Contacts of the helix formed by residues 366 - 372 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B VAL* 2.7 33.5 + - - +
294B ASN* 3.8 8.7 - - + -
295B ALA* 3.4 31.6 - - + +
298B MET* 4.0 21.5 - - - -
317B HIS 3.1 8.0 + - - +
319B PHE* 5.4 2.7 - - + -
365B GLY* 1.3 73.6 - - - -
367B PRO* 1.3 65.4 - - - +
368B ALA 3.3 3.3 + - - -
369B ILE* 3.5 10.2 - - + +
370B THR* 2.5 37.6 + - - -
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Residues in contact with PRO 367 (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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33B ILE 5.5 0.9 - - - +
34B ALA* 4.1 8.1 - - - +
36B GLU 4.0 14.6 - - - +
37B ASN* 3.8 9.8 - - - +
230B THR* 3.9 14.1 - - + +
287B TYR* 2.7 28.4 + - - +
291B VAL* 3.9 10.8 - - + -
317B HIS* 3.7 34.5 - - + +
365B GLY* 3.3 9.6 - - - -
366B THR* 1.3 94.2 - - - +
368B ALA* 1.3 61.3 + - - +
370B THR* 3.8 0.2 - - - -
371B ARG* 3.1 14.0 + - - +
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Residues in contact with ALA 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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31B GLU* 3.4 31.4 - - + +
33B ILE 5.5 3.5 + - - +
36B GLU 4.4 5.9 + - - +
37B ASN* 4.3 17.3 - - - +
38B TYR* 3.5 28.1 - - + -
365B GLY 5.0 0.8 + - - +
366B THR 3.3 0.6 - - - -
367B PRO* 1.3 76.6 - - - +
369B ILE* 1.3 66.4 + - - +
371B ARG* 3.2 3.6 + - - +
372B ARG* 3.0 21.3 + - - +
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Residues in contact with ILE 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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30B ILE* 3.7 31.2 - - + -
31B GLU 3.8 14.1 + - - +
32B LEU* 4.1 16.6 - - + -
294B ASN* 5.1 1.6 - - + -
298B MET* 4.3 13.2 - - - -
366B THR* 3.5 21.3 - - + +
368B ALA* 1.3 75.9 - - - +
370B THR* 1.3 66.2 + - - +
372B ARG* 3.2 14.6 + - - +
373B GLY 3.2 5.0 + - - -
374B PHE* 2.9 58.9 + - + +
379B ALA* 4.6 9.2 - - + -
382B LEU* 4.2 7.0 - - + -
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Residues in contact with THR 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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287B TYR* 3.7 10.0 - - + +
290B GLN* 3.4 33.9 - - + -
291B VAL* 3.5 29.1 - - + +
294B ASN* 2.9 23.8 + - - +
366B THR* 2.5 27.8 + - - -
367B PRO 3.8 0.2 - - - -
369B ILE* 1.3 74.7 - - - +
371B ARG* 1.3 57.3 + - - +
372B ARG 2.9 4.3 - - - -
373B GLY* 3.0 20.4 + - - -
374B PHE 4.0 4.1 - - - +
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Residues in contact with ARG 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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2A LEU* 4.1 32.5 - - + +
37B ASN* 3.3 14.8 - - - +
38B TYR* 2.5 52.6 + - + -
40B SER* 3.8 18.8 - - - +
232B ALA* 3.8 22.5 + - - +
278B GLU* 5.0 11.1 + - - +
284B PHE* 5.1 11.9 - - - -
287B TYR* 3.3 29.1 - - + +
367B PRO 3.1 16.9 + - - +
368B ALA 3.6 3.4 - - - +
370B THR* 1.3 77.9 - - - +
372B ARG* 1.3 59.5 + - - +
373B GLY 3.6 0.3 + - - -
415B VAL 5.7 0.5 - - - +
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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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26B GLN 3.9 1.8 + - - -
27B GLU* 2.5 34.1 + - - +
29B HIS 2.8 29.5 + - - -
30B ILE* 4.3 5.8 - - - +
31B GLU 4.9 0.2 - - - +
38B TYR* 3.8 20.4 + - + -
368B ALA 3.0 15.0 + - - +
369B ILE* 3.3 15.0 - - - +
370B THR 2.9 0.2 - - - -
371B ARG* 1.3 80.0 - - - +
373B GLY* 1.3 56.1 + - - +
374B PHE* 3.7 11.6 - - + -
410B CYS* 3.3 28.5 + - - +
413B TYR* 2.6 44.1 + - + +
414B PRO 4.3 8.2 - - - +
415B VAL* 3.5 25.3 - - + +
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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