Contacts of the helix formed by residues 370 - 377 (chain J) in PDB entry 6ASX
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 370 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191H ARG* 4.2 25.6 - - - +
195H ARG 5.7 3.1 - - - -
196H THR 5.1 5.6 - - - -
369J PRO* 1.3 74.0 - - - +
371J LYS* 1.3 60.0 + - + +
373J ALA* 3.3 5.8 + - - +
374J LEU* 3.0 30.1 + - - +
409J TRP* 3.9 34.5 - - + +
413J ASP* 5.5 0.2 + - - -
441J LEU* 3.4 40.3 + - + +
442J ILE 2.9 19.3 + - - +
443J GLU* 3.2 43.7 - - - +
444J GLY 5.0 1.0 + - - -
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Residues in contact with LYS 371 (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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1243I MET* 4.2 28.3 - - + -
369J PRO* 3.3 1.7 - - + +
370J LYS* 1.3 79.2 - - + +
372J MET* 1.3 60.8 + - - +
374J LEU* 3.5 5.9 + - - +
375J GLU* 3.0 29.3 + - - +
409J TRP* 5.8 2.9 - - + -
443J GLU* 5.0 13.0 - - - +
444J GLY 4.7 11.9 - - - +
445J LYS* 3.5 26.6 - - - +
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Residues in contact with MET 372 (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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1243I MET* 3.8 30.1 - - + -
1244I HIS 4.0 5.6 - - - +
1245I ALA* 4.4 17.2 - - + +
351J GLY* 4.3 2.5 - - - -
352J ARG 3.9 20.0 - - - +
353J SER* 3.8 19.7 - - - +
368J LEU* 4.3 6.5 - - + -
369J PRO* 3.7 35.4 + - + +
371J LYS* 1.3 73.8 - - - +
373J ALA* 1.3 60.5 + - - +
375J GLU* 3.7 0.7 - - - +
376J LEU* 2.9 37.3 + - + +
447J ILE* 4.4 4.3 - - + -
468J VAL* 3.7 29.6 - - + -
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Residues in contact with ALA 373 (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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368J LEU* 3.7 16.1 - - + +
369J PRO 3.1 18.8 + - - +
370J LYS* 3.6 7.2 - - - +
372J MET* 1.3 77.9 - - - +
374J LEU* 1.3 57.6 + - - +
376J LEU* 4.7 3.6 - - - -
377J PHE* 3.0 39.6 + - + +
412J LEU* 3.9 24.7 - - + -
416J ILE* 4.9 7.0 - - + -
441J LEU* 4.9 6.5 - - + -
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Residues in contact with LEU 374 (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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370J LYS 3.0 16.5 + - - +
371J LYS* 4.0 4.9 - - - +
373J ALA* 1.3 77.7 - - - +
375J GLU* 1.3 69.3 + - - +
377J PHE 4.3 0.9 - - - -
378J LYS* 3.3 28.2 + - - +
381J ILE* 4.5 11.1 - - + +
401J VAL* 4.2 24.2 - - + +
404J GLU* 4.5 15.3 - - + +
408J VAL* 4.7 15.0 - - + -
409J TRP* 3.6 32.5 - - + -
412J LEU* 3.8 17.4 - - + +
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Residues in contact with GLU 375 (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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1245I ALA* 3.8 37.0 - - + +
1246I ARG 4.6 0.2 - - - +
1247I SER* 3.2 30.4 + - - +
1265I PHE* 3.7 21.9 - - + -
371J LYS 3.0 18.5 + - - +
372J MET 4.0 0.2 - - - +
373J ALA 3.2 0.2 - - - -
374J LEU* 1.3 88.2 - - - +
376J LEU* 1.3 58.9 + - - +
378J LYS* 3.7 23.8 + - - +
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Residues in contact with LEU 376 (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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1245I ALA* 4.7 4.7 - - + -
1246I ARG 4.0 5.8 - - - +
1247I SER* 4.5 2.3 - - - -
349J TYR* 3.5 47.8 - - - +
350J SER 3.3 28.5 - - - +
368J LEU* 5.2 9.6 - - + -
372J MET* 2.9 26.0 + - + +
373J ALA* 3.9 5.2 - - - +
375J GLU* 1.3 79.8 - - - +
377J PHE* 1.3 74.6 + - + +
378J LYS 3.4 3.1 + - - -
379J PRO* 4.4 2.3 - - - +
380J PHE* 4.8 0.7 - - - -
421J VAL* 5.8 1.8 - - + -
468J VAL* 4.1 25.1 - - + +
470J VAL* 3.9 16.8 - - + +
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Residues in contact with PHE 377 (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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368J LEU* 6.2 2.5 - - + -
373J ALA* 3.0 24.5 + - + +
374J LEU 3.9 0.4 + - - -
375J GLU 3.5 0.4 - - - -
376J LEU* 1.3 88.1 - - + +
378J LYS* 1.3 57.5 + - - +
379J PRO* 3.5 2.5 - - - -
380J PHE* 3.4 26.2 + + + -
381J ILE* 3.0 40.9 + - + +
412J LEU* 5.2 1.8 - - + -
415J VAL* 4.4 16.4 - - + -
416J ILE* 3.5 32.8 - - + -
419J HIS* 4.0 22.2 - + + -
421J VAL* 4.4 16.8 - - + -
439J PRO* 5.3 0.7 - - + -
470J VAL* 3.6 38.4 - - + -
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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