Contacts of the helix formed by residues 435 - 447 (chain A) in PDB entry 5K7W
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 ARG 435 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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399A ASP* 2.7 38.8 + - - +
400A ILE* 3.9 15.2 + - + +
401A HIS* 3.5 47.0 + - - -
411A ASP* 2.7 40.6 + - - -
433A THR 3.4 0.2 + - - -
434A GLY* 1.3 72.3 - - - -
436A ALA* 1.3 59.9 + - - +
437A MET 3.2 0.4 - - - -
438A GLU* 3.2 17.2 + - - +
439A LEU* 3.1 36.9 + - - +
255B ARG* 4.3 1.8 - - - +
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Residues in contact with ALA 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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398A TRP* 3.4 52.5 - - + +
432A VAL* 3.3 8.8 - - + +
433A THR 2.9 16.9 + - - +
435A ARG* 1.3 77.5 - - + +
437A MET* 1.3 58.6 + - - +
438A GLU 3.1 1.6 - - - -
439A LEU* 3.9 10.3 - - + +
440A GLY* 2.7 27.4 + - - -
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Residues in contact with MET 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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432A VAL* 3.5 37.9 - - - +
433A THR* 3.7 11.2 + - - +
434A GLY 3.0 22.5 + - - +
436A ALA* 1.3 77.3 - - - +
438A GLU* 1.3 73.1 + - - +
441A ARG* 3.0 37.0 + - - +
454A GLU* 5.3 2.2 - - - +
482A HIS* 3.6 38.4 - - + +
484A LEU* 4.7 1.0 - - - +
245B ARG* 3.6 14.1 - - - +
255B ARG* 3.6 15.5 - - - +
258B ASP* 6.0 3.6 - - + -
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Residues in contact with GLU 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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435A ARG* 3.2 11.6 + - - +
436A ALA 3.1 0.2 - - - -
437A MET* 1.3 76.4 - - - +
439A LEU* 1.3 66.4 + - - +
440A GLY 3.2 1.3 - - - -
441A ARG* 3.1 9.4 + - - +
442A GLU* 3.0 20.1 + - - +
245B ARG* 2.8 38.2 + - + +
255B ARG* 2.8 50.8 + - + +
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Residues in contact with LEU 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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398A TRP* 3.7 29.4 - - + -
399A ASP 5.4 1.6 - - - +
411A ASP* 3.3 37.7 - - + +
414A MET* 5.1 0.7 - - + -
415A ARG* 3.7 22.0 - - - +
435A ARG* 3.1 29.3 + - - +
436A ALA* 3.9 6.1 - - + -
438A GLU* 1.3 75.6 - - - +
440A GLY* 1.3 58.3 + - - +
442A GLU* 3.2 28.6 + - - +
443A CYS* 2.9 34.7 + - - -
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Residues in contact with GLY 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A TRP* 3.9 20.6 - - - -
430A LEU* 3.7 7.7 - - - +
432A VAL* 4.0 9.4 - - - -
436A ALA* 2.7 24.6 + - - +
439A LEU* 1.3 74.5 - - - +
441A ARG* 1.3 56.1 + - - +
443A CYS 3.3 0.7 + - - -
444A LEU* 2.9 29.8 + - - +
484A LEU* 3.9 6.5 - - - -
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Residues in contact with ARG 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 MET* 3.0 28.4 + - - +
438A GLU* 3.1 11.6 + - - +
440A GLY* 1.3 76.3 - - - +
442A GLU* 1.3 62.9 + - - +
444A LEU* 3.3 5.7 + - - +
445A ASN* 3.1 33.5 + - - +
451A ARG* 3.5 23.3 - - + +
454A GLU* 2.8 28.7 + - - -
484A LEU* 3.9 22.6 - - + +
241B LEU* 3.7 8.3 + - - +
242B ASP* 2.8 24.8 + - - +
245B ARG* 3.4 51.1 - - - +
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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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415A ARG* 2.6 48.9 + - + +
438A GLU 3.0 11.2 + - - +
439A LEU* 3.2 18.8 + - - +
441A ARG* 1.3 77.5 - - - +
443A CYS* 1.3 57.1 + - - +
445A ASN* 3.3 6.1 + - - +
446A LEU* 2.9 36.1 + - + +
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Residues in contact with CYS 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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398A TRP* 4.1 19.7 - - + -
414A MET* 4.3 11.0 - - - -
415A ARG* 4.4 15.7 - - - -
430A LEU* 4.8 0.2 - - + -
439A LEU* 2.9 29.9 + - - +
440A GLY* 3.7 6.7 - - - +
442A GLU* 1.3 73.6 - - - +
444A LEU* 1.3 61.4 + - - +
446A LEU* 3.2 7.0 + - - +
447A TRP* 2.9 70.4 + - + -
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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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428A LEU* 4.3 15.3 - - + -
430A LEU* 4.9 2.9 - - + -
440A GLY 2.9 16.3 + - - +
441A ARG* 3.3 6.9 + - - +
443A CYS* 1.3 78.4 - - - +
445A ASN* 1.3 65.3 + - - +
447A TRP* 3.5 13.0 + - - -
448A GLY 3.5 0.3 + - - -
449A TYR* 3.0 45.6 + - + +
450A GLU 3.6 6.3 - - - -
451A ARG* 3.3 39.9 - - + +
484A LEU* 4.0 30.3 - - + -
486A GLY* 3.9 20.4 - - - +
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Residues in contact with ASN 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 ARG* 3.1 25.0 + - - +
442A GLU* 3.9 5.0 - - - +
444A LEU* 1.3 81.4 - - - +
446A LEU* 1.3 65.9 - - - +
448A GLY* 3.1 14.7 + - - -
449A TYR 3.0 19.2 + - - +
450A GLU* 4.3 3.8 - - - -
451A ARG 4.6 1.0 + - - -
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Residues in contact with LEU 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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415A ARG* 3.5 44.6 - - + +
420A PRO* 5.0 2.9 - - - +
442A GLU* 2.9 24.0 + - + +
443A CYS* 3.6 6.5 - - - +
445A ASN* 1.3 78.0 - - - +
447A TRP* 1.3 68.6 + - + +
448A GLY* 3.1 1.8 + - - -
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Residues in contact with TRP 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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414A MET* 3.2 37.5 - - + -
415A ARG* 3.4 23.1 + - - +
417A LEU* 3.6 10.5 + - + -
419A ILE* 3.6 35.7 - - + -
420A PRO* 3.9 33.4 - - + +
428A LEU* 4.0 22.4 - - + -
430A LEU* 4.1 26.7 - - + -
443A CYS* 2.9 43.9 + - + +
445A ASN 3.2 0.4 - - - -
446A LEU* 1.3 83.1 - - + +
448A GLY* 1.3 57.7 + - - +
449A TYR* 3.7 18.5 - - + -
488A LYS* 3.6 18.5 - - - -
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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