Contacts of the helix formed by residues 331 - 343 (chain A) in PDB entry 6Q6Q
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 THR 331 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A VAL 3.9 1.8 - - - +
323A VAL* 3.8 35.6 + - + -
326A LEU* 3.7 26.9 - - + +
327A PRO 3.3 17.0 + - - +
328A GLU* 3.4 10.9 - - - -
329A GLU 3.6 0.2 - - - -
330A LYS* 1.3 75.9 - - - +
332A GLN* 1.3 56.4 + - - +
333A MET 3.6 0.9 - - - -
334A TYR* 4.0 18.2 - - + -
335A HIS* 2.6 50.0 + - - +
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Residues in contact with GLN 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 GLU* 3.2 35.3 + - - +
329A GLU* 4.2 4.3 - - - +
330A LYS 3.2 3.2 - - - -
331A THR* 1.3 75.6 - - - +
333A MET* 1.3 66.9 + - - +
335A HIS* 3.4 8.6 + - - +
336A ALA* 3.4 14.6 + - - +
419A SER* 3.1 20.6 - - - +
423A GLU 3.9 10.2 - - - +
424A PHE* 3.8 26.0 - - - +
425A VAL* 3.3 47.1 + - + +
426A SER* 5.6 0.6 + - - -
533A ILE* 5.3 8.7 - - - +
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Residues in contact with MET 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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330A LYS 4.5 2.3 + - - +
332A GLN* 1.3 79.1 - - - +
334A TYR* 1.3 64.6 + - + +
336A ALA* 3.3 5.4 + - - +
337A LEU* 3.2 24.7 + - + +
371A ILE* 3.6 33.4 - - - +
372A LEU* 4.3 3.1 - - + -
375A GLY* 3.4 39.3 - - - +
377A CYS* 3.8 20.2 - - - -
416A ILE* 3.5 25.8 - - + -
417A PRO* 4.3 12.6 - - + +
419A SER* 4.5 6.4 + - - -
425A VAL* 3.6 19.0 - - + +
446A ARG* 6.1 1.1 - - - -
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Residues in contact with TYR 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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304A LEU* 3.2 28.6 + - + +
319A LEU* 3.8 23.9 - - + +
322A VAL* 4.0 17.7 - - + -
323A VAL* 4.1 13.5 - - + -
330A LYS 4.1 5.6 - - - -
331A THR* 4.0 19.5 - - + +
332A GLN 3.3 0.6 - - - -
333A MET* 1.3 76.4 - - + +
335A HIS* 1.3 60.4 + - - +
337A LEU* 3.3 10.2 + - + +
338A LEU* 2.9 35.8 + - + +
416A ILE* 3.0 45.1 + - + -
417A PRO 3.7 6.9 - - - -
418A TYR* 3.1 40.3 - + - -
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Residues in contact with HIS 335 (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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323A VAL* 3.5 34.0 + - + +
328A GLU* 4.3 20.0 + - + +
331A THR* 2.6 42.0 + - - +
332A GLN* 3.4 9.2 + - - +
333A MET 3.3 0.2 - - - -
334A TYR* 1.3 79.9 - - - +
336A ALA* 1.3 57.6 + - - +
338A LEU* 3.4 7.7 + - + +
339A LYS* 3.0 29.3 + - - +
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Residues in contact with ALA 336 (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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332A GLN 3.4 8.9 + - - +
333A MET 3.3 10.1 + - - +
335A HIS* 1.3 77.6 - - - +
337A LEU* 1.3 62.6 + - - +
339A LYS* 3.5 14.3 + - - +
340A HIS 3.5 5.7 + - - -
371A ILE* 3.3 34.5 - - + +
425A VAL* 4.6 10.1 - - + +
426A SER* 4.6 6.5 - - - -
427A ALA* 4.0 23.4 - - + +
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Residues in contact with LEU 337 (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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315A VAL* 5.8 2.2 - - + -
319A LEU* 4.0 24.5 - - + -
333A MET* 3.2 16.0 + - + +
334A TYR* 3.7 9.2 - - + +
336A ALA* 1.3 74.0 - - - +
338A LEU* 1.3 59.7 + - - +
339A LYS 3.3 0.3 + - - -
340A HIS* 3.4 1.9 + - - +
341A LEU* 2.9 38.1 + - + +
368A LEU* 4.3 17.9 - - + +
371A ILE* 3.8 27.1 - - + -
372A LEU* 3.8 35.4 - - + -
416A ILE* 4.6 20.9 - - + -
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Residues in contact with LEU 338 (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 LYS* 3.3 42.2 + - + +
319A LEU* 3.4 34.8 - - + +
320A ALA* 3.4 14.1 - - + +
323A VAL* 3.6 22.0 - - + -
334A TYR 2.9 23.3 + - - +
335A HIS* 3.8 9.2 - - + +
337A LEU* 1.3 75.7 - - - +
339A LYS* 1.3 62.6 + - - +
341A LEU* 4.1 5.9 - - - +
342A GLY* 3.3 16.8 + - - -
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Residues in contact with LYS 339 (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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335A HIS 3.0 17.3 + - - +
336A ALA* 3.6 8.5 - - - +
337A LEU 3.1 0.8 - - - -
338A LEU* 1.3 80.0 - - - +
340A HIS* 1.3 72.7 + - + +
342A GLY* 3.5 7.1 + - - -
343A THR* 3.9 14.8 + - + +
426A SER* 6.0 0.8 - - - -
427A ALA* 2.6 34.8 + - + +
428A PHE* 4.0 18.3 - - - +
529A GLU* 4.7 6.1 + - - -
555A ASP* 3.9 25.7 + - - +
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Residues in contact with HIS 340 (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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336A ALA 3.5 0.8 + - - -
337A LEU 3.4 1.8 + - - -
339A LYS* 1.3 92.5 - - + +
341A LEU* 1.3 61.7 + - - +
342A GLY 3.1 1.6 - - - -
343A THR* 3.3 8.5 + - + -
344A LEU* 2.9 28.6 + - - +
367A ASP* 3.0 36.7 + - + +
368A LEU* 4.3 4.7 - - + -
370A PRO* 6.0 0.7 - - + -
371A ILE* 3.4 15.5 - - + +
427A ALA* 3.6 11.8 + - + -
428A PHE* 3.0 50.7 + - - -
429A ARG* 3.7 25.6 + - + +
442A ASN* 4.5 4.7 - - + -
443A SER 4.0 3.4 - - - -
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Residues in contact with LEU 341 (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 LEU* 3.6 34.8 - - + +
315A VAL* 4.0 15.0 - - + -
316A LYS* 3.2 42.3 + - + +
319A LEU* 5.0 3.6 - - + -
337A LEU* 2.9 25.9 + - + +
338A LEU* 4.1 3.8 - - - +
339A LYS 3.4 0.2 - - - -
340A HIS* 1.3 76.4 - - - +
342A GLY* 1.3 61.0 + - - +
343A THR 3.4 0.2 - - - -
344A LEU* 3.5 20.1 - - + +
350A ARG* 3.3 20.9 - - - -
368A LEU* 3.7 31.9 - - + -
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Residues in contact with GLY 342 (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 LYS* 3.3 16.0 + - - +
338A LEU 3.3 12.7 + - - -
339A LYS 3.5 4.2 + - - -
340A HIS 3.1 0.8 - - - -
341A LEU* 1.3 79.0 - - - +
343A THR* 1.3 60.6 + - - +
344A LEU 3.3 1.0 + - - -
350A ARG* 3.7 13.2 + - - -
435A GLU* 3.9 12.8 - - - +
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Residues in contact with THR 343 (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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339A LYS* 3.9 11.2 - - + +
340A HIS* 3.3 11.4 + - + -
342A GLY* 1.3 78.1 - - - +
344A LEU* 1.3 58.2 + - - +
345A ALA 3.0 11.0 + - - -
367A ASP* 4.1 0.9 + - - +
429A ARG* 3.2 35.4 + - - -
434A GLN* 3.7 27.6 - - + +
435A GLU* 4.1 10.5 - - + +
436A ASN 3.8 11.8 + - - -
557A HIS* 5.8 8.3 - - + -
3003A FAD 4.3 4.2 - - - +
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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