Contacts of the strand formed by residues 311 - 316 (chain N) in PDB entry 1A14
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 311 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256N TYR* 3.6 2.9 - - - -
264N LYS* 4.7 5.8 - - - +
266N GLU* 3.5 11.0 - - - +
304N ARG 4.1 0.2 - - - +
306N ASP* 2.7 40.1 + - - +
309N ALA* 4.0 21.4 - - + +
310N MET* 1.3 81.6 - - - +
312N HIS* 1.3 59.9 + - - +
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Residues in contact with HIS 312 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254N ILE* 3.3 27.1 - - + +
256N TYR* 3.8 8.5 - - - +
266N GLU* 2.8 30.5 + - - +
267N PRO 3.1 23.1 - - - -
268N LEU* 4.5 1.3 - - + -
269N ALA* 2.8 39.3 + - + +
303N ILE* 3.9 17.9 - - + -
304N ARG 3.1 14.8 - - - +
305N ILE* 3.9 10.5 - - + -
311N THR* 1.3 77.8 - - - +
313N THR* 1.3 84.7 + - - +
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Residues in contact with THR 313 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269N ALA* 3.8 7.4 - - - -
270N GLY* 4.1 9.0 + - - -
303N ILE* 3.1 7.6 - - - +
304N ARG* 3.1 41.3 + - + +
312N HIS* 1.3 85.2 - - - +
314N SER* 1.3 70.7 + - - +
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Residues in contact with SER 314 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268N LEU* 3.7 9.9 - - - +
269N ALA 2.4 26.6 + - - -
270N GLY* 3.2 2.8 - - - -
271N THR* 2.7 27.8 + - - +
272N ALA* 3.0 33.0 + - - +
302N VAL 2.9 11.4 - - - -
303N ILE* 3.9 4.9 - - - -
313N THR* 1.3 83.2 + - - +
315N GLN* 1.3 62.8 + - - +
338N ASN* 4.9 0.2 + - - -
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Residues in contact with GLN 315 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271N THR* 3.3 10.8 - - - -
272N ALA* 5.2 0.7 - - - -
301N PRO* 3.2 2.7 - - - +
302N VAL* 2.4 45.5 + - + +
314N SER* 1.3 78.4 - - - +
316N TYR* 1.3 86.7 + - - +
318N CYS* 3.8 10.7 - - - -
337N CYS* 3.3 12.0 + - + +
338N ASN* 3.3 12.3 - - - +
383N LEU* 3.2 40.9 + - - +
384N THR* 5.0 4.0 - - - +
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Residues in contact with TYR 316 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271N THR 3.1 24.7 - - - -
272N ALA* 4.1 3.8 - - - -
273N LYS* 3.4 17.4 + - - -
293N ASP* 2.8 36.1 + - + -
299N ASN* 3.6 37.5 - - - +
300N ARG 3.2 20.9 - - - +
301N PRO* 3.8 7.2 - - + -
315N GLN* 1.3 104.2 + - - +
317N ILE* 1.3 63.4 + - - +
318N CYS 3.1 1.4 + - - -
336N LYS 4.2 0.2 - - - +
337N CYS 3.0 16.3 + - - +
338N ASN* 3.5 5.2 - - - -
339N ASP* 3.4 31.0 - - - -
340N PRO* 3.0 23.3 - - + +
383N LEU* 4.2 1.8 - - - -
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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