Contacts of the helix formed by residues 364 - 375 (chain B) in PDB entry 2Y1M
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 364 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362B LYS 5.7 0.2 - - - +
363B VAL* 1.3 76.2 - - - +
365B GLN* 1.3 65.0 + - - +
366B GLU* 2.7 20.2 + - - +
367B GLN* 2.8 45.6 + - - +
368B TYR* 3.2 8.6 + - - -
166C LYS 4.0 3.4 - - - +
167C GLY* 3.6 35.2 - - - +
170C PRO* 4.0 19.3 - - + -
175C GLN* 6.2 0.4 - - + -
179C PHE* 5.1 7.4 - - + -
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Residues in contact with GLN 365 (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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217B SER* 3.1 31.0 + - - -
219B LEU* 3.2 47.7 - - + +
363B VAL 3.8 3.8 + - - +
364B THR* 1.3 71.7 - - - +
366B GLU* 1.3 73.3 + - - +
368B TYR* 3.5 10.1 + - - -
369B GLU* 3.1 19.1 + - - +
398B HIS* 5.5 1.7 + - + +
419B CYS* 4.4 12.5 - - - +
166C LYS 5.8 0.2 + - - -
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Residues in contact with GLU 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B THR* 2.7 16.1 + - - +
365B GLN* 1.3 91.4 + - - +
367B GLN* 1.3 60.6 + - + +
369B GLU* 3.2 12.6 + - - +
370B LEU* 2.9 37.9 + - + +
163C ALA 5.5 3.7 - - - +
166C LYS* 5.4 4.5 - - - +
167C GLY* 5.3 5.2 - - - -
239C PHE* 5.9 8.0 - - + -
246C ARG* 6.1 2.9 - - - +
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Residues in contact with GLN 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B VAL* 4.1 8.0 - - + +
264B THR* 3.7 32.0 + - + +
362B LYS 4.7 1.9 - - - +
363B VAL* 3.8 14.7 - - + -
364B THR* 2.8 38.8 + - - +
366B GLU* 1.3 79.5 - - + +
368B TYR* 1.3 57.1 + - - +
370B LEU* 4.0 11.4 - - + +
371B TYR* 3.1 28.6 + - - +
180C ARG* 4.6 21.2 - - - +
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Residues in contact with TYR 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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216B SER* 6.5 0.2 - - - -
217B SER* 4.6 4.7 - - - -
219B LEU* 4.0 20.0 - - + +
220B GLU* 3.0 47.4 + - + -
223B ALA* 3.8 16.5 - - + +
258B TRP* 4.0 6.1 - + - -
259B ASN* 3.1 27.0 + - - -
263B VAL* 3.7 14.6 - - + -
363B VAL* 3.2 39.2 - - + +
364B THR 3.2 10.0 + - - -
365B GLN* 3.7 21.1 - - - +
366B GLU 3.2 0.6 - - - -
367B GLN* 1.3 77.2 - - - +
369B GLU* 1.3 57.0 + - - +
371B TYR* 3.5 4.2 + - - +
372B CYS* 3.0 33.4 + - - -
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Residues in contact with GLU 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B LEU* 4.4 14.3 - - + +
365B GLN 3.1 17.4 + - - +
366B GLU* 3.2 12.2 + - - +
368B TYR* 1.3 75.6 - - - +
370B LEU* 1.3 72.2 + - - +
372B CYS* 3.1 15.4 + - + +
373B GLU* 3.3 23.3 - - + +
398B HIS* 3.5 28.5 + - + +
399B LEU* 5.0 2.1 + - - +
418B PHE* 6.2 3.1 - - + -
299C ARG* 3.4 32.7 + - - -
302C GLN* 5.6 1.2 + - - -
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Residues in contact with LEU 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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366B GLU* 2.9 23.6 + - + +
367B GLN* 4.0 11.7 - - + +
369B GLU* 1.3 81.6 - - + +
371B TYR* 1.3 55.6 + - - +
373B GLU* 2.6 35.1 + - + +
374B MET* 3.3 6.1 + - - +
182C THR* 4.1 23.8 - - + +
246C ARG* 5.5 14.1 - - - +
302C GLN* 5.7 7.4 - - - +
320C HIS* 5.8 6.3 - - - +
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Residues in contact with TYR 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ALA* 3.5 42.2 - - + -
226B SER* 4.3 6.0 + - - -
227B THR* 2.4 26.8 + - - +
258B TRP* 3.5 6.5 + + - -
262B ALA* 3.8 4.9 - - - +
263B VAL* 3.5 49.6 - - + +
268B TYR* 3.7 16.5 + + - -
367B GLN 3.1 18.4 + - - +
368B TYR 3.7 3.4 - - - +
370B LEU* 1.3 79.4 - - - +
372B CYS* 1.3 58.8 + - - +
373B GLU 3.1 4.0 + - - -
374B MET* 3.3 51.1 + - + +
375B GLY 4.7 1.0 + - - -
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Residues in contact with CYS 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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219B LEU* 4.5 8.1 - - + -
222B MET* 4.0 16.2 - - - -
223B ALA* 3.7 32.8 - - - -
226B SER* 4.8 8.1 - - - -
368B TYR 3.0 20.3 + - - +
369B GLU* 3.3 14.1 - - + +
370B LEU 3.0 0.8 + - - -
371B TYR* 1.3 77.5 - - - +
373B GLU* 1.3 59.6 + - + +
374B MET 3.6 0.2 - - - -
375B GLY 5.3 1.0 + - - -
382B LYS* 3.2 27.4 - - + +
418B PHE* 4.9 12.1 - - + -
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Residues in contact with GLU 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 GLU* 3.3 24.9 - - + +
370B LEU* 2.6 21.0 + - + +
372B CYS* 1.3 74.9 - - + +
374B MET* 1.3 63.3 + - - +
375B GLY 3.5 1.6 - - - -
376B SER 3.7 11.8 + - - +
377B THR 4.9 1.6 - - - +
378B PHE* 3.6 21.3 + - + -
382B LYS* 2.9 41.1 + - - +
389B LYS* 2.9 34.6 + - - -
399B LEU* 5.7 0.3 - - - +
418B PHE* 5.9 1.0 - - - -
320C HIS* 5.3 11.8 - - + +
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Residues in contact with MET 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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262B ALA 5.1 0.7 - - - +
263B VAL 5.6 0.7 - - - +
268B TYR* 4.0 32.1 - - + +
269B MET* 4.8 3.8 - - - +
270B ALA* 4.4 15.3 - - + -
370B LEU 3.3 4.7 + - - +
371B TYR* 3.3 51.1 + - + +
373B GLU* 1.3 79.1 - - - +
375B GLY* 1.3 64.3 + - - +
376B SER 3.1 11.4 + - - +
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Residues in contact with GLY 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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153B LYS* 3.5 31.2 + - - +
270B ALA* 6.2 1.8 - - - -
371B TYR 4.7 1.6 + - - -
372B CYS 5.3 1.0 + - - -
373B GLU 3.5 0.8 - - - -
374B MET* 1.3 82.4 - - - +
376B SER* 1.3 59.2 + - - +
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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