Contacts of the helix formed by residues 438 - 450 (chain A) in PDB entry 6C90
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 LEU 438 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434A GLU 4.1 1.3 + - - +
435A ASP* 3.0 36.5 + - + +
436A LYS 3.2 0.8 - - - -
437A LYS* 1.3 79.9 - - - +
439A PRO* 1.3 77.7 - - + +
440A GLN* 4.4 3.6 - - + +
441A VAL* 3.1 19.7 + - + +
442A GLU* 3.1 10.6 + - - +
460A LEU* 4.1 9.0 - - + -
979A PHE* 3.8 24.0 - - + -
980A ALA* 3.6 43.5 - - + +
983A CYS* 5.3 2.5 - - + -
990A GLU* 6.2 1.6 - - + -
1034A ILE* 3.7 26.5 - - + -
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Residues in contact with PRO 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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437A LYS 3.4 4.4 - - - +
438A LEU* 1.3 94.0 - - + +
440A GLN* 1.3 57.9 + - - +
442A GLU* 3.2 10.0 + - + +
443A HIS* 2.9 30.3 + - - +
980A ALA* 5.3 5.4 - - + -
983A CYS* 6.5 1.6 - - + -
990A GLU* 4.8 9.2 - - - +
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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
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400A GLU* 5.0 5.3 + - - +
438A LEU* 3.3 1.5 - - + -
439A PRO* 1.3 80.3 - - - +
441A VAL* 1.3 62.9 + - - +
443A HIS* 3.2 15.8 + - + +
444A VAL* 3.2 29.2 + - + +
458A GLY 3.3 22.6 + - - -
459A LEU* 3.5 18.8 - - + +
460A LEU* 2.7 50.1 + - + +
463A LEU* 3.6 9.3 - - + +
989A PHE* 4.8 4.4 - - - -
990A GLU* 3.5 29.9 + - - +
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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
----------------------------------------------------------
424A PHE* 3.6 29.3 - - + -
428A ILE* 4.1 15.9 - - + -
431A LEU* 4.8 9.6 - - + -
435A ASP 3.9 17.5 - - - +
436A LYS* 3.3 19.5 - - - +
438A LEU* 3.1 10.0 + - + +
440A GLN* 1.3 78.2 - - - +
442A GLU* 1.3 62.5 + - + +
443A HIS 3.2 0.7 + - - -
444A VAL* 3.4 15.2 + - - +
445A LEU* 3.8 3.1 + - - +
460A LEU* 3.7 23.8 - - + -
462A ILE* 5.8 0.2 - - + -
463A LEU* 3.9 15.3 - - + -
1034A ILE* 5.0 0.2 - - + -
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Residues in contact with GLU 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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436A LYS 4.3 8.3 - - - +
437A LYS* 3.5 32.6 - - - +
438A LEU 3.1 9.1 + - - +
439A PRO* 3.2 9.9 + - + +
441A VAL* 1.3 76.6 - - + +
443A HIS* 1.3 57.5 + - - +
445A LEU* 4.8 2.3 - - - +
446A PRO* 3.3 22.3 - - - +
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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
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400A GLU* 5.4 8.8 + - + -
404A LEU* 3.7 36.3 - - + +
439A PRO 2.9 15.8 + - - +
440A GLN* 3.7 9.6 - - - +
441A VAL 3.1 0.6 - - - -
442A GLU* 1.3 78.6 - - - +
444A VAL* 1.3 71.8 + - - +
446A PRO* 3.4 11.0 - - - +
447A LEU* 3.9 26.7 - - + +
454A ILE* 4.9 8.5 - - + -
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Residues in contact with VAL 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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424A PHE* 3.5 22.9 - - + -
440A GLN* 3.3 21.1 - - + +
441A VAL 3.4 13.5 - - - +
443A HIS* 1.3 86.6 - - - +
445A LEU* 1.3 69.8 + - - +
447A LEU* 2.9 22.4 + - + +
448A LEU* 2.9 24.5 + - + +
454A ILE* 5.8 6.5 - - + -
459A LEU* 5.2 8.3 - - + -
463A LEU* 4.1 20.4 - - + -
467A ILE* 5.0 13.2 - - + -
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Residues in contact with LEU 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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420A VAL* 4.2 17.3 - - + -
421A GLU* 4.6 10.5 - - + +
424A PHE* 3.6 52.7 - - + -
441A VAL 3.8 4.2 + - - +
442A GLU* 4.8 2.2 - - - +
444A VAL* 1.3 83.1 - - - +
446A PRO* 1.3 69.7 - - + +
447A LEU 3.2 0.2 + - - -
448A LEU* 3.2 4.2 + - + -
449A LYS* 3.0 40.8 + - + +
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Residues in contact with PRO 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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442A GLU 3.3 22.0 - - - +
443A HIS* 3.4 12.6 - - - +
445A LEU* 1.3 93.4 - - + +
447A LEU* 1.3 62.8 + - + +
449A LYS* 3.7 13.9 + - + +
450A ARG* 3.5 39.0 + - - +
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Residues in contact with LEU 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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403A ALA* 4.3 20.6 - - + +
404A LEU* 4.6 17.0 - - + -
443A HIS* 3.9 25.8 - - + +
444A VAL* 2.9 14.3 + - + +
446A PRO* 1.3 76.9 - - + +
448A LEU* 1.3 62.3 + - + +
450A ARG* 2.8 49.6 + - - +
451A GLY 3.3 0.2 + - - -
452A ILE* 3.0 33.9 + - + +
454A ILE* 3.7 31.4 - - + -
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Residues in contact with LEU 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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412A ASN* 3.4 7.6 + - - -
420A VAL* 3.7 19.8 - - + +
424A PHE* 3.8 35.0 - - + -
444A VAL* 2.9 24.3 + - + +
445A LEU* 3.8 3.8 - - - +
447A LEU* 1.3 75.2 - - + +
449A LYS* 1.3 58.6 + - - +
451A GLY* 2.7 20.8 + - - -
452A ILE 3.3 17.9 - - - +
453A GLY* 3.9 11.9 - - - -
466A THR* 4.9 0.9 - - + -
467A ILE* 3.8 33.2 - - + -
470A LEU* 3.9 17.0 - - + -
475A LEU 4.1 1.7 - - - +
476A ILE* 4.1 13.9 - - + +
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Residues in contact with LYS 449 (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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412A ASN* 3.3 14.8 + - - +
417A LYS* 3.2 45.9 + - + +
420A VAL* 4.2 10.1 - - + -
421A GLU* 3.1 43.6 + - + +
445A LEU* 3.0 38.7 + - + +
446A PRO* 3.9 12.3 - - + +
447A LEU 3.2 0.2 + - - -
448A LEU* 1.3 75.3 - - - +
450A ARG* 1.3 59.1 + - + +
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Residues in contact with ARG 450 (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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407A THR* 3.2 44.4 + - - +
409A LEU 3.3 25.0 + - - +
410A ASP* 3.4 23.6 - - - +
411A PHE* 2.9 33.6 + - - -
412A ASN* 4.1 1.8 - - - -
417A LYS* 4.6 4.0 - - - +
446A PRO* 3.5 32.6 + - - +
447A LEU* 2.8 39.5 + - - +
449A LYS* 1.3 78.0 - - + +
451A GLY* 1.3 58.0 + - - +
452A ILE* 3.2 9.8 + - + +
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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
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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