Contacts of the helix formed by residues 316 - 332 (chain A) in PDB entry 3G0H
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 SER 316 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A CYS* 3.8 0.4 - - - +
315A SER* 1.3 81.4 + - - +
317A ARG* 1.3 58.9 + - - +
318A ASP* 3.2 13.7 + - - +
319A GLU* 3.1 22.1 + - - +
320A LYS* 3.1 30.1 + - - +
444A ASP* 3.7 12.3 + - - +
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Residues in contact with ARG 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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316A SER* 1.3 72.9 - - - +
318A ASP* 1.3 63.8 + - - +
320A LYS* 3.3 14.6 + - - +
321A PHE* 3.0 27.2 + - - +
345A THR* 4.6 17.5 + - - +
348A TRP* 3.4 67.4 - - + +
408A PHE* 4.0 18.0 - - + -
444A ASP* 4.9 1.2 + - - +
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Residues in contact with ASP 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A SER* 3.2 11.0 + - - +
317A ARG* 1.3 79.1 + - - +
319A GLU* 1.3 57.8 + - - +
321A PHE* 3.3 11.1 + - - +
322A GLN* 3.0 31.9 + - - +
348A TRP* 4.5 15.0 - - - -
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Residues in contact with GLU 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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313A LEU 4.3 3.3 - - - +
314A CYS* 3.5 20.8 - - + -
315A SER* 2.7 33.3 + - - -
316A SER* 3.1 23.9 + - - +
318A ASP* 1.3 73.6 - - - +
320A LYS* 1.3 63.6 + - - +
322A GLN* 3.6 7.6 + - + +
323A ALA* 3.2 22.2 + - - +
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Residues in contact with LYS 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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314A CYS* 4.0 19.1 - - + -
316A SER 3.1 12.7 + - - +
317A ARG* 3.3 16.9 + - - +
319A GLU* 1.3 74.5 - - - +
321A PHE* 1.3 65.5 + - - +
323A ALA* 3.5 3.2 + - - +
324A LEU* 3.2 25.3 + - - +
408A PHE* 3.1 53.9 + - + +
409A ASP* 3.3 15.8 + - - +
442A MET* 3.5 29.2 + - + +
444A ASP* 3.1 37.5 + - + +
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Residues in contact with PHE 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 ARG 3.0 13.4 + - - +
318A ASP* 3.4 12.3 - - + +
320A LYS* 1.3 78.0 - - - +
322A GLN* 1.3 70.2 + - + +
324A LEU* 3.6 3.1 + - + +
325A CYS* 3.0 48.2 + - - -
348A TRP* 4.2 13.2 - + + -
349A LEU* 4.0 16.8 - - + -
352A GLU* 3.3 62.4 - - + -
353A LEU* 3.6 18.8 - - + -
356A GLU* 4.2 13.7 - - + -
408A PHE* 3.8 5.3 - - - -
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Residues in contact with GLN 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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318A ASP 3.0 18.1 + - - +
319A GLU* 3.9 8.5 - - + +
320A LYS 3.3 0.4 - - - -
321A PHE* 1.3 87.0 - - + +
323A ALA* 1.3 65.3 + - - +
325A CYS* 3.2 11.4 - - - +
326A ASN* 3.0 44.5 + - - +
356A GLU* 4.3 14.0 + - - +
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Residues in contact with ALA 323 (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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312A VAL* 5.0 10.8 - - + -
314A CYS* 4.5 11.2 - - - -
319A GLU 3.2 17.4 + - - +
320A LYS* 3.7 7.6 - - - +
321A PHE 3.4 0.2 - - - -
322A GLN* 1.3 74.8 - - - +
324A LEU* 1.3 57.0 + - - +
326A ASN* 2.8 29.1 + - - +
327A LEU* 3.0 22.2 + - + +
442A MET* 4.6 11.9 - - + -
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Residues in contact with LEU 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LYS 3.2 13.1 + - - +
321A PHE* 3.9 3.4 - - - +
323A ALA* 1.3 78.9 - - - +
325A CYS* 1.3 56.8 + - - +
327A LEU* 3.1 7.7 + - - -
328A TYR* 2.9 34.6 + - + +
331A ILE* 3.6 30.3 - - + -
338A ILE* 3.8 30.1 - - + -
349A LEU* 3.9 28.5 - - + -
353A LEU* 4.5 13.7 - - + -
406A ILE* 4.8 7.2 - - + -
408A PHE* 4.0 17.7 - - + -
442A MET* 4.5 14.5 - - + +
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Residues in contact with CYS 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A PHE* 3.0 53.7 + - - +
322A GLN* 3.2 23.1 - - - +
324A LEU* 1.3 77.5 - - - +
326A ASN* 1.3 62.5 + - - +
328A TYR* 3.4 14.7 + - - +
329A GLY 4.9 0.7 + - - -
353A LEU* 4.7 4.0 - - - +
356A GLU* 3.9 25.4 - - + +
358A HIS* 4.3 17.7 + - + -
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Residues in contact with ASN 326 (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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61A LEU* 5.1 6.2 - - - +
322A GLN* 3.0 31.9 + - - +
323A ALA* 2.8 15.1 + - - +
325A CYS* 1.3 74.5 - - - +
327A LEU* 1.3 68.4 + - + +
328A TYR 3.4 0.6 + - - -
329A GLY* 4.6 3.6 + - - -
330A ALA 5.5 0.3 + - - -
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Residues in contact with LEU 327 (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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61A LEU* 4.0 25.1 - - + -
63A ASN* 4.4 21.1 - - + +
312A VAL* 5.1 5.8 - - + -
323A ALA* 3.0 22.6 + - + +
324A LEU* 3.1 8.0 + - + +
326A ASN* 1.3 85.7 - - + +
328A TYR* 1.3 62.0 + - - +
329A GLY 3.3 3.1 - - - -
330A ALA* 3.0 18.3 + - - +
331A ILE* 3.1 22.5 + - + +
406A ILE* 5.4 4.0 - - + -
440A VAL* 5.0 10.5 - - + -
442A MET* 4.6 19.7 - - + -
466A LEU* 5.1 10.5 - - + -
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Residues in contact with TYR 328 (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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324A LEU* 2.9 23.0 + - + +
325A CYS 3.6 14.1 - - - +
326A ASN 3.4 2.0 - - - -
327A LEU* 1.3 78.4 - - - +
329A GLY* 1.3 57.5 + - - +
331A ILE* 3.2 6.3 + - + +
332A THR* 2.9 60.3 + - + +
353A LEU* 3.9 31.0 - - + -
358A HIS* 3.3 44.4 - + + +
359A GLN 2.7 26.2 + - - -
360A VAL* 3.8 8.3 - - - +
386A VAL* 3.4 34.0 - - + +
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Residues in contact with GLY 329 (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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64A LYS* 6.3 0.4 - - - -
325A CYS 4.9 0.6 + - - -
326A ASN 4.6 3.6 + - - -
327A LEU 3.3 1.2 - - - -
328A TYR* 1.3 77.7 - - - +
330A ALA* 1.3 58.1 + - - +
332A THR* 3.4 14.3 + - - -
333A ILE* 3.4 15.1 + - - +
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Residues in contact with ALA 330 (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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61A LEU* 4.2 13.2 - - + +
63A ASN* 3.4 38.1 - - + +
64A LYS* 4.2 5.2 - - - +
66A ILE* 3.0 19.0 - - + +
327A LEU* 3.0 13.0 + - - +
329A GLY* 1.3 75.5 - - - +
331A ILE* 1.3 63.8 + - - +
333A ILE* 3.2 26.2 - - - +
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Residues in contact with ILE 331 (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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63A ASN* 5.1 5.6 - - - +
66A ILE* 4.2 6.4 - - - +
324A LEU* 3.6 31.6 - - + -
327A LEU* 3.1 21.8 + - + +
328A TYR* 3.2 12.1 + - + +
330A ALA* 1.3 77.6 - - - +
332A THR* 1.3 57.7 + - - +
333A ILE 3.5 0.7 + - - -
334A ALA 3.9 1.2 + - - +
335A GLN* 3.8 22.2 + - - +
336A ALA* 3.1 26.3 - - + +
338A ILE* 5.3 2.0 - - + -
385A LYS 4.7 0.5 - - - +
386A VAL* 3.5 23.6 - - + -
403A SER* 5.5 0.3 + - - -
404A VAL* 4.6 14.7 - - + +
406A ILE* 4.1 20.4 - - + -
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Residues in contact with THR 332 (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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328A TYR* 2.9 48.3 + - + +
329A GLY* 3.4 11.6 + - - -
331A ILE* 1.3 74.8 - - - +
333A ILE* 1.3 66.6 + - - +
334A ALA 3.3 11.4 - - - +
359A GLN 5.6 0.9 - - - +
385A LYS* 4.0 26.1 - - + +
386A VAL* 4.1 11.9 - - + -
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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