Contacts of the helix formed by residues 433 - 446 (chain A) in PDB entry 3KSS
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 LYS 433 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434A THR* 1.3 62.5 + - + +
435A ARG* 4.7 2.0 - - + +
436A TRP* 3.0 58.5 - - + +
437A GLN* 3.1 25.7 + - - +
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Residues in contact with THR 434 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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433A LYS* 1.3 75.6 - - + +
435A ARG* 1.3 71.6 + - + +
437A GLN* 2.5 41.2 + - - +
438A VAL* 2.9 13.8 + - - +
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Residues in contact with ARG 435 (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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418A LEU* 5.8 5.5 - - - +
421A TRP* 4.4 26.9 - - + +
433A LYS* 5.3 1.1 - - + -
434A THR* 1.3 83.4 - - + +
436A TRP* 1.3 137.1 + - - +
437A GLN 3.1 1.1 - - - -
438A VAL* 3.0 21.0 - - + +
439A ILE* 2.9 25.9 - - - +
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Residues in contact with TRP 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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433A LYS* 3.0 77.3 - - + +
435A ARG* 1.3 124.4 - - - +
437A GLN* 1.3 53.5 + - - +
439A ILE* 3.4 14.5 + - + +
440A THR* 2.6 30.3 + - - +
501A MET* 4.9 7.3 - - + +
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Residues in contact with GLN 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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7A ARG* 4.5 17.1 - - - +
10A VAL* 6.5 1.1 - - + -
433A LYS 3.1 16.3 + - - +
434A THR* 2.5 41.5 + - - +
436A TRP* 1.3 74.3 - - - +
438A VAL* 1.3 58.3 + - - +
440A THR* 2.6 22.2 + - - +
441A ASP* 2.6 58.1 + - - +
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Residues in contact with VAL 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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417A ARG* 5.0 1.0 - - + +
421A TRP* 4.0 34.3 - - + +
434A THR 2.9 14.3 + - - +
435A ARG* 3.0 28.3 - - + +
437A GLN* 1.3 72.9 + - - +
439A ILE* 1.3 66.3 + - + +
441A ASP* 3.0 25.5 + - + +
442A ALA* 3.2 15.0 + - + +
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Residues in contact with ILE 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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414A ALA* 4.1 9.2 - - + +
417A ARG* 3.8 37.8 - - + +
418A LEU* 3.9 20.9 - - + +
421A TRP* 4.2 26.2 - - + +
435A ARG* 2.9 23.3 - - - +
436A TRP* 3.5 15.5 - - + +
437A GLN 3.2 0.2 - - - -
438A VAL* 1.3 78.8 - - + +
440A THR* 1.3 51.7 + - - +
442A ALA* 3.6 3.5 + - - +
443A SER* 2.7 34.3 + - - +
501A MET* 5.0 7.9 - - + -
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Residues in contact with THR 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 ARG* 5.5 4.7 - - + -
10A VAL* 4.8 17.9 - - + -
436A TRP 2.6 15.4 + - - -
437A GLN* 2.6 19.9 + - - +
439A ILE* 1.3 73.6 - - - +
441A ASP* 1.3 54.1 + - - +
442A ALA 3.1 1.6 - - - -
443A SER* 2.8 10.3 + - - -
444A VAL* 2.7 42.0 + - + +
497A ILE* 5.5 4.7 - - + -
501A MET* 3.3 41.4 - - + +
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Residues in contact with ASP 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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7A ARG* 3.9 21.9 - - - +
437A GLN* 2.6 64.0 + - - +
438A VAL* 3.0 21.4 + - + +
440A THR* 1.3 72.7 - - - +
442A ALA* 1.3 58.9 + - - +
444A VAL* 2.8 29.8 + - - +
445A GLU* 3.0 10.5 + - - +
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Residues in contact with ALA 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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413A ASN* 2.8 20.1 - - - +
417A ARG* 2.9 49.4 - - + +
438A VAL* 3.2 9.4 + - + +
439A ILE 3.9 0.2 - - - -
440A THR 3.1 0.2 - - - -
441A ASP* 1.3 74.7 - - - +
443A SER* 1.3 57.1 + - - +
444A VAL 3.0 5.2 - - - -
445A GLU* 3.4 18.2 + - + +
446A VAL* 3.2 9.7 + - - +
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Residues in contact with SER 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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6A ILE* 4.8 7.1 - - - +
410A MET* 5.3 4.3 - - - -
413A ASN* 4.4 2.0 - - - -
414A ALA* 4.1 22.4 - - - +
417A ARG* 4.9 0.2 - - - +
439A ILE* 2.7 21.7 + - - +
440A THR* 2.8 17.7 + - - -
442A ALA* 1.3 76.8 - - - +
444A VAL* 1.3 57.3 + - - +
446A VAL* 3.0 23.8 - - - +
447A GLY* 3.6 7.6 + - - -
497A ILE* 4.6 19.7 - - - +
501A MET* 4.4 7.4 - - - +
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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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5A ILE 5.2 6.3 - - - +
6A ILE* 3.3 39.5 - - + -
7A ARG* 3.5 31.9 - - + -
440A THR* 2.7 22.7 + - + +
441A ASP* 2.8 13.7 + - - +
443A SER* 1.3 77.9 - - - +
445A GLU* 1.3 53.2 + - + +
446A VAL 3.1 2.0 - - - -
447A GLY* 3.0 1.1 + - - +
448A PRO* 2.7 38.5 - - + +
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Residues in contact with GLU 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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413A ASN* 6.1 0.2 - - - +
417A ARG* 4.6 12.3 - - - +
441A ASP 3.0 13.2 + - - +
442A ALA* 3.4 16.5 + - + +
444A VAL* 1.3 77.4 - - + +
446A VAL* 1.3 56.5 + - - +
447A GLY 3.2 0.8 + - - -
448A PRO* 3.8 12.3 - - - +
946A MET* 4.2 29.4 - - - +
950A HIS* 5.9 3.5 - - - -
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Residues in contact with VAL 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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409A VAL* 3.6 31.2 - - + +
410A MET* 4.7 7.2 - - + +
413A ASN* 3.4 39.2 - - + +
442A ALA 3.2 13.0 - - - +
443A SER* 3.0 28.3 - - - +
445A GLU* 1.3 77.2 - - - +
447A GLY* 1.3 63.2 + - - +
448A PRO* 3.9 0.2 - - - -
449A ALA 4.9 0.8 + - - -
450A LEU* 3.5 18.4 + - + +
943A VAL* 5.8 1.6 - - + -
947A TYR* 4.3 7.9 - - + +
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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