Contacts of the helix formed by residues 322 - 334 (chain A) in PDB entry 6Q3W
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 CYS 322 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A HIS* 4.0 15.5 - - + -
321A SER* 1.3 79.4 + - - +
323A PRO* 1.3 78.1 - - + +
324A GLU* 3.1 21.5 - - - +
325A LEU* 3.0 20.7 + - - -
326A ASP* 2.9 27.1 + - - -
348A PHE* 3.9 5.6 - - + -
349A GLY* 3.5 29.4 - - - -
231D LEU* 5.6 4.5 - - + -
234D SER* 5.7 2.2 - - - -
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Residues in contact with PRO 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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229A HIS* 5.2 2.7 - - + +
322A CYS* 1.3 87.3 - - + +
324A GLU* 1.3 66.6 + - - +
326A ASP* 3.9 8.8 - - + +
327A GLN* 3.0 31.2 + - - +
231D LEU* 5.2 4.5 - - + -
233D SER* 4.6 22.2 - - - +
234D SER* 4.5 17.7 - - - -
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Residues in contact with GLU 324 (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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225A SER* 4.3 2.9 - - - -
227A VAL* 3.7 26.8 - - + +
229A HIS* 3.0 34.5 + - - -
322A CYS* 3.2 11.7 - - - +
323A PRO* 1.3 86.5 - - - +
325A LEU* 1.3 63.4 + - - +
327A GLN* 3.8 3.0 - - - +
328A LEU* 3.0 28.6 + - - +
372A TYR* 3.7 32.4 - - + +
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Residues in contact with LEU 325 (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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225A SER* 4.7 4.9 - - - +
311A HIS* 4.5 0.2 - - - -
321A SER* 3.5 20.6 - - - +
322A CYS* 3.0 15.5 + - - +
324A GLU* 1.3 78.3 - - - +
326A ASP* 1.3 58.5 + - - +
328A LEU* 3.2 6.5 + - - +
329A VAL* 2.9 33.7 + - - +
343A MET* 3.8 23.1 - - + -
344A THR 6.0 0.2 - - - +
347A GLY* 4.2 2.7 - - - -
348A PHE 4.0 8.5 - - - +
349A GLY* 3.5 39.9 - - - +
350A GLY 3.8 11.7 - - - +
351A CYS 3.7 12.6 - - - +
352A THR* 3.7 21.4 - - + +
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Residues in contact with ASP 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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311A HIS* 2.9 20.0 + - - -
315A ARG* 3.4 32.1 - - - +
321A SER* 2.6 25.3 + - - -
322A CYS* 2.9 21.5 + - - +
323A PRO* 3.9 8.2 - - + +
325A LEU* 1.3 77.2 - - - +
327A GLN* 1.3 56.9 + - - +
329A VAL* 3.3 1.9 + - - +
330A GLU* 2.9 31.6 + - - +
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Residues in contact with GLN 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A PRO 3.0 19.4 + - - +
324A GLU* 3.8 4.9 - - - +
326A ASP* 1.3 76.9 - - - +
328A LEU* 1.3 61.9 + - - +
330A GLU* 4.2 5.4 - - - +
331A ALA* 3.1 25.6 + - - +
371A HIS 5.0 11.2 - - - +
372A TYR* 4.8 11.8 - - + -
373A GLY 5.9 0.9 - - - +
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Residues in contact with LEU 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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223A THR* 4.0 20.6 - - + +
224A ASN 4.8 0.2 - - - +
225A SER* 3.7 38.4 - - - +
324A GLU 3.0 16.5 + - - +
325A LEU* 3.2 8.9 + - + +
327A GLN* 1.3 78.0 - - - +
329A VAL* 1.3 62.0 + - - +
331A ALA* 3.8 3.6 - - + +
332A ALA* 3.2 23.0 + - - +
352A THR* 3.8 24.4 + - + +
368A ILE* 3.7 28.3 - - + +
372A TYR* 3.5 33.4 - - + -
376A ALA* 4.5 0.2 - - + -
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Residues in contact with VAL 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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308A VAL* 6.0 1.1 - - + -
311A HIS* 3.4 41.5 - - + +
325A LEU 2.9 20.1 + - - +
326A ASP 3.7 4.0 - - - +
328A LEU* 1.3 74.1 - - - +
330A GLU* 1.3 66.8 + - - +
332A ALA* 3.1 4.0 + - - +
333A LEU* 3.0 38.1 + - + +
341A SER* 3.7 26.2 - - - +
342A ARG* 3.9 14.8 - - - +
343A MET 3.9 3.1 - - - +
352A THR* 4.0 9.0 - - + -
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Residues in contact with GLU 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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326A ASP 2.9 21.4 + - - +
327A GLN* 4.2 5.6 - - - +
329A VAL* 1.3 76.5 - - - +
331A ALA* 1.3 63.0 + - - +
333A LEU* 3.5 9.6 + - - +
334A ALA* 3.5 18.0 + - - +
2B ALA* 4.5 17.9 - - + +
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Residues in contact with ALA 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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327A GLN 3.1 20.2 + - - +
328A LEU* 3.8 6.7 - - - +
329A VAL 3.2 0.2 - - - -
330A GLU* 1.3 77.9 - - - +
332A ALA* 1.3 60.2 + - - +
334A ALA* 3.1 11.4 + - - +
335A VAL* 3.5 1.9 - - - +
367A HIS* 3.3 27.5 + - - +
368A ILE* 4.1 18.4 - - + +
371A HIS* 3.9 28.3 - - + -
2B ALA* 5.0 3.6 - - - +
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Residues in contact with ALA 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 LEU 3.2 14.4 + - - +
329A VAL 3.1 5.0 + - - +
331A ALA* 1.3 78.8 - - - +
333A LEU* 1.3 61.7 + - - +
334A ALA 3.1 0.4 - - - -
335A VAL* 3.1 14.2 + - - +
338A VAL* 3.3 22.8 - - + +
341A SER* 3.7 21.8 - - - +
352A THR* 6.0 0.4 - - - +
354A THR* 3.9 11.9 - - + +
368A ILE* 3.8 24.6 - - + +
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Residues in contact with LEU 333 (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 VAL* 3.8 33.2 - - + -
329A VAL* 3.0 37.5 + - + +
330A GLU* 3.9 8.7 - - - +
331A ALA 3.3 0.4 - - - -
332A ALA* 1.3 76.1 - - - +
334A ALA* 1.3 58.8 + - - +
335A VAL 3.2 5.5 + - - +
338A VAL* 4.4 8.7 - - + +
339A TYR 5.0 1.6 - - - +
340A GLY* 4.0 8.5 - - - +
341A SER* 3.7 26.9 - - - +
375B THR* 4.4 10.4 + - - +
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Residues in contact with ALA 334 (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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330A GLU 3.5 7.9 + - - +
331A ALA 3.1 10.3 + - - +
332A ALA 3.1 1.0 - - - -
333A LEU* 1.3 78.0 - - - +
335A VAL* 1.3 59.8 + - - +
336A PRO* 3.7 4.3 - - - +
367A HIS* 3.9 4.7 + - + -
2B ALA* 3.4 34.8 - - + +
3B ALA* 3.8 13.3 - - + +
369B GLN* 5.3 4.0 - - - +
375B THR* 3.4 18.2 - - - +
376B ALA 4.2 6.4 - - - +
377B THR* 4.5 3.6 + - - -
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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