Contacts of the helix formed by residues 366 - 372 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D VAL* 2.7 34.1 + - - +
294D ASN* 3.8 9.6 - - + -
295D ALA* 3.4 31.8 - - + +
298D MET* 3.9 20.9 - - - -
317D HIS 3.1 7.1 + - - +
319D PHE* 5.4 3.1 - - + -
365D GLY* 1.3 74.6 - - - -
367D PRO* 1.3 67.6 - - - +
368D ALA 3.3 2.5 - - - -
369D ILE* 3.4 10.0 - - + +
370D THR* 2.5 36.7 + - - -
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Residues in contact with PRO 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D ILE 5.4 0.9 - - - +
34D ALA* 4.1 7.4 - - - +
36D GLU 4.0 14.6 - - - +
37D ASN* 4.1 14.8 - - - +
230D THR* 4.0 13.2 - - + +
287D TYR* 2.8 24.6 + - - +
291D VAL* 3.9 12.1 - - + -
317D HIS* 3.7 33.9 - - + +
365D GLY* 3.2 11.0 - - - -
366D THR* 1.3 94.2 - - - +
368D ALA* 1.3 62.0 + - - +
370D THR* 3.8 0.2 - - - -
371D ARG* 3.1 13.9 + - - +
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Residues in contact with ALA 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D GLU* 3.4 31.6 + - + +
33D ILE 5.5 3.1 + - - +
36D GLU 4.3 7.0 + - - +
37D ASN* 4.3 17.3 - - - +
38D TYR* 3.5 27.4 - - + +
365D GLY 5.0 1.0 + - - +
366D THR 3.3 0.8 - - - -
367D PRO* 1.3 76.9 - - - +
369D ILE* 1.3 66.3 + - - +
371D ARG* 3.1 3.6 + - - +
372D ARG* 3.0 21.5 + - - +
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Residues in contact with ILE 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ILE* 3.7 31.6 - - + -
31D GLU 3.8 12.8 + - - +
32D LEU* 4.1 16.4 - - + -
294D ASN* 5.0 2.0 - - + +
298D MET* 4.3 14.1 - - - -
366D THR* 3.4 20.8 - - + +
368D ALA* 1.3 78.7 - - + +
370D THR* 1.3 67.3 + - - +
372D ARG* 3.2 15.5 + - - +
373D GLY 3.2 5.0 + - - -
374D PHE* 2.9 58.0 + - + +
379D ALA* 4.6 9.4 - - + -
382D LEU* 4.2 7.2 - - + -
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Residues in contact with THR 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287D TYR* 3.7 9.8 - - + +
290D GLN* 3.4 33.9 - - + -
291D VAL* 3.5 29.4 - - + +
294D ASN* 3.0 23.7 + - - +
366D THR* 2.5 27.9 + - - -
367D PRO 3.8 0.4 - - - -
369D ILE* 1.3 73.9 - - - +
371D ARG* 1.3 57.9 + - - +
372D ARG 2.9 4.7 - - - -
373D GLY* 3.0 20.1 + - - -
374D PHE 4.0 4.4 - - - +
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Residues in contact with ARG 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET 4.2 12.5 + - - -
2C LEU* 4.0 29.6 - - + +
37D ASN* 3.3 15.7 - - - +
38D TYR* 2.6 52.4 + - + -
39D THR 3.9 0.2 - - - -
40D SER* 3.7 17.4 - - - +
232D ALA* 3.9 21.8 + - - +
278D GLU* 5.1 10.7 + - - +
284D PHE* 5.1 11.7 - - - -
287D TYR* 3.3 28.4 - - + +
367D PRO 3.1 18.4 + - - +
368D ALA 3.6 3.8 - - - +
370D THR* 1.3 76.0 - - - +
372D ARG* 1.3 59.3 + - - +
373D GLY 3.4 0.6 + - - -
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Residues in contact with ARG 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET 4.5 9.9 + - - +
26D GLN 3.9 1.0 + - - -
27D GLU* 2.4 36.6 + - - +
29D HIS 2.8 27.9 + - - -
30D ILE* 4.3 6.4 - - - +
31D GLU 4.9 0.2 - - - +
38D TYR* 3.9 19.4 + - + -
368D ALA 3.0 11.0 + - - +
369D ILE* 3.3 18.1 - - - +
370D THR 2.9 0.6 - - - -
371D ARG* 1.3 79.3 - - - +
373D GLY* 1.3 55.4 + - - +
374D PHE* 3.7 11.4 - - + -
410D CYS* 3.4 30.3 + - - +
413D TYR* 2.6 45.5 + - + +
414D PRO 4.5 5.9 - - - +
415D VAL* 3.6 21.1 - - + +
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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