Contacts of the helix formed by residues 393 - 404 (chain J) in PDB entry 6C6U
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 THR 393 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386J GLU* 4.4 9.1 - - - +
391J ALA* 4.0 8.3 - - - +
392J THR* 1.3 84.7 - - - +
394J ILE* 1.3 74.9 + - - +
395J LYS* 3.4 23.6 + - + +
396J ALA* 3.7 15.2 - - + +
397J ALA* 3.8 13.5 + - - +
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Residues in contact with ILE 394 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1305I TYR* 4.6 10.3 - - + +
1309I VAL* 4.5 14.4 - - + -
382J TYR* 3.6 45.5 - - + -
386J GLU* 4.6 12.6 + - - +
393J THR* 1.3 86.9 + - - +
395J LYS* 1.3 75.1 + - + +
396J ALA 3.4 0.2 - - - -
397J ALA* 3.3 5.5 + - + +
398J LYS* 2.9 31.2 + - - +
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Residues in contact with LYS 395 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393J THR* 3.4 13.2 - - + +
394J ILE* 1.3 88.7 - - + +
396J ALA* 1.3 59.9 + - - +
398J LYS* 3.3 35.1 + - + +
399J LYS* 3.0 44.0 + - - +
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Residues in contact with ALA 396 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391J ALA* 3.9 19.5 - - + -
392J THR* 4.5 4.9 - - - +
393J THR* 3.7 15.0 - - + +
394J ILE 3.4 0.2 - - - -
395J LYS* 1.3 77.4 - - - +
397J ALA* 1.3 58.7 + - - +
399J LYS* 3.4 10.8 + - - +
400J MET* 2.9 34.6 + - + +
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Residues in contact with ALA 397 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382J TYR* 4.0 18.6 - - + +
385J LEU* 3.8 27.4 - - + -
386J GLU* 5.7 1.3 - - + +
391J ALA* 3.5 18.5 - - + +
393J THR 3.8 7.0 + - - +
394J ILE* 3.3 11.8 + - + +
395J LYS 3.3 0.6 - - - -
396J ALA* 1.3 76.1 - - - +
398J LYS* 1.3 60.6 + - - +
400J MET* 3.3 3.0 + - - +
401J VAL* 3.0 34.0 + - - +
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Residues in contact with LYS 398 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1305I TYR* 5.4 3.1 + - - -
378J LYS* 5.4 2.2 - - - +
382J TYR* 3.3 36.5 - - + +
394J ILE* 2.9 22.2 + - - +
395J LYS* 3.3 36.0 + - + +
397J ALA* 1.3 76.1 - - - +
399J LYS* 1.3 60.0 + - + +
401J VAL* 3.4 3.9 - - + +
402J GLU* 2.9 34.4 + - + +
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Residues in contact with LYS 399 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395J LYS* 3.0 32.6 + - - +
396J ALA* 4.0 7.4 - - - +
397J ALA 3.3 0.2 - - - -
398J LYS* 1.3 77.6 - - + +
400J MET* 1.3 61.5 + - - +
402J GLU* 3.8 14.9 - - - +
403J ARG* 3.0 47.8 + - - +
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Residues in contact with MET 400 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385J LEU* 4.3 20.4 - - + -
390J LEU* 3.4 31.4 - - + +
391J ALA* 4.0 10.3 - - - -
396J ALA* 2.9 23.2 + - + +
397J ALA* 3.6 7.0 - - - +
398J LYS 3.3 0.2 - - - -
399J LYS* 1.3 77.9 - - - +
401J VAL* 1.3 57.3 + - + +
403J ARG* 3.3 10.8 + - - +
404J GLU 3.0 22.0 + - - -
405J GLU* 3.6 32.0 + - + +
407J VAL* 4.0 26.7 - - + -
408J VAL* 4.6 6.4 - - + +
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Residues in contact with VAL 401 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374J LEU* 4.0 18.7 - - + +
378J LYS* 3.7 22.7 + - + +
381J ILE* 3.7 30.5 - - + -
382J TYR* 3.6 25.8 - - + +
385J LEU* 4.0 6.5 - - + -
397J ALA 3.0 11.9 + - - +
398J LYS 3.4 9.9 - - - +
400J MET* 1.3 72.9 - - - +
402J GLU* 1.3 64.1 + - + +
404J GLU* 3.7 18.2 - - - +
408J VAL* 4.0 20.0 - - + -
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Residues in contact with GLU 402 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378J LYS* 5.9 1.8 - - - +
398J LYS* 2.9 23.7 + - + +
399J LYS* 3.8 15.9 - - - +
401J VAL* 1.3 78.4 - - - +
403J ARG* 1.3 63.9 + - - +
404J GLU* 3.2 6.5 + - - +
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Residues in contact with ARG 403 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399J LYS* 3.0 42.9 + - - +
400J MET* 3.3 7.9 + - - +
402J GLU* 1.3 77.2 - - - +
404J GLU* 1.3 68.9 + - - +
405J GLU* 2.8 35.4 + - + -
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Residues in contact with GLU 404 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371J LYS* 5.4 8.4 - - - +
374J LEU* 3.9 24.5 - - + +
400J MET 3.0 9.8 + - - -
401J VAL 3.7 16.6 - - - +
402J GLU 3.2 5.8 - - - +
403J ARG* 1.3 82.3 - - - +
405J GLU* 1.3 66.7 + - - +
408J VAL* 4.3 7.2 - - + -
409J TRP* 3.7 33.4 + - + +
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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