Contacts of the helix formed by residues 368 - 379 (chain E) in PDB entry 6CAJ
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 GLU 368 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220E SER* 5.2 5.5 - - - -
337E GLY* 3.6 8.1 - - - +
338E CYS* 3.3 52.2 + - + +
362E ASP* 3.5 3.8 + - - +
366E TRP* 3.3 18.7 - - + +
367E LEU* 1.3 73.6 - - - +
369E GLY* 1.3 62.6 + - - +
370E ARG 3.2 2.4 + - - -
371E HIS* 3.5 24.6 + - + +
372E THR 4.2 0.5 + - - -
417E ARG* 2.9 54.3 + - - +
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Residues in contact with GLY 369 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337E GLY* 4.2 7.4 - - - -
360E VAL* 3.8 9.2 - - - +
361E VAL 5.1 0.4 - - - -
362E ASP* 3.2 27.4 + - - -
367E LEU 3.2 0.6 - - - -
368E GLU* 1.3 77.5 - - - +
370E ARG* 1.3 58.8 + - - +
371E HIS 3.2 0.4 - - - -
372E THR* 3.3 14.7 - - - +
373E LEU* 2.9 28.3 + - - +
385E TYR* 4.4 5.4 - - - -
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Residues in contact with ARG 370 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294D VAL 3.2 24.2 + - - -
295D LEU* 3.6 10.1 - - + +
296D PRO* 3.4 22.9 - - - +
299D GLU* 3.5 25.1 + - - +
362E ASP* 3.5 1.6 - - - -
367E LEU* 3.3 50.3 + - - +
368E GLU 3.2 0.6 - - - -
369E GLY* 1.3 78.7 - - - +
371E HIS* 1.3 58.7 + - + +
373E LEU* 3.5 9.1 - - + +
374E ARG* 2.9 51.9 + - - +
385E TYR* 2.7 29.1 + - + +
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Residues in contact with HIS 371 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220E SER* 6.4 2.0 - - - -
338E CYS* 3.8 25.3 - - - +
367E LEU 5.6 0.8 + - - -
368E GLU* 3.5 21.7 + - + +
369E GLY 3.2 0.4 - - - -
370E ARG* 1.3 78.6 - - + +
372E THR* 1.3 57.9 + - - +
374E ARG* 3.3 23.5 + - - +
375E SER* 2.9 26.6 + - - -
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Residues in contact with THR 372 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335E VAL* 4.8 10.6 - - + +
337E GLY 3.5 24.7 - - - +
338E CYS* 4.9 7.3 - - - -
339E SER 5.5 0.4 - - - -
343E SER* 2.9 27.1 + - - -
346E LEU* 5.1 1.6 - - - +
360E VAL* 4.1 15.0 - - + -
368E GLU 4.2 0.8 + - - +
369E GLY 3.3 16.1 - - - +
371E HIS* 1.3 76.4 - - - +
373E LEU* 1.3 59.3 + - - +
375E SER* 3.7 7.3 - - - -
376E LEU* 2.9 41.6 + - - +
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Residues in contact with LEU 373 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295D LEU* 3.9 20.0 - - + -
299D GLU* 4.9 0.2 - - - +
302D ILE* 3.8 22.2 - - + -
306D VAL* 3.8 15.5 - - + -
360E VAL* 4.3 13.2 - - + -
369E GLY 2.9 17.8 + - - +
370E ARG* 3.5 8.3 - - - +
371E HIS 3.2 0.2 - - - -
372E THR* 1.3 76.2 - - - +
374E ARG* 1.3 60.2 + - - +
376E LEU* 3.3 3.6 + - - +
377E VAL* 3.0 36.1 + - + +
383E ALA* 3.7 28.9 - - + -
385E TYR* 3.7 35.9 - - + -
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Residues in contact with ARG 374 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299D GLU* 2.9 41.0 + - - +
302D ILE* 3.7 26.9 - - + +
370E ARG* 2.9 47.2 + - - +
371E HIS* 3.7 19.2 - - - +
373E LEU* 1.3 74.8 - - - +
375E SER* 1.3 58.2 + - - +
377E VAL 3.9 0.2 - - - -
378E HIS* 2.9 53.3 + - + +
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Residues in contact with SER 375 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343E SER* 4.2 14.4 - - - -
347E GLN* 2.5 42.4 + - - +
371E HIS 2.9 18.2 + - - -
372E THR* 3.7 11.7 - - - -
373E LEU 3.3 0.2 - - - -
374E ARG* 1.3 76.8 - - - +
376E LEU* 1.3 59.8 + - - +
378E HIS* 4.2 5.6 - - - +
379E ALA* 3.4 14.2 + - - +
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Residues in contact with LEU 376 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335E VAL* 5.0 0.7 - - + -
343E SER* 5.1 3.1 - - - +
346E LEU* 3.7 37.7 - - + -
347E GLN* 5.0 4.9 - - + +
358E VAL* 3.7 34.1 - - + -
360E VAL* 4.2 11.2 - - + -
372E THR* 2.9 29.8 + - - +
373E LEU 3.9 2.7 - - - +
374E ARG 3.3 0.2 - - - -
375E SER* 1.3 79.1 - - - +
377E VAL* 1.3 62.7 + - - +
379E ALA* 3.5 2.3 + - - -
380E GLY 3.4 2.9 + - - -
381E VAL* 2.9 58.6 + - + +
383E ALA* 4.7 9.9 - - + -
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Residues in contact with VAL 377 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301D ASP* 5.0 2.5 - - - +
302D ILE* 3.7 50.9 - - + +
305D LYS* 4.5 23.1 - - + +
306D VAL* 5.4 0.2 - - + -
373E LEU* 3.0 26.3 + - + +
374E ARG 4.1 0.2 - - - +
376E LEU* 1.3 78.4 - - - +
378E HIS* 1.3 66.3 + - + +
380E GLY* 3.1 13.3 + - - -
381E VAL 4.2 6.1 - - - +
383E ALA* 4.4 17.5 - - + -
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Residues in contact with HIS 378 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301D ASP* 4.6 12.5 + - - -
302D ILE* 4.5 17.5 - - + +
374E ARG* 2.9 36.3 + - + +
375E SER* 4.3 5.9 - - - +
377E VAL* 1.3 78.9 - - + +
379E ALA* 1.3 60.1 + - - +
380E GLY 3.3 0.4 + - - -
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Residues in contact with ALA 379 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347E GLN* 3.8 28.7 - - + +
350E TRP* 3.2 22.2 + - + -
351E THR* 5.5 5.0 - - + +
375E SER 3.4 17.6 + - - +
376E LEU* 3.9 5.8 - - - +
377E VAL 3.2 1.0 - - - -
378E HIS* 1.3 76.9 - - - +
380E GLY* 1.3 58.8 + - - +
381E VAL* 3.4 10.5 - - + -
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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