Contacts of the helix formed by residues 307 - 317 (chain A) in PDB entry 4M83
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 307 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304A THR* 4.5 0.6 + - - -
305A HIS* 3.3 34.1 + - - -
306A ALA* 1.3 77.9 - - - +
308A ALA* 1.3 64.6 + - - -
309A GLY 3.3 2.5 - - - -
310A GLY 3.5 0.2 + - - -
311A SER* 2.7 27.3 + - - -
329A ASP* 3.9 13.2 - - - -
333A ASN* 3.9 0.4 - - - -
1401A UDP 3.7 5.2 - - - -
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Residues in contact with ALA 308 (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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132A PRO 5.4 4.9 - - - +
192A ILE* 5.4 13.0 - - + -
196A LEU* 4.6 4.3 - - - +
307A GLY* 1.3 71.0 - - - +
309A GLY* 1.3 57.4 + - - +
311A SER* 3.9 2.3 - - - -
312A GLN* 3.0 29.8 + - - +
329A ASP* 4.5 3.4 + - - +
333A ASN* 3.8 15.1 - - - +
1401A UDP 3.4 6.0 + - - +
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Residues in contact with GLY 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ALA* 1.3 74.2 - - - +
310A GLY* 1.3 54.3 + - - +
312A GLN* 3.0 9.6 + - - +
313A GLU* 2.7 54.8 + - - -
1401A UDP 3.0 20.7 + - - -
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Residues in contact with GLY 310 (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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292A GLN* 4.0 4.3 - - - -
302A PHE* 3.4 26.8 - - - -
304A THR* 4.3 7.2 - - - -
305A HIS* 5.4 0.7 - - - -
307A GLY 3.5 1.7 + - - -
308A ALA 3.5 0.2 - - - -
309A GLY* 1.3 72.0 - - - +
311A SER* 1.3 57.0 + - - +
313A GLU* 3.6 12.6 + - - -
314A GLY* 2.8 27.2 + - - -
321A MET* 4.3 0.2 - - - +
1401A UDP 2.8 19.2 + - - -
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Residues in contact with SER 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LEU* 3.7 24.2 - - - -
304A THR* 4.7 1.4 + - - -
306A ALA* 3.2 26.9 + - - +
307A GLY 2.7 23.0 + - - -
308A ALA* 3.9 1.6 - - - -
310A GLY* 1.3 75.7 - - - +
312A GLN* 1.3 63.1 + - - +
314A GLY* 4.0 0.7 - - - -
315A LEU* 3.3 28.2 + - - +
321A MET* 4.4 5.2 - - - +
333A ASN* 4.0 3.8 - - - +
337A LEU* 3.8 19.4 - - - +
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Residues in contact with GLN 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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193A PRO* 4.2 20.7 - - + +
196A LEU* 4.1 6.9 - - + +
213A ALA* 3.4 35.6 - - + +
217A ASP* 3.6 14.7 + - - +
293A LEU* 5.2 1.7 - - - +
308A ALA 3.0 17.6 + - - +
309A GLY* 3.2 13.7 - - - +
311A SER* 1.3 76.4 - - - +
313A GLU* 1.3 75.0 + - + +
315A LEU* 3.4 3.8 + - - +
316A ALA* 2.8 29.2 + - - +
380A MET* 3.4 22.5 - - - +
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Residues in contact with GLU 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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292A GLN* 2.3 37.2 + - - +
293A LEU* 3.7 26.0 - - + -
296A LEU* 3.7 15.5 - - + -
309A GLY* 2.7 28.5 + - - +
310A GLY* 3.6 3.5 - - - +
312A GLN* 1.3 86.2 - - - +
314A GLY* 1.3 56.8 + - - +
316A ALA* 3.3 4.6 + - - +
317A THR* 2.7 38.2 + - - +
1401A UDP 2.5 33.7 + - - -
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Residues in contact with GLY 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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296A LEU* 4.3 1.7 - - - +
302A PHE* 4.2 10.1 - - - -
310A GLY 2.8 15.8 + - - -
312A GLN 3.4 0.2 - - - -
313A GLU* 1.3 77.2 - - - +
315A LEU* 1.3 59.2 + - - +
317A THR* 3.2 5.8 + - - -
318A ALA 3.1 3.5 + - - -
319A THR* 3.0 31.0 + - - -
321A MET* 3.7 24.7 - - - -
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Residues in contact with LEU 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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193A PRO* 4.5 7.0 - - + -
195A ALA* 4.1 20.0 - - + -
196A LEU* 4.1 26.9 - - + -
311A SER 3.3 15.9 + - - +
312A GLN 3.8 4.9 - - - +
314A GLY* 1.3 75.7 - - - +
316A ALA* 1.3 63.5 + - - +
318A ALA* 3.1 11.5 + - - +
321A MET* 3.8 8.3 - - + +
337A LEU* 3.8 23.6 - - + -
340A LEU* 4.4 1.1 - - + -
342A VAL* 4.0 10.1 - - + -
373A LEU* 4.1 8.7 - - + +
376A ILE* 3.7 30.1 - - + +
377A GLN* 3.5 13.7 - - - +
380A MET* 3.8 15.0 - - - +
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Residues in contact with ALA 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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217A ASP* 4.5 20.8 - - + +
218A ARG* 4.9 9.2 + - - +
293A LEU* 5.2 0.7 - - + -
312A GLN* 2.8 28.9 + - - +
313A GLU* 3.6 8.5 - - - +
314A GLY 3.3 0.2 - - - -
315A LEU* 1.3 76.2 - - - +
317A THR* 1.3 62.0 + - + +
318A ALA 3.5 0.2 - - - -
377A GLN* 3.1 18.7 + - - +
380A MET* 3.8 20.8 - - + -
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Residues in contact with THR 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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218A ARG* 4.8 12.6 - - + -
293A LEU* 4.2 18.4 - - + +
296A LEU* 3.7 33.2 - - + +
297A ARG* 4.2 9.2 - - + +
299A ALA 5.5 0.7 - - - +
313A GLU 2.7 22.4 + - - +
314A GLY 3.2 2.3 + - - -
316A ALA* 1.3 80.4 - - + +
318A ALA* 1.3 69.8 + - - +
319A THR* 2.8 25.6 + - - -
377A GLN* 3.8 4.4 + - - +
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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