Contacts of the helix formed by residues 267 - 272 (chain P) in PDB entry 5C7O
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 ALA 267 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264P SER* 2.7 28.2 + - - +
265P ARG 3.2 0.2 - - - -
266P LYS* 1.3 84.4 - - + +
268P TRP* 1.3 64.9 + - - +
269P ARG 3.3 2.5 - - - -
270P ASP* 3.1 29.9 + - - +
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Residues in contact with TRP 268 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352O GLU* 3.8 39.8 + - + +
264P SER* 3.5 17.5 + - - -
265P ARG* 3.4 22.9 + - - +
266P LYS 5.2 0.2 - - - -
267P ALA* 1.3 70.8 - - - +
269P ARG* 1.3 64.2 + - - +
271P GLY* 3.0 15.6 + - - -
272P ARG* 4.0 8.8 + - - +
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Residues in contact with ARG 269 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351O ASP 3.8 4.6 + - - -
352O GLU* 3.0 38.4 + - + +
353O VAL 2.8 40.9 + - - +
354O VAL* 4.0 3.4 - - + -
368O ASP* 2.8 41.6 + - - -
370O LYS* 3.4 26.5 - - - +
371O ALA* 3.6 6.4 - - - +
267P ALA 3.3 0.6 + - - -
268P TRP* 1.3 75.7 - - - +
270P ASP* 1.3 62.2 + - - +
272P ARG* 3.1 27.9 + - - +
279P ILE* 3.4 26.6 - - + +
280P PRO* 3.5 34.7 + - - +
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Residues in contact with ASP 270 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256P THR* 4.6 6.3 - - - +
257P GLN* 4.0 34.0 + - + +
258P LYS* 4.1 2.6 + - - +
264P SER* 3.6 9.1 - - - +
267P ALA* 3.1 30.6 + - - +
269P ARG* 1.3 77.7 - - - +
271P GLY* 1.3 59.5 + - - +
272P ARG 3.3 5.8 - - - +
279P ILE* 4.1 11.3 - - - +
280P PRO 4.6 1.4 - - - +
281P ALA* 4.0 21.9 - - - +
306P ARG* 5.3 4.3 - - - +
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Residues in contact with GLY 271 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258P LYS* 3.5 15.8 - - - +
261P ASP* 3.4 0.9 - - - -
262P GLY 2.8 43.2 + - - -
264P SER* 3.4 15.2 - - - -
268P TRP 3.0 10.0 + - - -
270P ASP* 1.3 76.8 - - - +
272P ARG* 1.3 66.5 + - - +
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Residues in contact with ARG 272 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352O GLU 4.4 9.8 + - - +
354O VAL* 3.4 26.4 - - + +
356O THR* 3.7 9.9 + - - -
357O ASP* 2.8 43.6 + - - -
257P GLN* 4.8 0.3 + - - -
258P LYS 4.1 2.4 + - - +
261P ASP* 3.2 31.3 + - - +
262P GLY 6.0 0.2 - - - +
268P TRP 4.1 10.1 - - - +
269P ARG* 3.1 17.8 + - - +
270P ASP 4.1 4.2 - - - +
271P GLY* 1.3 81.2 - - - +
273P GLY* 1.3 67.5 + - - +
274P ALA* 3.1 4.0 + - - +
277P ASN* 4.0 10.0 - - - +
279P ILE* 3.5 12.4 - - + +
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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