Contacts of the helix formed by residues 367 - 377 (chain B) in PDB entry 1EWV
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 TRP 367 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B SER* 2.8 44.2 - - - -
38B VAL* 4.3 0.2 - - - -
39B ALA* 4.0 20.9 - - + -
53B VAL* 3.8 30.5 - - + -
54B HIS* 4.5 15.0 + + - -
70B ILE* 4.1 3.8 - - + -
76B ILE* 3.9 14.8 - - + -
79B VAL* 4.1 17.9 - - + -
105B ILE* 4.0 18.6 - - + -
106B ARG 4.5 0.2 - - - -
107B ASP* 4.1 28.5 + - + -
365B ASN* 2.9 10.1 + - - +
366B PRO* 1.3 81.5 - - + +
368B PHE* 1.3 56.3 + - - +
369B PRO* 3.1 3.1 - - - -
370B GLU* 2.7 26.1 + - - +
371B PHE* 2.6 33.0 + - - -
385B LEU* 5.1 1.6 - - + -
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Residues in contact with PHE 368 (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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76B ILE* 4.0 13.5 - - + -
80B GLU* 3.2 31.6 - - + -
354B PHE* 4.9 0.2 - + - -
357B LEU* 3.4 44.4 - - + -
358B ARG 4.8 7.0 - - - -
359B LEU* 4.9 14.1 - - + -
362B ASN* 3.8 26.2 - - + +
365B ASN* 3.0 30.4 + - - +
367B TRP* 1.3 74.1 - - - +
369B PRO* 1.3 62.7 - - + +
371B PHE* 3.8 22.9 - + - -
372B TRP* 2.6 49.2 + + - +
400B LEU* 5.9 1.1 - - + -
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Residues in contact with PRO 369 (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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359B LEU* 4.4 19.5 - - + -
362B ASN 5.5 2.2 - - - +
365B ASN 4.3 1.8 - - - +
366B PRO* 3.2 20.4 - - + +
367B TRP 3.3 0.4 - - - -
368B PHE* 1.3 95.8 - - + +
370B GLU* 1.3 64.6 + - - +
372B TRP* 3.4 7.0 + - + +
373B GLN* 3.6 20.0 + - - +
380B LEU* 4.5 7.9 - - + +
383B HIS* 4.0 23.1 - - + -
385B LEU* 3.4 19.1 - - + -
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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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54B HIS* 2.8 38.8 + - - -
68B GLY 5.0 2.3 - - - +
70B ILE* 3.8 19.0 + - + +
367B TRP* 2.7 23.7 + - - +
369B PRO* 1.3 78.4 - - - +
371B PHE* 1.3 65.2 + - - +
372B TRP 3.4 0.2 + - - -
373B GLN* 3.7 6.1 + - - +
374B HIS* 3.6 15.2 + - - +
385B LEU* 3.4 34.4 - - + +
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Residues in contact with PHE 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE* 3.3 30.2 - - + +
72B GLU* 3.0 46.9 - - + -
76B ILE* 3.5 39.5 - - + -
354B PHE* 4.3 12.3 - + - -
367B TRP 2.6 15.3 + - - +
368B PHE* 3.4 27.8 - + - +
370B GLU* 1.3 71.9 - - - +
372B TRP* 1.3 71.7 + + - +
374B HIS* 3.1 7.1 + - + +
375B ARG* 3.0 42.7 + - + +
400B LEU* 4.7 6.5 - - + -
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Residues in contact with TRP 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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357B LEU 4.5 11.4 - - - -
358B ARG* 5.8 0.7 - - - -
359B LEU* 3.8 45.3 - - + +
368B PHE* 2.6 35.1 + + + +
369B PRO* 3.7 5.8 - - + +
371B PHE* 1.3 81.2 - + - +
373B GLN* 1.3 67.1 + - + +
375B ARG* 3.0 9.5 + - + +
376B PHE* 2.9 62.8 + + - +
378B CYS* 4.6 13.7 - - - -
380B LEU* 5.2 2.2 - - + -
394B CYS* 4.7 7.4 - - + +
396B GLY* 4.8 10.0 - - - -
398B GLU* 3.6 31.8 + - - -
400B LEU* 3.8 31.9 - - + -
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Residues in contact with GLN 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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369B PRO 3.6 11.3 + - - +
370B GLU* 4.0 6.6 - - - +
371B PHE 3.4 1.0 - - - -
372B TRP* 1.3 78.6 - - + +
374B HIS* 1.3 55.7 + - - +
376B PHE 3.0 0.3 + - - -
377B GLN* 2.2 40.7 + - - -
378B CYS* 2.7 41.2 - - - +
379B ARG* 3.2 13.5 - - - -
380B LEU* 3.4 26.6 - - + +
385B LEU* 2.8 29.9 + - - +
386B GLU* 4.0 3.2 - - - +
387B ASN* 3.0 26.9 + - + +
390B PHE* 4.5 4.9 - - + -
394B CYS* 4.6 0.2 - - - -
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Residues in contact with HIS 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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69B GLU* 3.6 27.0 + - + +
70B ILE* 3.2 42.9 + - + +
73B GLN* 5.9 3.4 - - - -
370B GLU 3.6 6.0 + - - +
371B PHE* 3.1 10.7 + + + +
373B GLN* 1.3 79.4 - - - +
375B ARG* 1.3 66.3 + - - +
376B PHE 3.1 0.2 + - - -
377B GLN* 3.4 16.4 + - + +
390B PHE* 4.8 9.9 - + - -
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Residues in contact with ARG 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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72B GLU* 3.2 35.1 + - - +
354B PHE* 5.3 0.2 - - - -
371B PHE* 3.0 35.1 + - + +
372B TRP* 3.5 10.8 - - + +
374B HIS* 1.3 79.3 - - - +
376B PHE* 1.4 81.7 + - + +
377B GLN* 5.0 3.5 + - - +
400B LEU* 2.7 58.4 + - - +
402B GLU* 3.2 23.5 + - - +
403B ASN* 4.7 1.0 + - - +
404B TYR* 4.0 12.7 - - - +
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Residues in contact with PHE 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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372B TRP* 2.9 51.2 + + - +
373B GLN 3.2 0.7 - - - +
375B ARG* 1.4 101.0 - - + +
377B GLN* 1.4 75.9 + - - +
378B CYS* 3.4 10.0 + - + +
392B LYS* 4.1 15.8 + - - -
398B GLU* 3.1 43.5 - - + +
399B SER 3.4 25.6 - - - -
400B LEU* 3.9 7.4 - - + -
402B GLU* 2.8 33.4 - - + -
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Residues in contact with GLN 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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373B GLN 2.2 22.8 + - - -
374B HIS* 3.6 15.5 + - + +
375B ARG 5.0 2.6 + - - -
376B PHE* 1.4 74.0 - - - +
378B CYS* 1.4 56.0 + - - +
390B PHE* 3.7 47.2 - - + +
392B LYS* 3.9 15.9 - - - +
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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