Contacts of the helix formed by residues 328 - 336 (chain X) in PDB entry 2W6C
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 328 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288X PHE* 5.6 0.4 - - - -
326X ASP 3.2 1.8 + - - -
327X GLU* 1.3 78.0 - - - +
329X SER* 1.3 67.3 + - - +
330X PHE 3.3 0.2 - - - -
331X PHE* 3.0 18.8 + - - +
332X LEU* 3.4 10.7 + - - +
392X ASP* 3.4 10.5 + - - -
395X VAL* 3.7 30.6 - - - +
396X GLY* 3.8 8.6 - - - -
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Residues in contact with SER 329 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326X ASP 3.5 7.6 + - - -
327X GLU 3.6 0.6 - - - -
328X GLY* 1.3 76.6 - - - +
330X PHE* 1.3 64.9 + - - +
332X LEU* 3.1 9.3 + - - +
333X LEU* 3.0 22.7 + - - +
392X ASP* 3.2 24.6 + - - -
435X TRP* 3.8 12.2 - - - -
436X MET* 2.5 45.5 + - - +
439X ILE* 4.4 4.3 - - - +
440X HIS 5.4 0.2 + - - -
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Residues in contact with PHE 330 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81X SER* 5.8 0.2 - - - -
84X TRP* 5.8 0.2 - + - -
327X GLU 4.6 1.2 + - - -
328X GLY 3.0 2.8 + - - -
329X SER* 1.3 77.3 + - - +
331X PHE* 1.3 76.1 + - + +
333X LEU* 3.2 2.6 + - - +
334X TYR* 2.9 48.9 + + - +
432X TRP* 3.4 50.3 - + - -
436X MET* 3.8 12.9 - - + +
439X ILE* 3.1 43.1 - - + -
440X HIS* 3.9 14.1 - - + +
442X TYR* 4.0 4.7 - + - -
601X BM4 3.6 45.5 - - + -
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Residues in contact with PHE 331 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287X ILE* 3.1 26.1 - - + +
288X PHE* 3.3 74.9 - + + +
290X PHE* 4.2 5.6 - + - -
327X GLU 3.6 15.3 - - - -
328X GLY* 3.0 13.4 + - - +
330X PHE* 1.3 85.2 - - + +
332X LEU* 1.3 58.3 - - - +
334X TYR* 3.6 5.2 + - - +
335X GLY 3.2 12.8 + - - -
395X VAL* 4.4 7.6 - - + -
440X HIS* 3.5 27.1 - + - -
601X BM4 3.7 43.5 - + + -
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Residues in contact with LEU 332 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287X ILE* 5.0 4.3 - - + -
328X GLY 3.4 9.4 + - - +
329X SER* 3.1 9.0 + - - +
331X PHE* 1.3 76.4 - - - +
333X LEU* 1.3 63.4 + - - +
336X ALA* 2.8 52.5 + - + +
339X PHE* 3.6 37.2 - - + +
355X GLY* 5.2 1.8 - - - -
359X SER* 4.7 4.3 - - - +
391X LEU* 3.7 18.8 - - + +
392X ASP* 3.5 39.0 - - + +
395X VAL* 3.9 21.3 - - + -
435X TRP* 5.3 0.4 - - + -
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Residues in contact with LEU 333 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74X GLN* 5.3 2.6 - - - +
75X PHE* 4.3 12.4 - - + -
329X SER 3.0 12.2 + - - +
330X PHE 3.4 8.1 - - - +
332X LEU* 1.3 79.4 - - - +
334X TYR* 1.3 76.4 + - + +
335X GLY 3.3 0.3 + - - -
336X ALA 4.8 1.0 + - - +
339X PHE* 4.0 13.7 - - - +
340X SER* 3.4 16.2 - - - +
341X LYS* 3.4 32.8 - - + +
432X TRP* 3.8 23.1 - - + -
435X TRP* 4.0 10.9 - - + -
436X MET* 3.7 28.7 - - + -
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Residues in contact with TYR 334 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72X ASP* 2.5 42.6 + - - -
74X GLN* 3.6 27.9 - - + +
75X PHE* 3.7 24.7 - + - -
81X SER* 3.4 16.3 - - - -
287X ILE* 5.3 0.2 - - - -
330X PHE* 2.9 45.8 + + - +
331X PHE 4.3 3.1 - - - +
333X LEU* 1.3 86.8 - - + +
335X GLY* 1.3 57.3 + - - +
432X TRP* 3.9 2.8 - + - -
601X BM4 3.6 53.5 - - + +
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Residues in contact with GLY 335 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287X ILE* 3.3 25.0 - - - +
331X PHE 3.2 6.5 + - - -
332X LEU 3.1 2.8 + - - -
333X LEU 3.3 0.4 + - - -
334X TYR* 1.3 82.4 - - - +
336X ALA* 1.3 64.6 + - - +
337X PRO* 3.7 4.5 - - - +
358X LEU* 4.1 4.5 - - - +
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Residues in contact with ALA 336 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287X ILE* 3.7 4.9 - - + +
332X LEU* 2.8 42.3 + - + +
333X LEU 5.0 0.7 - - - +
335X GLY* 1.3 73.9 - - - -
337X PRO* 1.3 73.8 - - + +
338X GLY 3.5 1.2 + - - -
339X PHE* 3.4 31.5 + - + +
351X ASP 6.0 0.2 - - - +
355X GLY* 4.7 8.5 - - - -
358X LEU* 4.1 10.8 - - + -
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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