Contacts of the helix formed by residues 366 - 372 (chain A) in PDB entry 1EQB
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 THR 366 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291A VAL* 2.7 34.7 + - - +
294A ASN* 3.8 9.2 - - + -
295A ALA* 3.4 31.8 - - + +
298A MET* 4.0 20.4 - - - -
317A HIS 3.2 8.0 + - - +
319A PHE* 5.4 2.9 - - + -
365A GLY* 1.3 75.9 - - - -
367A PRO* 1.4 65.2 - - - +
368A ALA 3.2 2.6 + - - -
369A ILE* 3.4 9.7 - - + +
370A THR* 2.5 36.6 + - - -
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Residues in contact with PRO 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE 5.5 0.9 - - - +
34A ALA* 4.1 8.3 - - - +
36A GLU 4.0 14.4 - - - +
37A ASN* 4.0 14.6 - - - +
229A LYS 5.7 0.2 - - - -
230A THR* 3.9 14.4 - - + -
287A TYR* 2.8 24.0 + - - +
291A VAL* 3.9 10.8 - - + -
317A HIS* 3.7 34.1 - - + -
365A GLY* 3.3 10.3 - - - -
366A THR* 1.4 93.3 - - - +
368A ALA* 1.3 62.5 + - - +
370A THR* 3.8 0.2 - - - -
371A ARG* 3.1 13.5 + - - +
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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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31A GLU* 3.3 31.4 - - + +
33A ILE 5.4 3.3 + - - +
36A GLU* 4.4 6.1 + - + +
37A ASN* 4.3 17.3 - - - -
38A TYR* 3.5 27.3 - - + +
365A GLY 5.0 1.2 + - - +
366A THR 3.3 0.6 - - - -
367A PRO* 1.3 79.1 - - - +
369A ILE* 1.3 64.3 + - + +
371A ARG* 3.2 4.0 + - - +
372A ARG* 3.0 21.1 + - - +
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Residues in contact with ILE 369 (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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30A ILE* 3.7 31.9 - - + -
31A GLU 3.8 13.4 + - - +
32A LEU* 4.1 17.3 - - + -
294A ASN* 5.0 1.8 - - + +
298A MET* 4.3 13.9 - - - -
366A THR* 3.4 20.6 - - + +
368A ALA* 1.3 78.2 - - - +
370A THR* 1.3 66.0 + - - +
372A ARG* 3.2 14.8 + - - +
373A GLY 3.2 5.2 + - - -
374A PHE* 2.9 57.6 + - + +
379A ALA* 4.6 9.6 - - + -
382A LEU* 4.2 7.2 - - + -
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Residues in contact with THR 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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287A TYR* 3.7 10.4 - - + +
290A GLN* 3.4 33.7 - - + -
291A VAL* 3.5 29.7 - - + +
294A ASN* 2.9 24.2 + - - +
366A THR* 2.5 27.4 + - - -
367A PRO 3.8 0.7 - - - -
369A ILE* 1.3 73.1 - - - +
371A ARG* 1.3 58.4 + - - +
372A ARG 2.9 4.5 - - - -
373A GLY* 3.0 20.1 + - - -
374A PHE 4.0 5.2 - - - +
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Residues in contact with ARG 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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37A ASN* 3.3 14.6 - - - +
38A TYR* 2.6 51.9 + - + -
39A THR* 3.9 0.4 - - - +
40A SER* 3.7 16.4 - - - +
232A ALA* 3.9 22.6 + - - +
278A GLU* 5.1 10.7 + - - +
284A PHE* 5.1 11.3 - - - -
287A TYR* 3.3 29.2 - - + +
367A PRO 3.1 19.0 + - - +
368A ALA 3.6 3.4 - - - +
370A THR* 1.3 75.1 - - - +
372A ARG* 1.3 58.8 + - - +
373A GLY 3.3 0.4 + - - -
1B MET 4.0 13.3 + - - -
2B LEU* 3.9 29.0 - - + +
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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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26A GLN 3.8 1.6 + - - -
27A GLU* 2.4 36.4 + - - +
29A HIS 2.8 28.1 + - - -
30A ILE* 4.4 5.8 - - - +
31A GLU 4.9 0.2 - - - +
38A TYR* 3.8 20.1 + - + -
368A ALA 3.0 11.9 + - - +
369A ILE* 3.3 19.1 - - - +
370A THR 2.9 0.2 - - - -
371A ARG* 1.3 80.1 - - - +
373A GLY* 1.3 55.6 + - - +
374A PHE* 3.7 12.5 - - + -
410A CYS* 3.5 23.5 + - - +
413A TYR* 2.7 52.0 + - + +
414A PRO 4.6 3.2 - - - +
415A VAL* 3.6 22.8 - - + +
1B MET* 4.5 12.6 + - - +
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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