Contacts of the helix formed by residues 368 - 381 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A TYR* 3.2 38.6 - - + +
196A TYR* 4.0 16.6 - - + +
198A VAL* 3.7 16.8 - - + -
200A GLY* 4.2 7.6 - - - +
201A ASN* 3.6 40.2 - - - +
202A LYS* 6.5 0.4 - - - -
366B GLU 4.7 1.6 - - - +
367B MET* 1.3 74.8 - - - +
369B VAL* 1.3 60.9 + - - +
370B GLU* 3.3 15.3 - - + +
371B GLN* 2.9 29.1 + - + +
372B ARG* 2.8 26.6 + - - +
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Residues in contact with VAL 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ALA* 4.9 3.1 - - + +
61B LEU* 4.1 24.0 - - + -
62B LEU* 3.8 32.4 - - + +
65B LEU* 3.8 19.1 - - + -
367B MET 4.0 0.2 + - - -
368B MET* 1.3 74.0 - - - +
370B GLU* 1.3 80.7 + - - +
372B ARG* 3.2 13.8 + - - +
373B ALA* 2.8 27.2 + - - +
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Residues in contact with GLU 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A TYR* 3.5 23.2 + - - +
176A LEU* 5.4 12.3 - - + -
196A TYR* 6.5 0.7 - - + -
65B LEU* 4.5 10.4 - - + +
368B MET* 3.8 10.9 - - + +
369B VAL* 1.3 95.4 - - - +
371B GLN* 1.3 62.6 + - + +
373B ALA* 3.3 8.4 + - - +
374B ALA* 3.0 28.6 + - - +
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Residues in contact with GLN 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A GLU* 5.0 6.5 + - - +
194A LEU* 2.9 35.6 + - - +
195A ALA* 5.1 0.2 - - - -
196A TYR* 3.6 30.4 + - + -
366B GLU 4.5 1.7 - - - +
367B MET* 3.5 27.0 - - + +
368B MET* 2.9 44.1 + - + +
370B GLU* 1.3 80.1 - - + +
372B ARG* 1.3 64.3 + - - +
374B ALA* 3.4 7.6 + - - +
375B VAL* 3.2 18.9 + - - +
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Residues in contact with ARG 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A LYS* 4.3 20.7 - - - +
62B LEU* 4.2 24.7 - - + +
363B LEU* 3.9 17.6 - - + +
364B SER 4.1 4.1 + - - +
365B GLY* 3.4 29.9 + - - -
367B MET* 2.9 33.9 + - + +
368B MET 2.8 16.3 + - - +
369B VAL* 3.4 13.4 - - - +
371B GLN* 1.3 75.7 - - - +
373B ALA* 1.3 62.8 + - - +
375B VAL* 3.2 3.8 + - - +
376B ILE* 3.0 27.8 + - - +
392B VAL 5.2 0.8 + - - -
393B CYS* 3.6 34.6 + - - +
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Residues in contact with ALA 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B LEU* 3.8 12.5 - - + +
65B LEU* 4.0 15.9 - - + -
66B ILE* 3.9 19.2 - - + +
369B VAL 2.8 16.5 + - - +
370B GLU* 3.5 11.2 - - - +
372B ARG* 1.3 72.4 - - - +
374B ALA* 1.3 56.9 + - - +
376B ILE* 3.3 2.8 + - - +
377B GLU* 2.8 45.9 + - - +
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Residues in contact with ALA 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B GLU 3.0 16.5 + - - +
371B GLN* 3.7 8.1 - - - +
372B ARG 3.3 0.4 - - - -
373B ALA* 1.3 77.0 - - - +
375B VAL* 1.3 58.8 + - + +
377B GLU* 3.4 15.6 + - - +
378B ARG* 3.0 36.9 + - + +
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Residues in contact with VAL 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A LYS* 5.7 9.9 - - - -
361B ALA* 4.1 21.3 - - + -
362B LEU 3.9 13.0 - - - +
363B LEU* 3.9 19.3 - - + -
367B MET* 3.5 25.1 - - + -
371B GLN 3.2 4.0 + - - +
372B ARG 3.2 7.9 + - - +
374B ALA* 1.3 75.4 - - + +
376B ILE* 1.3 66.9 + - - +
378B ARG* 3.5 10.0 + - - +
379B PHE* 3.1 22.7 + - - +
384B GLU* 5.1 1.0 - - - +
387B LEU* 5.0 6.5 - - + -
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Residues in contact with ILE 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B LEU* 3.9 31.4 - - + -
66B ILE* 4.1 20.6 - - + -
363B LEU* 4.1 25.8 - - + -
372B ARG 3.0 19.6 + - - +
373B ALA 3.6 6.1 - - - +
375B VAL* 1.3 77.3 - - - +
377B GLU* 1.3 61.6 + - - +
379B PHE* 3.5 7.5 + - - +
380B ARG* 3.2 41.1 + - - +
387B LEU* 4.7 6.3 - - + -
397B ILE* 4.2 15.0 - - + -
399B VAL* 4.4 19.1 - - + -
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Residues in contact with GLU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B LEU 4.2 10.0 - - - +
66B ILE* 5.1 11.4 - - + +
373B ALA* 2.8 39.8 + - - +
374B ALA* 3.5 14.3 + - - +
376B ILE* 1.3 73.2 - - - +
378B ARG* 1.3 67.7 + - + +
380B ARG* 2.8 24.4 + - - +
381B GLU* 2.9 24.6 + - - +
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Residues in contact with ARG 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B ALA* 3.0 20.3 + - + +
375B VAL* 3.9 9.2 - - - +
377B GLU* 1.3 77.8 - - + +
379B PHE* 1.3 62.9 + - - +
381B GLU* 3.1 20.9 + - + +
383B LYS* 3.2 49.2 + - + +
384B GLU* 2.6 35.4 + - + +
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Residues in contact with PHE 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B GLN* 3.8 30.3 - - + +
336B ALA 3.9 7.4 - - - -
337B MET* 4.3 9.6 - - + -
361B ALA* 5.5 0.4 - - + -
375B VAL 3.1 16.9 + - - +
376B ILE 3.6 7.0 - - - +
377B GLU 3.1 0.6 - - - -
378B ARG* 1.3 77.6 - - - +
380B ARG* 1.3 65.6 + - + +
382B GLY* 3.1 10.7 + - - -
384B GLU* 3.4 40.1 - - + +
385B LYS 3.5 21.8 - - - -
387B LEU* 3.7 38.1 - - + -
399B VAL* 4.3 11.0 - - + -
400B GLU 4.2 9.2 - - - -
401B GLN* 4.2 4.0 - - + -
402B VAL* 4.0 19.5 - - + -
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Residues in contact with ARG 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ILE* 2.8 50.7 + - - +
67B ARG* 5.0 0.4 - - - +
68B SER* 4.4 10.5 + - - +
376B ILE* 3.2 20.3 + - + +
377B GLU* 2.8 17.5 + - - +
379B PHE* 1.3 74.8 - - + +
381B GLU* 1.3 60.6 + - - +
382B GLY* 2.9 7.1 + - - -
398B ASP 2.8 28.9 + - - -
399B VAL* 3.7 1.2 - - - +
400B GLU* 3.7 51.3 + - - +
401B GLN* 5.0 15.9 - - + +
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Residues in contact with GLU 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B GLU* 2.9 25.3 + - + +
378B ARG* 3.1 19.3 + - + +
380B ARG* 1.3 76.2 - - - +
382B GLY* 1.3 56.1 + - - +
383B LYS* 3.2 21.3 + - + +
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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