Contacts of the helix formed by residues 292 - 299 (chain M) in PDB entry 7PRC
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 TRP 292 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H ALA* 4.3 3.6 - - + -
191M TYR* 2.8 30.1 + - + +
193M ASN 3.9 8.3 - - - +
194M PHE* 3.9 16.8 - + - -
196M TYR* 3.6 16.7 - - - +
197M CYS* 3.5 29.8 - - + -
198M PRO* 3.4 24.9 - - + -
199M TRP* 3.5 26.7 - + - -
281M GLY 4.1 5.8 - - - -
284M LEU* 4.2 8.3 - - + -
285M THR* 2.9 28.8 + - - +
289M VAL* 3.3 44.1 - - + +
290M ASP 4.0 0.4 - - - -
291M ASN* 1.3 68.1 - - - +
293M TYR* 1.3 65.6 + - - +
295M TRP* 3.3 22.0 + + - +
296M CYS* 2.9 26.3 + - - +
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Residues in contact with TYR 293 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C GLN* 3.4 35.2 + - + +
252C THR* 3.7 31.4 - - + -
254C GLU* 4.2 4.5 - - - +
255C SER* 4.3 6.1 - - - -
259C LYS* 3.4 24.6 + - - -
192M GLY 2.9 21.9 + - - +
196M TYR* 3.8 34.3 - + + +
291M ASN* 3.1 4.5 + - - +
292M TRP* 1.3 73.5 - - - +
294M LEU* 1.3 65.4 + - + +
296M CYS* 3.1 5.0 + - - +
297M VAL* 2.7 58.9 + - + +
302M ALA* 3.8 7.1 - - + +
303M PRO 4.5 3.1 + - - -
304M ASP* 5.2 1.4 + - - +
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Residues in contact with LEU 294 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C GLN* 3.3 44.6 - - - +
207C THR* 3.6 5.6 - - - +
208C ALA* 3.7 13.2 - - - +
254C GLU* 5.0 1.6 - - + +
255C SER* 5.6 3.4 - - - +
291M ASN* 2.9 37.1 + - + +
293M TYR* 1.3 91.7 - - + +
295M TRP* 1.3 56.9 + - - +
297M VAL* 3.5 11.8 - - + +
298M LYS* 2.6 34.8 + - - +
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Residues in contact with TRP 295 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C ALA* 3.5 14.3 - - + +
209C LEU* 4.5 9.9 - - + -
11H ASP* 2.9 26.6 + - - -
13H ALA* 4.0 13.7 - - + +
14H GLN* 3.7 27.4 - - + -
17H TRP* 5.0 4.9 - - + -
702L LDA 3.7 32.3 - - + -
198M PRO* 3.2 32.5 - - + -
199M TRP* 5.1 0.2 - + - -
289M VAL* 4.0 18.8 - - + -
291M ASN 2.9 11.7 + - - +
292M TRP* 3.5 27.8 - + - +
294M LEU* 1.3 78.3 - - - +
296M CYS* 1.3 80.9 + - - +
298M LYS* 3.2 3.3 + - + +
299M HIS* 3.1 49.7 + + - -
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Residues in contact with CYS 296 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151L LEU* 5.7 0.2 - - - -
702L LDA 3.7 26.0 - - - -
196M TYR* 3.2 51.8 - - + -
292M TRP 2.9 9.5 + - - +
293M TYR 3.2 9.2 - - - +
295M TRP* 1.3 86.9 - - - +
297M VAL* 1.3 57.9 + - - +
299M HIS* 2.9 17.4 + - - +
300M GLY 3.0 10.9 + - - -
301M ALA* 3.2 22.5 + - + -
302M ALA* 4.3 3.8 - - + +
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Residues in contact with VAL 297 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293M TYR* 2.7 61.7 + - + +
294M LEU* 3.5 15.0 - - + +
295M TRP 3.2 0.2 - - - -
296M CYS* 1.3 71.1 - - - +
298M LYS* 1.3 65.8 + - - +
299M HIS 3.0 0.9 + - - -
300M GLY* 3.2 11.4 + - - +
302M ALA* 3.8 13.9 - - + +
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Residues in contact with LYS 298 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C ALA* 4.1 16.1 - - + +
209C LEU* 3.6 31.5 - - - +
2H TYR* 6.3 0.2 - - - -
5H ALA* 5.8 0.6 - - - +
9H HIS* 3.2 59.3 - - + +
10H LEU 5.7 0.6 + - - +
11H ASP* 3.5 21.5 + - - +
294M LEU 2.6 21.5 + - - +
295M TRP* 3.4 6.5 - - + +
297M VAL* 1.3 74.5 - - - +
299M HIS* 1.3 70.5 + - + +
300M GLY 3.7 0.3 + - - -
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Residues in contact with HIS 299 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H HIS* 4.0 15.7 + - - -
11H ASP* 2.9 23.0 + - - -
14H GLN* 3.0 35.9 + - + +
702L LDA 3.7 45.6 + - + +
295M TRP* 3.1 51.6 + + - +
296M CYS* 2.9 6.6 + - - +
298M LYS* 1.3 93.3 + - + +
300M GLY* 1.3 55.7 - - - +
301M ALA 3.4 4.3 + - - -
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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