Contacts of the helix formed by residues 395 - 406 (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 SER 395 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A SER* 3.2 3.6 + - - -
394A PHE* 1.3 80.7 - - - +
396A LYS* 1.3 64.3 + - - +
397A LYS* 3.3 16.3 + - - +
398A ASP* 3.2 28.1 + - - +
399A CYS* 3.2 22.5 + - - -
482A THR* 4.0 5.5 - - - +
1106A MLI 4.7 2.7 - - - -
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Residues in contact with LYS 396 (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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395A SER* 1.3 72.1 + - - +
397A LYS* 1.3 62.4 + - - +
399A CYS* 3.1 12.4 + - - +
400A GLU* 3.1 19.4 + - - +
456A HIS* 3.8 23.9 - - + +
457A GLY* 3.5 6.7 - - - -
458A GLY 3.5 26.9 - - - +
482A THR* 4.0 4.1 - - - +
916A GLU* 5.8 3.4 - - - -
989A PHE* 3.6 31.9 - - + -
992A SER* 4.4 11.4 - - - -
995A ARG* 4.2 6.7 - - - +
1106A MLI 2.9 47.9 + - - +
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Residues in contact with LYS 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A SER* 3.2 9.6 + - - +
396A LYS* 1.3 78.6 - - - +
398A ASP* 1.3 68.5 + - - +
400A GLU* 3.2 8.1 + - - +
401A ALA* 2.9 28.2 + - + +
989A PHE* 4.9 8.4 - - + -
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Residues in contact with ASP 398 (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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393A SER* 3.9 11.1 - - - -
394A PHE 5.3 1.0 + - - -
395A SER* 3.2 26.7 + - - +
397A LYS* 1.3 80.2 - - - +
399A CYS* 1.3 63.8 + - - +
401A ALA* 4.4 5.3 - - - +
402A TYR* 2.9 60.3 + - + -
499A THR* 5.5 0.7 + - - -
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Residues in contact with CYS 399 (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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393A SER* 4.1 10.5 - - - -
395A SER 3.2 17.5 + - - -
396A LYS 3.1 10.3 + - - +
398A ASP* 1.3 76.3 - - - +
400A GLU* 1.3 56.3 + - - +
402A TYR* 4.9 2.2 - - - -
403A ALA* 3.0 31.0 + - - +
454A ILE* 4.3 3.6 - - + -
455A HIS 4.7 1.8 - - - -
456A HIS* 4.1 10.8 - - + -
480A PHE* 3.7 26.6 - - - +
481A ALA* 3.5 36.1 - - - -
482A THR* 3.8 11.4 - - - -
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Residues in contact with GLU 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A LYS 3.1 18.0 + - - +
397A LYS* 3.2 6.8 + - - +
399A CYS* 1.3 72.8 - - - +
401A ALA* 1.3 66.1 + - - +
403A ALA* 3.5 1.9 + - - +
404A LEU* 3.1 35.2 + - + +
440A GLN* 5.0 4.5 + - - +
443A HIS* 5.4 7.9 + - + -
454A ILE* 4.0 19.9 - - + +
456A HIS* 3.3 27.7 + - + +
459A LEU* 4.2 9.7 - - - +
989A PHE* 3.3 24.3 - - - -
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Residues in contact with ALA 401 (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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371A PRO* 6.4 1.1 - - + -
397A LYS* 2.9 22.6 + - + +
398A ASP* 3.8 6.1 - - - +
400A GLU* 1.3 77.4 - - - +
402A TYR* 1.3 68.7 + - + +
404A LEU* 3.1 18.2 + - - +
405A GLN* 3.2 24.4 + - - +
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Residues in contact with TYR 402 (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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370A GLY 3.5 18.7 + - - -
371A PRO* 3.8 21.2 - - + +
374A VAL* 3.6 30.0 - - + +
393A SER* 3.6 24.2 - - - -
398A ASP* 2.9 47.9 + - + +
401A ALA* 1.3 74.5 - - + +
403A ALA* 1.3 64.8 + - - +
405A GLN* 3.0 32.3 + - - +
406A MET* 3.4 13.2 - - - +
480A PHE* 3.6 24.0 - + + -
499A THR* 3.9 24.3 + - + -
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Residues in contact with ALA 403 (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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399A CYS 3.0 20.0 + - - +
400A GLU 3.8 1.1 - - - +
402A TYR* 1.3 75.3 - - - +
404A LEU* 1.3 62.0 + - - +
406A MET* 3.1 19.4 + - - +
407A THR 4.1 1.9 + - - -
447A LEU* 4.3 7.6 - - + +
452A ILE* 3.9 14.6 - - + +
454A ILE* 3.5 33.2 - - + -
480A PHE* 3.8 22.4 - - + -
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Residues in contact with LEU 404 (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* 3.1 25.2 + - + +
401A ALA* 3.1 8.1 + - - +
403A ALA* 1.3 75.4 - - - +
405A GLN* 1.3 62.4 + - + +
406A MET 3.1 0.2 - - - -
407A THR* 3.2 30.2 + - + +
443A HIS* 3.7 36.8 - - + +
447A LEU* 4.6 15.7 - - + -
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Residues in contact with GLN 405 (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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371A PRO* 2.8 55.9 + - - +
372A SER* 4.7 0.8 - - - +
374A VAL* 4.5 0.6 - - - +
375A PHE* 3.1 34.5 - - + +
401A ALA* 3.2 19.4 + - - +
402A TYR* 3.0 26.5 + - - +
404A LEU* 1.3 77.4 - - - +
406A MET* 1.3 62.6 + - + +
407A THR* 3.3 3.8 + - - +
408A LYS* 4.1 12.4 - - - +
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Residues in contact with MET 406 (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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374A VAL* 3.8 20.2 - - + -
375A PHE* 3.6 42.8 - - + -
378A VAL* 3.7 25.8 - - + -
402A TYR 3.4 22.4 - - - +
403A ALA 3.1 5.9 + - - +
405A GLN* 1.3 78.4 - - + +
407A THR* 1.3 58.7 + - - +
408A LYS 3.1 3.6 - - - -
409A LEU* 2.9 28.3 + - + +
411A PHE* 4.6 6.3 - - + -
452A ILE* 3.2 31.9 - - + +
478A ALA* 5.8 0.2 - - + -
480A PHE* 3.5 25.4 - - + -
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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