Contacts of the helix formed by residues 311 - 322 (chain A) in PDB entry 2W3C
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 GLY 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A LYS* 3.1 21.8 + - - +
308A PHE 3.0 8.2 + - - -
309A GLN 3.4 1.2 + - - -
310A CYS* 1.3 74.0 - - - +
312A LEU* 1.3 58.0 + - - +
314A GLN* 3.2 26.8 - - - +
315A GLN* 3.1 21.0 + - - +
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Residues in contact with LEU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A ILE* 4.2 7.4 - - + +
259A MET* 3.9 19.7 - - + +
260A LYS* 4.0 14.8 - - + -
263A PHE* 3.4 38.6 - - + -
287A VAL* 4.1 16.2 - - + -
307A MET* 2.9 50.5 + - + +
310A CYS* 3.5 12.8 + - - -
311A GLY* 1.3 72.1 - - - +
313A LEU* 1.3 64.9 + - - +
315A GLN* 3.2 1.3 + - + +
316A LEU* 3.0 36.7 + - + +
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Residues in contact with LEU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A MET* 3.1 14.4 + - - +
308A PHE* 4.0 10.5 - - + +
312A LEU* 1.3 71.6 - - - +
314A GLN* 1.3 73.7 + - - +
316A LEU* 3.0 18.0 + - - +
317A CYS* 3.1 18.9 + - - -
337A VAL* 4.2 15.7 - - + -
340A VAL* 3.6 27.4 - - + -
341A ILE* 3.4 26.9 - - + -
347A ASN* 3.6 38.1 - - + +
350A TYR* 3.8 26.2 - - + -
351A PHE* 5.7 0.2 - - + -
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Residues in contact with GLN 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A PHE* 3.4 51.5 + - - +
311A GLY* 3.2 27.2 - - - +
313A LEU* 1.3 83.2 + - - +
315A GLN* 1.3 59.9 + - - +
317A CYS* 3.2 11.4 + - - +
318A THR* 3.3 16.4 + - - -
350A TYR* 3.5 39.3 + - + +
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Residues in contact with GLN 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A LYS* 4.0 24.3 + - + +
263A PHE* 3.1 39.3 + - + +
264A GLU* 3.5 27.4 + - - +
265A VAL* 5.0 3.6 - - - +
311A GLY 3.1 18.8 + - - +
312A LEU* 3.6 5.2 - - + +
313A LEU 3.1 0.4 + - - -
314A GLN* 1.3 72.1 - - - +
316A LEU* 1.3 65.2 + - - +
318A THR* 3.4 27.2 + - - +
319A ILE* 3.4 11.0 + - - +
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Residues in contact with LEU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A PHE* 3.9 39.0 - - + -
284A LEU* 4.0 11.7 - - + -
287A VAL* 4.4 7.9 - - + -
312A LEU* 3.0 23.8 + - + +
313A LEU* 3.5 10.8 - - - +
315A GLN* 1.3 76.2 - - - +
317A CYS* 1.3 63.8 + - - +
319A ILE* 3.1 22.0 + - + +
320A LEU* 3.4 5.5 + - - +
333A THR* 3.7 16.1 - - + +
336A THR* 3.6 26.7 - - + -
337A VAL* 3.6 20.2 - - + -
340A VAL* 4.4 13.2 - - + -
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Residues in contact with CYS 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A LEU* 3.1 19.3 + - - -
314A GLN 3.2 9.4 + - - +
316A LEU* 1.3 75.3 - - - +
318A THR* 1.3 59.0 + - - +
320A LEU* 3.0 31.6 + - + +
321A MET* 3.6 14.5 + - + +
337A VAL* 4.4 14.1 - - - -
350A TYR* 4.1 23.6 - - + +
351A PHE* 4.0 29.4 - - - -
354A VAL* 4.4 15.6 - - + +
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Residues in contact with THR 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A VAL* 5.3 9.2 - - + -
314A GLN 3.3 12.2 + - - -
315A GLN* 3.5 25.2 + - - +
316A LEU 3.3 0.2 - - - -
317A CYS* 1.3 77.7 - - - +
319A ILE* 1.3 60.6 + - - +
321A MET* 3.6 21.0 + - + +
322A ALA* 3.3 22.8 + - + +
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Residues in contact with ILE 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A PHE* 3.3 54.1 - - + +
265A VAL* 4.7 15.5 - - + +
272A TRP* 6.1 3.6 - - + -
280A LEU* 5.2 9.2 - - + -
284A LEU* 5.6 0.4 - - + -
315A GLN* 3.4 7.7 + - - +
316A LEU* 3.1 17.0 + - + +
318A THR* 1.3 78.2 - - - +
320A LEU* 1.3 63.9 + - + +
321A MET 3.4 0.9 + - - -
322A ALA* 3.5 16.7 + - - +
325A VAL* 4.2 21.6 - - + +
329A ILE* 4.8 6.1 - - + -
330A LEU* 4.1 7.9 - - + +
333A THR* 3.7 27.1 - - + +
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Residues in contact with LEU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A LEU 3.4 10.3 + - - +
317A CYS* 3.0 16.8 + - - +
319A ILE* 1.3 78.9 - - - +
321A MET* 1.3 59.1 + - + +
322A ALA 4.0 0.7 + - - +
330A LEU* 3.8 23.0 - - + +
333A THR* 3.9 23.3 - - + +
334A ILE* 3.7 34.3 - - + +
337A VAL* 4.5 14.4 - - + -
351A PHE* 4.3 22.0 - - + -
368A LEU* 5.9 0.2 - - + -
388A CYS* 5.7 0.2 - - - -
1630A PEG 3.8 40.5 - - - +
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Residues in contact with MET 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A CYS* 3.9 8.7 - - + +
318A THR* 4.0 27.1 - - + +
319A ILE 3.3 0.2 - - - -
320A LEU* 1.3 77.6 - - + +
322A ALA* 1.3 65.5 + - - +
323A THR* 4.0 2.9 + - - -
354A VAL* 3.8 26.0 - - + -
355A ASN 3.7 23.8 - - - +
356A ALA* 4.7 16.4 - - + -
357A PRO* 4.9 14.4 - - + +
1630A PEG 6.2 0.4 - - - -
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Residues in contact with ALA 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A VAL* 4.2 23.1 - - + -
318A THR* 3.3 18.4 + - + +
319A ILE* 3.5 12.3 + - - +
320A LEU 4.7 1.7 - - - +
321A MET* 1.3 81.9 - - - +
323A THR* 1.3 62.6 + - - +
324A GLY 4.0 0.5 + - - -
325A VAL* 3.9 19.3 + - + +
330A LEU* 5.3 2.6 - - - +
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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