Contacts of the helix formed by residues 435 - 444 (chain A) in PDB entry 4KXA
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 GLN 435 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428A ASN* 5.3 2.6 + - - -
431A GLU 5.3 0.2 + - - -
432A THR 4.4 4.0 + - - -
433A ASP* 3.3 10.0 + - - +
434A TRP* 1.3 79.2 - - - +
436A MET* 1.3 63.7 + - - +
437A ARG* 3.4 2.7 - - - -
438A ASP* 3.1 25.2 + - + +
439A GLN* 3.1 21.0 + - + +
652A SER* 6.2 0.3 - - - -
688A ASN* 5.9 0.7 + - - -
689A PHE* 5.9 0.7 - - - +
690A LEU* 5.4 6.5 - - + +
738A ASP* 5.1 2.4 + - - -
740A VAL* 4.0 32.4 - - + +
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Residues in contact with MET 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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385A GLN* 3.9 33.0 - - - +
389A THR* 4.1 11.0 - - - +
424A PHE* 3.4 56.8 - - + +
427A VAL* 3.6 32.1 - - + -
428A ASN* 4.0 18.8 + - + +
431A GLU 4.8 0.4 + - - +
434A TRP* 3.8 30.1 - - + -
435A GLN* 1.3 76.1 - - - +
437A ARG* 1.3 59.6 + - - +
439A GLN* 2.8 26.2 + - + +
440A MET 3.1 8.8 + - - -
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Residues in contact with ARG 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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421A PHE* 4.4 6.1 - - - -
424A PHE* 4.9 6.5 - - - -
425A LEU* 3.6 41.7 - - - +
428A ASN* 4.6 19.7 + - - +
435A GLN 3.4 0.6 - - - -
436A MET* 1.3 76.7 - - - +
438A ASP* 1.3 64.4 + - - +
440A MET* 3.3 39.2 - - - +
441A LEU 4.5 0.3 + - - -
487A ARG* 4.6 11.8 + - - +
490A GLU* 3.2 37.6 + - - -
495A PRO* 5.6 3.0 - - - +
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Residues in contact with ASP 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 GLN* 3.1 29.0 + - + +
437A ARG* 1.3 80.5 - - - +
439A GLN* 1.3 63.6 + - - +
441A LEU* 3.1 27.2 + - - +
442A LEU 4.2 0.3 + - - -
622A ASP* 4.4 14.2 - - - +
652A SER* 6.0 1.7 - - - -
653A ALA* 4.4 11.6 + - - +
690A LEU* 3.6 29.3 - - + +
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Residues in contact with GLN 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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385A GLN* 2.9 41.5 + - - +
424A PHE* 4.1 8.3 - - + -
434A TRP 3.0 21.9 + - - +
435A GLN* 3.1 14.3 + - + +
436A MET* 2.8 15.4 + - - +
438A ASP* 1.3 73.2 - - - +
440A MET* 1.3 59.0 + - - +
441A LEU 3.1 2.7 - - - -
442A LEU* 3.0 12.2 + - + +
443A GLU* 2.9 38.3 + - + +
689A PHE* 3.9 25.8 - - + -
690A LEU* 4.7 7.2 - - + -
739A HIS* 4.4 1.2 - - - -
740A VAL* 4.2 5.8 - - + +
743A LEU* 3.9 13.3 - - - +
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Residues in contact with MET 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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421A PHE* 3.6 35.4 - - + +
424A PHE* 3.4 54.9 - - + -
425A LEU* 5.5 0.2 - - - -
436A MET 3.1 4.0 + - - +
437A ARG* 3.3 34.3 - - - +
438A ASP 3.1 0.4 - - - -
439A GLN* 1.3 75.7 - - - +
441A LEU* 1.3 57.8 + - - +
444A ASP* 2.9 26.6 + - + +
445A VAL* 3.1 12.3 + - + +
483A SER* 3.8 13.9 - - - +
487A ARG* 3.9 31.6 - - + -
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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
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438A ASP* 3.1 15.0 + - - +
439A GLN 3.1 0.6 - - - -
440A MET* 1.3 78.5 - - - +
442A LEU* 1.3 61.3 + - + +
445A VAL* 3.8 20.9 - - + -
446A LEU* 3.1 47.3 + - + +
487A ARG* 3.5 25.4 - - - +
622A ASP 3.5 20.4 - - - +
623A HIS* 3.8 21.3 - - + +
653A ALA* 4.1 28.5 - - + +
656A ALA* 5.4 1.8 - - + -
657A SER* 5.3 0.4 - - - -
690A LEU* 4.2 13.9 - - + -
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Residues in contact with LEU 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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439A GLN* 3.0 13.7 + - + +
441A LEU* 1.3 78.2 - - + +
443A GLU* 1.3 69.1 + - - +
446A LEU* 5.3 0.4 - - + -
447A PRO* 3.2 20.4 - - - +
656A ALA* 5.4 0.2 - - + -
689A PHE* 3.4 33.4 - - + -
690A LEU* 3.7 37.0 - - + +
693A GLN* 3.7 27.6 - - + +
694A ARG* 3.6 36.7 + - + +
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Residues in contact with GLU 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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385A GLN* 4.5 11.6 + - - +
423A GLU* 5.7 0.2 - - - +
424A PHE* 3.6 29.4 - - + -
439A GLN* 2.9 32.0 + - + +
442A LEU* 1.3 86.9 - - - +
444A ASP* 1.3 67.8 + - - +
447A PRO* 3.8 10.0 - - - +
480A SER* 4.3 2.1 + - - -
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Residues in contact with ASP 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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420A SER* 3.9 8.2 + - - +
423A GLU* 4.2 3.6 - - - +
424A PHE* 3.2 29.2 - - + -
440A MET* 2.9 11.6 + - + +
442A LEU 3.6 0.6 - - - -
443A GLU* 1.3 86.1 - - - +
445A VAL* 1.3 68.5 + - + +
446A LEU 3.6 0.9 - - - -
447A PRO* 3.8 2.2 - - - +
448A VAL* 3.1 27.0 + - - +
479A TYR* 4.8 1.6 - - - +
480A SER* 2.7 42.8 + - - +
483A SER* 3.7 14.7 + - - +
484A SER* 4.0 3.8 - - - +
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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