3 - - + -
390A LEU* 3.6 24.0 - - + -
425A SER 3.8 7.4 - - - -
426A LEU* 3.7 34.8 - - + +
427A GLY 3.1 9.4 + - - +
429A VAL* 1.3 75.2 - - + +
431A GLY* 1.3 60.3 + - - +
433A PHE 3.4 0.5 + - - -
434A ALA* 2.8 31.3 + - - +
457A PHE* 3.9 15.7 - + - -
460A MET* 3.9 20.4 - - + -
461A PHE* 4.2 14.6 - + - -
464A ALA* 5.1 0.4 - - + -
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Residues in contact with GLY 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU* 4.6 1.3 - - - -
294A ALA* 4.2 19.7 - - - -
297A ILE* 3.8 17.4 - - - +
298A VAL* 4.9 3.8 - - - -
387A PHE* 4.3 6.1 - - - -
427A GLY 3.0 12.9 + - - -
428A ALA 3.1 5.8 + - - -
430A PHE* 1.3 75.3 - - - +
432A ILE* 1.3 61.6 + - - +
434A ALA* 3.4 7.4 + - - +
435A GLY 3.1 17.7 + - - -
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Residues in contact with ILE 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A HEA 3.8 45.1 - - + -
111A VAL* 3.9 28.0 - - + -
114A ALA* 4.1 18.8 - - + -
115A LEU* 3.7 28.5 - - + -
119A PHE* 3.9 10.4 - - + -
428A ALA 2.9 18.1 + - - +
429A VAL* 3.1 11.3 + - - +
431A GLY* 1.3 75.6 - - - +
433A PHE* 1.3 65.2 + - + +
435A GLY* 3.3 2.4 + - - -
436A ILE* 3.0 31.3 + - + +
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Residues in contact with PHE 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A HEA 4.2 22.7 - - + -
383A TRP* 3.5 45.5 - + + +
429A VAL* 2.9 41.8 + - + +
430A PHE 4.0 0.2 - - - +
432A ILE* 1.3 71.6 - - + +
434A ALA* 1.3 66.4 + - - +
436A ILE* 3.2 5.8 + - + +
437A TYR* 3.1 30.4 + + + -
456A HIS* 3.7 29.2 - + - -
460A MET* 4.6 6.5 - - + -
508A PHE* 4.0 22.7 - + - -
511A PHE* 3.7 35.9 - + - -
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Residues in contact with ALA 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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297A ILE* 4.2 11.9 - - + -
298A VAL* 5.5 2.5 - - + -
301A VAL* 4.4 6.1 - - + -
380A PRO* 3.8 17.7 - - - +
383A TRP* 3.7 21.4 - - + +
384A ALA* 4.4 8.1 - - + +
430A PHE 2.8 22.5 + - - +
431A GLY* 3.6 9.0 - - - +
433A PHE* 1.3 72.5 - - - +
435A GLY* 1.3 57.6 + - - +
438A PHE* 3.0 31.1 + - - +
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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
----------------------------------------------------------
119A PHE* 3.6 12.7 - - - -
297A ILE* 3.9 16.4 - - - +
431A GLY 3.1 11.6 + - - -
432A ILE 3.3 2.9 + - - -
434A ALA* 1.3 74.6 - - - +
436A ILE* 1.3 58.9 + - - +
438A PHE* 4.1 2.9 - - - -
439A TRP* 2.9 46.5 + - - +
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Residues in contact with ILE 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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1A HEA 4.0 13.7 - - + -
7A DMU 4.1 25.1 - - + -
34A LEU* 5.2 1.6 - - + -
119A PHE* 3.7 17.0 - - + -
432A ILE* 3.0 35.3 + - + +
433A PHE* 3.2 8.9 + - + +
435A GLY* 1.3 75.3 - - - +
437A TYR* 1.3 62.6 + - + +
440A ILE* 2.8 40.2 + - + +
443A MET* 5.0 2.0 - - - -
511A PHE* 3.7 27.4 - - + -
515A ILE* 3.8 27.4 - - + -
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Residues in contact with TYR 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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379A THR* 3.5 12.3 - - + -
380A PRO* 3.9 18.2 - - + -
383A TRP* 3.3 26.2 - + - -
433A PHE* 3.1 25.2 + - + +
434A ALA 4.1 1.1 - - - +
436A ILE* 1.3 77.2 - - + +
438A PHE* 1.3 65.5 + - - +
439A TRP 3.4 0.2 + - - -
440A ILE* 4.1 5.2 - - + +
447A GLN* 4.4 1.4 - - - +
448A TYR* 3.2 58.3 - + + -
453A GLY* 3.7 22.4 - - - -
456A HIS* 2.8 39.2 + + - +
511A PHE* 3.7 20.4 - + - -
514A VAL* 4.1 15.3 - - + +
515A ILE* 5.8 2.2 - - + -
530A TYR* 5.0 0.3 + - - -
531A TRP* 3.7 4.7 - - - -
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Residues in contact with PHE 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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297A ILE* 5.6 0.4 - - + -
300A HIS* 4.1 21.8 - - + -
301A VAL* 3.8 17.5 - - + -
304A THR* 3.7 25.8 - - + -
305A PHE* 3.8 22.9 - + - -
380A PRO* 3.7 7.2 - - + +
434A ALA 3.0 20.0 + - - +
435A GLY* 3.6 6.1 - - - +
437A TYR* 1.3 76.3 - - - +
439A TRP* 1.3 105.1 + + - +
530A TYR* 3.0 16.1 + - - -
531A TRP* 3.0 42.0 + + - -
535A ALA* 5.5 0.2 - - - -
539A GLU* 4.7 0.7 - - - -
540A TRP* 3.5 22.1 - + - -
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Residues in contact with TRP 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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119A PHE* 3.5 31.9 - + + -
123A PHE* 3.2 42.2 - + + -
127A HIS* 3.9 20.2 - + - -
228A PHE* 4.4 8.3 - + + -
297A ILE* 3.8 35.0 - - + -
300A HIS* 4.8 3.8 - - + -
435A GLY* 2.9 25.1 + - - +
438A PHE* 1.3 101.7 - + - +
440A ILE* 1.3 65.1 + - - +
441A GLY 3.2 3.4 - - - -
442A LYS* 3.0 5.6 + - + +
443A MET* 2.9 29.4 + - + +
530A TYR* 3.7 2.2 - - - -
539A GLU* 3.1 28.4 + - + -
540A TRP* 3.6 20.5 - + - -
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Residues in contact with ILE 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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7A DMU 4.4 17.0 - - + -
436A ILE* 2.8 27.7 + - + +
437A TYR* 4.1 2.5 - - + +
438A PHE 3.8 0.2 - - - -
439A TRP* 1.3 72.2 - - - +
441A GLY* 1.3 56.8 + - - +
443A MET* 3.9 9.6 - - + +
444A SER* 2.7 47.5 + - - +
446A ARG 3.7 3.6 - - - +
447A GLN* 4.3 1.8 - - - +
448A TYR* 3.9 33.2 - - + +
515A ILE* 3.8 28.7 - - + -
518A THR* 3.8 21.8 - - + +
519A LEU* 4.1 18.2 - - + -
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Residues in contact with GLY 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 TYR 5.1 0.2 + - - -
438A PHE 5.0 0.2 + - - -
439A TRP 3.2 0.6 - - - -
440A ILE* 1.3 83.0 - - - +
442A LYS* 1.3 56.2 + - - +
445A GLY* 2.9 30.3 + - - -
446A ARG 3.2 16.4 - - - -
447A GLN* 4.3 5.6 + - - -
525A VAL* 3.7 10.4 - - - +
530A TYR* 3.3 21.1 + - - -
544A SER* 3.6 5.5 - - - -
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Residues in contact with LYS 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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122A TYR* 5.1 0.9 - - + -
123A PHE* 4.1 22.7 - - + -
439A TRP* 3.0 11.4 + - + +
441A GLY* 1.3 75.1 - - - +
443A MET* 1.3 56.3 + - - +
528A ASN 2.7 28.9 + - - -
530A TYR* 2.8 17.7 + - - +
539A GLU* 2.8 27.1 + - + +
540A TRP* 3.7 19.5 - - + -
542A LEU 2.7 23.2 + - - -
543A THR 2.9 15.7 + - - +
544A SER* 3.2 11.7 + - - -
545A PRO* 3.1 27.5 - - - +
546A PRO* 3.4 15.2 - - + +
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Residues in contact with MET 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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7A DMU 3.4 60.7 + - + +
31A VAL* 5.0 2.0 - - - -
34A LEU* 4.1 15.0 - - + -
119A PHE* 3.9 22.0 - - + -
122A TYR* 3.6 33.9 + - + +
123A PHE* 3.8 29.4 - - + -
436A ILE* 4.7 2.7 - - - +
439A TRP* 2.9 29.4 + - + +
440A ILE* 3.9 7.6 - - + +
442A LYS* 1.3 77.7 - - - +
444A SER* 1.3 58.9 + - - +
445A GLY 3.8 0.2 - - - -
545A PRO* 3.6 13.1 - - - +
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Residues in contact with SER 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A DMU 3.3 37.7 + - - +
440A ILE* 2.7 22.8 + - - +
443A MET* 1.3 79.3 - - - +
445A GLY* 1.3 57.9 + - - +
446A ARG* 3.0 28.4 + - - +
519A LEU* 3.5 30.8 - - - +
545A PRO* 4.1 7.9 - - - +
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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
----------------------------------------------------------
441A GLY 2.9 12.6 + - - -
443A MET 3.8 0.8 - - - -
444A SER* 1.3 77.4 - - - +
446A ARG* 1.3 62.4 + - - +
524A ARG* 3.8 5.5 - - - +
525A VAL* 2.9 30.9 + - - +
544A SER 3.5 22.0 - - - -
545A PRO* 3.8 6.8 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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