Contacts of the helix formed by residues 367 - 382 (chain A) in PDB entry 2E8A
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 367 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ASP* 6.1 0.2 - - - -
17A CYS* 4.0 17.7 - - - -
28A ILE* 3.6 19.1 - - + +
36A ARG* 2.7 56.8 + - - +
37A THR* 4.6 4.0 - - + -
342A ARG* 5.0 1.6 + - - -
363A ILE* 4.4 5.8 - - + +
364A ASN* 2.9 36.4 + - + +
366A ASP* 1.3 88.6 - - - +
368A ALA* 1.3 61.9 + - - +
369A VAL 3.3 2.5 - - - -
370A ALA* 3.3 5.2 + - - +
371A TYR* 2.9 29.5 + - - +
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Residues in contact with ALA 368 (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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178A ALA 4.1 1.7 - - - +
179A ALA* 4.5 8.5 - - + -
182A ALA* 3.4 11.8 - - + +
183A TYR* 4.7 12.6 - - + -
336A LEU 4.4 13.5 - - - +
337A VAL* 4.4 11.9 - - + -
363A ILE* 3.9 17.3 - - + +
364A ASN 3.1 8.6 + - - +
365A PRO* 3.5 12.5 + - + +
367A GLU* 1.3 77.9 - - - +
369A VAL* 1.3 61.3 + - - +
371A TYR* 3.4 1.7 + - - -
372A GLY* 3.1 19.1 + - - -
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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
----------------------------------------------------------
10A ASP* 3.8 23.5 + - + +
145A THR* 3.1 39.0 - - + +
175A GLU* 3.7 32.8 - - + +
178A ALA* 3.5 10.2 - - + +
179A ALA* 4.5 4.0 - - + +
199A ASP* 4.7 1.1 - - - +
337A VAL* 3.8 26.2 - - + +
365A PRO 4.9 1.0 + - - -
366A ASP 5.4 0.8 - - - -
367A GLU 3.3 1.0 - - - -
368A ALA* 1.3 76.2 - - - +
370A ALA* 1.3 65.2 + - - +
372A GLY 3.3 1.6 + - - -
373A ALA* 2.9 21.1 + - - +
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Residues in contact with ALA 370 (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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8A GLY 4.1 8.1 - - - +
10A ASP* 3.8 8.7 - - + +
17A CYS* 3.4 53.6 - - + +
18A VAL 4.1 1.3 - - - +
19A GLY 4.2 4.2 + - - +
28A ILE* 4.4 3.4 - - + -
367A GLU 3.3 3.3 + - - +
369A VAL* 1.3 78.4 - - - +
371A TYR* 1.3 64.5 + - - +
373A ALA* 3.3 8.2 + - - +
374A ALA* 2.9 25.3 + - - +
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Residues in contact with TYR 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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26A VAL* 3.7 45.9 + - + +
28A ILE* 4.0 17.9 - - + +
182A ALA* 3.6 31.2 + - + -
363A ILE* 3.9 32.0 - - + +
367A GLU 2.9 17.7 + - - +
368A ALA* 3.4 9.0 - - - +
369A VAL 3.2 0.2 - - - -
370A ALA* 1.3 75.9 - - - +
372A GLY* 1.3 61.8 + - - +
374A ALA* 3.1 6.2 + - - +
375A VAL* 3.1 26.2 + - + +
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Residues in contact with GLY 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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178A ALA* 3.2 29.2 - - - -
181A ILE* 3.9 8.0 - - - +
182A ALA* 3.6 14.3 - - - +
368A ALA 3.1 11.3 + - - -
369A VAL 3.8 0.4 - - - -
371A TYR* 1.3 72.5 - - - +
373A ALA* 1.3 60.8 + - - +
375A VAL* 3.1 4.1 + - - +
376A GLN* 2.8 30.9 + - - +
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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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8A GLY* 3.6 16.6 - - - -
9A ILE 3.9 8.5 - - - +
143A VAL* 3.7 16.7 - - + +
145A THR* 3.9 20.2 - - + -
173A ILE* 4.9 0.7 - - - -
178A ALA* 4.0 4.9 - - - +
369A VAL 2.9 17.5 + - - +
370A ALA* 3.5 6.7 - - - +
372A GLY* 1.3 75.8 - - - +
374A ALA* 1.3 57.9 + - - +
376A GLN* 3.3 4.7 + - - +
377A ALA* 2.8 29.3 + - - +
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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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6A ALA 5.1 1.4 - - - +
7A ILE 4.6 0.2 - - - -
8A GLY* 3.5 9.8 - - - +
19A GLY* 3.6 30.5 - - - +
20A VAL* 3.8 12.1 - - - +
21A PHE* 4.1 5.1 + - - +
26A VAL* 4.3 7.9 - - + -
370A ALA 2.9 13.4 + - - +
371A TYR 3.4 9.4 - - - +
373A ALA* 1.3 73.1 - - - +
375A VAL* 1.3 66.9 + - - +
377A ALA* 3.3 3.1 + - - +
378A ALA* 3.0 24.6 + - - +
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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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21A PHE* 5.0 8.3 - - + -
26A VAL* 3.6 20.9 - - + -
181A ILE* 3.8 25.8 - - + +
182A ALA 5.6 0.2 - - - +
371A TYR* 3.1 27.1 + - + +
372A GLY* 3.5 7.6 - - - +
374A ALA* 1.3 76.6 - - - +
376A GLN* 1.3 63.6 + - - +
378A ALA* 3.2 7.8 + - - +
379A ILE* 3.0 33.7 + - + +
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Residues in contact with GLN 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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143A VAL* 4.3 8.5 - - + -
171A ARG* 4.0 13.7 + - - +
173A ILE* 4.5 19.0 - - + +
181A ILE* 3.4 28.5 - - + +
372A GLY 2.8 16.3 + - - +
373A ALA* 3.6 8.1 - - - +
375A VAL* 1.3 77.7 - - - +
377A ALA* 1.3 57.1 + - - +
379A ILE* 3.3 15.3 + - - +
380A LEU* 2.9 67.1 + - + +
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Residues in contact with ALA 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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6A ALA* 3.8 17.0 - - + -
7A ILE 3.6 24.9 - - - +
143A VAL* 3.5 17.9 - - + +
170A LEU* 4.0 3.3 - - + +
373A ALA 2.8 17.9 + - - +
374A ALA 3.6 5.2 - - - +
375A VAL 3.2 0.2 - - - -
376A GLN* 1.3 78.4 - - - +
378A ALA* 1.3 62.6 + - - +
380A LEU* 3.4 3.2 + - - +
381A MET* 3.0 28.5 + - - +
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Residues in contact with ALA 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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6A ALA* 5.3 4.9 + - - +
21A PHE* 3.7 35.2 - - + +
374A ALA 3.0 16.6 + - - +
375A VAL 3.6 4.9 - - - +
377A ALA* 1.3 72.2 - - - +
379A ILE* 1.3 68.1 + - + +
381A MET* 3.2 17.6 + - - +
382A GLY 3.4 13.2 + - - +
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Residues in contact with ILE 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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375A VAL* 3.0 31.1 + - + +
376A GLN* 3.4 23.6 - - - +
378A ALA* 1.3 76.0 - - + +
380A LEU* 1.3 63.3 + - + +
382A GLY* 2.8 22.9 + - - -
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Residues in contact with LEU 380 (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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143A VAL* 3.9 22.4 - - + -
170A LEU* 4.1 21.0 - - + +
171A ARG* 3.5 46.2 - - + +
376A GLN* 2.9 47.5 + - + +
377A ALA 3.7 5.2 - - - +
379A ILE* 1.3 82.0 - - + +
381A MET* 1.3 62.1 + - - +
382A GLY* 3.1 1.9 + - - -
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Residues in contact with MET 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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3A LYS* 4.8 10.8 - - + +
4A ALA 3.8 20.4 - - - +
5A ALA* 5.8 0.2 - - - -
6A ALA* 3.5 18.4 - - + +
141A ASN* 3.4 35.2 - - + +
170A LEU* 4.0 16.8 - - + -
377A ALA 3.0 19.3 + - - +
378A ALA* 3.6 11.0 - - - +
379A ILE 3.2 0.8 - - - -
380A LEU* 1.3 75.7 - - - +
382A GLY* 1.3 65.1 + - - +
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Residues in contact with GLY 382 (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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378A ALA 3.4 9.6 + - - +
379A ILE* 2.8 17.2 + - - -
380A LEU 3.1 2.0 - - - -
381A MET* 1.3 85.7 - - - +
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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