Contacts of the helix formed by residues 368 - 381 (chain A) in PDB entry 3EWS
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 MET 368 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A GLU 4.3 0.2 - - - +
367A MET* 1.3 76.7 - - - +
369A VAL* 1.3 65.3 + - - +
370A GLU* 4.0 18.6 - - + +
371A GLN* 2.8 27.8 + - + +
372A ARG* 3.1 8.3 + - - +
172B TYR* 4.2 29.8 - - - -
176B LEU* 5.2 4.9 - - + -
196B TYR* 3.6 35.9 - - + +
198B VAL* 4.4 6.5 - - + -
200B GLY 5.0 4.0 - - - +
201B ASN* 3.6 41.3 - - + +
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Residues in contact with VAL 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ALA* 4.2 21.8 - - + +
61A LEU* 4.2 15.7 - - + -
62A LEU* 3.6 43.5 - - + +
65A LEU* 3.7 10.5 - - + -
367A MET 3.7 1.0 + - - -
368A MET* 1.3 72.8 - - - +
370A GLU* 1.3 67.2 + - - +
372A ARG* 3.2 22.6 + - - +
373A ALA* 2.9 26.0 + - - +
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Residues in contact with GLU 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 4.9 5.1 - - - +
65A LEU* 4.2 15.0 - - + +
173A GLU* 6.1 2.0 - - - +
368A MET* 4.0 15.9 - - + +
369A VAL* 1.3 93.4 + - - +
371A GLN* 1.3 58.9 - - + +
373A ALA* 3.3 9.4 + - - +
374A ALA* 3.0 26.3 + - - +
172B TYR* 4.7 10.4 + - - -
176B LEU* 4.8 12.6 - - - +
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Residues in contact with GLN 371 (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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366A GLU 4.6 0.9 - - - +
367A MET* 3.5 23.1 - - + -
368A MET* 2.8 41.8 + - + +
370A GLU* 1.3 77.2 - - + +
372A ARG* 1.3 66.3 + - - +
373A ALA 3.1 0.4 - - - -
374A ALA* 3.2 8.0 + - - +
375A VAL* 3.0 26.3 + - - +
183B GLU* 4.2 11.1 + - - +
194B LEU* 2.8 36.9 + - - +
196B TYR* 3.5 30.2 + - + -
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Residues in contact with ARG 372 (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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58A ALA* 4.8 13.9 + - - +
62A LEU* 4.0 24.7 - - + +
343A ARG* 5.5 0.2 - - - +
363A LEU* 3.6 25.7 - - + +
364A SER 4.0 6.9 + - - +
365A GLY* 3.4 20.8 + - - -
367A MET* 3.0 36.4 + - + -
368A MET 3.1 8.5 + - - +
369A VAL* 3.5 25.6 - - - +
371A GLN* 1.3 76.8 - - - +
373A ALA* 1.3 57.6 + - - +
375A VAL* 3.8 1.2 - - - +
376A ILE* 3.0 35.2 + - - +
393A CYS* 4.1 31.0 + - - +
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Residues in contact with ALA 373 (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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62A LEU* 3.7 18.1 - - + +
65A LEU* 3.9 17.3 - - + +
66A ILE* 3.9 13.8 - - + +
369A VAL 2.9 13.0 + - - +
370A GLU* 3.4 12.3 - - - +
371A GLN 3.1 0.2 - - - -
372A ARG* 1.3 77.9 - - - +
374A ALA* 1.3 58.7 + - - +
376A ILE* 3.4 2.4 + - - +
377A GLU* 2.9 40.2 + - - +
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Residues in contact with ALA 374 (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 GLU 3.0 14.3 + - - +
371A GLN* 3.2 9.8 + - - +
373A ALA* 1.3 73.2 - - - +
375A VAL* 1.3 65.6 + - + +
377A GLU* 3.4 7.4 + - - +
378A ARG* 3.0 31.3 + - + +
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Residues in contact with VAL 375 (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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361A ALA* 3.8 15.7 - - + -
362A LEU 4.2 6.7 - - - +
363A LEU* 4.1 14.4 - - + -
367A MET* 3.6 20.0 - - + -
371A GLN 3.0 19.8 + - - +
372A ARG 3.8 4.3 - - - +
374A ALA* 1.3 75.7 - - + +
376A ILE* 1.3 64.1 + - - +
378A ARG* 3.0 15.1 + - - +
379A PHE* 2.9 20.8 + - - +
384A GLU* 5.2 0.7 - - + +
387A LEU* 3.6 28.5 - - + -
193B LYS* 5.8 8.3 - - - -
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Residues in contact with ILE 376 (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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62A LEU* 4.0 30.3 - - + -
66A ILE* 4.0 18.8 - - + -
363A LEU* 4.2 22.4 - - + -
372A ARG 3.0 23.2 + - - +
373A ALA 3.7 3.1 - - - +
375A VAL* 1.3 77.8 - - - +
377A GLU* 1.3 57.8 + - - +
379A PHE* 3.2 10.1 + - - +
380A ARG* 3.0 45.1 + - - +
387A LEU* 4.6 5.2 - - + -
397A ILE* 4.0 18.4 - - + -
399A VAL* 4.0 20.2 - - + -
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Residues in contact with GLU 377 (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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65A LEU 4.1 18.4 - - - +
66A ILE* 4.1 13.6 - - + +
373A ALA* 2.9 29.3 + - - +
374A ALA* 3.9 7.0 - - - +
375A VAL 3.2 0.4 - - - -
376A ILE* 1.3 73.9 - - - +
378A ARG* 1.3 65.9 + - - +
380A ARG* 3.2 17.8 + - + +
381A GLU* 3.1 41.0 + - + +
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Residues in contact with ARG 378 (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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359A GLN* 4.8 6.1 + - - -
361A ALA* 5.2 2.6 - - - +
374A ALA* 3.0 19.5 + - + +
375A VAL* 3.0 15.1 + - - +
377A GLU* 1.3 75.7 - - + +
379A PHE* 1.3 63.1 + - - +
381A GLU* 3.3 8.6 + - - +
382A GLY 3.3 3.1 + - - -
383A LYS* 3.0 70.9 + - + +
384A GLU* 3.0 38.7 + - + +
190B PRO* 4.8 11.8 + - - +
193B LYS* 4.9 9.9 - - - +
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Residues in contact with PHE 379 (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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335A GLN* 3.6 19.7 - - - +
336A ALA 3.5 23.3 - - - -
337A MET* 4.3 2.7 - - + -
375A VAL 2.9 11.7 + - - +
376A ILE 3.3 9.2 - - - +
377A GLU 3.2 0.2 - - - -
378A ARG* 1.3 78.0 - - - +
380A ARG* 1.3 63.1 + - - +
382A GLY* 3.3 8.8 + - - -
384A GLU* 3.6 30.9 - - + +
385A LYS 3.7 16.6 - - - -
387A LEU* 3.8 31.9 - - + -
399A VAL* 3.9 18.6 - - + -
400A GLU 3.5 11.4 - - - -
401A GLN* 3.3 29.7 - - - +
402A VAL* 3.7 14.6 - - + -
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Residues in contact with ARG 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ILE* 2.8 52.2 + - - +
67A ARG* 4.9 1.0 - - - +
68A SER* 4.3 12.5 + - - +
376A ILE* 3.0 23.0 + - + +
377A GLU* 3.6 17.9 - - + +
378A ARG 3.2 0.2 - - - -
379A PHE* 1.3 75.4 - - + +
381A GLU* 1.3 57.7 + - + +
382A GLY* 3.0 8.8 + - - -
398A ASP 2.8 29.9 + - - -
399A VAL* 4.0 0.8 - - - +
400A GLU* 3.5 44.9 - - - +
401A GLN* 4.0 27.1 - - + +
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Residues in contact with GLU 381 (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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377A GLU* 3.1 30.9 + - - +
378A ARG* 3.3 9.7 + - - +
380A ARG* 1.3 76.5 - - + +
382A GLY* 1.3 58.4 + - - +
383A LYS* 3.2 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