Contacts of the helix formed by residues 330 - 347 (chain A) in PDB entry 6T2C
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 VAL 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329A GLY* 1.3 70.3 - - - -
331A ASN* 1.3 61.5 + - - +
332A THR* 4.0 12.3 - - + +
333A ASN* 2.9 44.7 + - - +
334A TYR 3.8 0.7 + - - -
363A TRP* 3.3 34.2 - - + +
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Residues in contact with ASN 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ILE* 3.8 23.6 - - + +
325A LYS* 3.4 19.8 - - + +
326A HIS* 2.6 44.3 + - - +
329A GLY 3.0 26.2 + - - -
330A VAL* 1.3 69.2 - - - +
332A THR* 1.3 65.9 + - + +
333A ASN 3.1 0.2 - - - -
334A TYR* 3.1 13.6 + - - +
335A LEU* 3.0 20.6 + - - +
536A CYS* 3.3 16.7 - - - -
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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
----------------------------------------------------------
322A ILE* 5.0 6.3 - - + -
330A VAL* 4.0 10.8 - - + +
331A ASN* 1.3 79.7 - - + +
333A ASN* 1.3 69.3 + - - +
335A LEU* 3.7 11.0 - - + +
336A MET* 2.9 42.7 + - - +
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Residues in contact with ASN 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A VAL* 2.9 24.4 + - - +
332A THR* 1.3 88.2 + - - +
334A TYR* 1.3 56.3 + - - +
336A MET* 3.8 2.6 - - - +
337A ILE* 2.9 36.2 + - - +
359A ASN 4.7 0.6 + - - -
360A HIS* 3.5 30.7 - - + +
363A TRP* 3.4 47.4 - - + +
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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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326A HIS* 3.8 29.0 + - + -
330A VAL 3.8 0.2 + - - -
331A ASN* 3.1 19.7 + - - +
333A ASN* 1.3 76.9 - - - +
335A LEU* 1.3 64.6 + - - +
337A ILE* 3.3 13.7 + - + +
338A TRP* 3.0 22.7 + - - +
363A TRP* 4.0 24.7 - + - -
364A GLY* 5.0 5.4 - - - -
516A ILE* 4.9 5.6 - - + -
534A LYS 5.5 1.7 + - - -
535A TYR 5.9 0.2 - - - -
536A CYS* 3.6 36.6 - - + -
538A LEU* 4.7 5.3 - - + +
560A VAL* 3.6 31.7 - - + +
561A ARG* 4.7 5.3 - - - -
562A THR* 2.5 39.7 + - - -
1V A 4.3 4.7 + - - -
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Residues in contact with LEU 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ALA* 3.4 44.4 - - + +
321A THR* 4.5 3.4 - - + +
322A ILE* 4.7 14.1 - - + -
331A ASN 3.0 12.6 + - - +
332A THR* 3.7 12.1 - - + +
333A ASN 3.3 0.2 - - - -
334A TYR* 1.3 77.0 - - - +
336A MET* 1.3 60.3 + - + +
338A TRP* 3.3 4.5 + - + +
339A GLU* 3.0 40.6 + - + +
538A LEU* 3.8 25.0 - - + +
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Residues in contact with MET 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 THR* 2.9 30.8 + - - +
333A ASN* 5.3 1.6 - - - +
335A LEU* 1.3 76.3 - - + +
337A ILE* 1.3 59.7 + - - +
339A GLU* 3.8 16.2 - - - +
340A GLN* 2.9 31.7 + - - +
360A HIS* 3.4 42.7 + - + +
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Residues in contact with ILE 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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333A ASN* 2.9 24.6 + - + +
334A TYR* 3.6 13.0 - - + +
335A LEU 3.3 0.2 - - - -
336A MET* 1.3 76.4 - - - +
338A TRP* 1.3 59.0 + - - +
340A GLN* 3.4 5.8 + - - +
341A LEU* 3.0 28.4 + - - +
355A LEU* 6.0 0.3 - - - +
360A HIS* 3.4 36.6 - - + +
361A LEU* 4.0 11.4 - - + -
364A GLY* 4.1 6.5 - - - -
500A ILE* 4.1 24.1 - - + +
516A ILE* 3.7 30.7 - - + -
518A LEU* 4.4 13.9 - - + -
560A VAL* 5.3 1.1 - - + -
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Residues in contact with TRP 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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311A LEU* 5.8 1.1 - - + -
317A TRP* 4.0 30.1 - + - -
320A ALA* 3.7 31.8 - - + +
334A TYR 3.0 14.3 + - - +
335A LEU 3.8 7.4 - - - +
337A ILE* 1.3 80.2 - - - +
339A GLU* 1.3 61.8 + - + +
341A LEU* 4.4 21.5 - - + +
342A LEU* 2.9 60.3 + - + +
345A ILE* 6.2 0.7 - - + -
498A PHE* 4.8 15.5 - + - -
518A LEU* 4.4 9.9 - - + -
520A PHE* 4.6 8.1 - + - -
538A LEU* 4.0 17.0 - - + -
540A ILE* 3.9 19.5 - - + +
558A LEU* 3.6 26.0 - - + -
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Residues in contact with GLU 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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319A LYS* 5.6 6.9 - - - +
320A ALA* 4.9 10.0 + - + +
335A LEU* 3.0 37.1 + - + +
336A MET* 3.8 16.7 - - - +
337A ILE 3.3 0.2 - - - -
338A TRP* 1.3 84.3 - - + +
340A GLN* 1.3 57.2 + - - +
342A LEU* 3.4 8.4 + - + +
343A GLU* 3.0 29.3 + - - +
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Residues in contact with GLN 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 MET 2.9 15.9 + - - +
337A ILE* 3.8 5.4 - - - +
339A GLU* 1.3 76.0 - - - +
341A LEU* 1.3 58.8 + - - +
343A GLU* 3.4 6.2 + - - +
344A SER* 2.9 41.4 + - - +
355A LEU* 4.2 9.9 - - + +
356A LYS* 3.2 35.2 + - - +
358A THR* 2.9 16.4 + - - +
360A HIS* 2.5 37.6 + - + +
361A LEU* 3.7 15.4 - - - +
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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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337A ILE 3.0 17.8 + - - +
338A TRP* 3.9 15.9 - - + +
340A GLN* 1.3 76.7 - - - +
342A LEU* 1.3 58.4 + - - +
344A SER* 4.6 2.9 - - - -
345A ILE* 3.0 53.8 + - + +
353A LEU* 4.6 2.9 - - + -
355A LEU* 4.9 5.6 - - + -
477A VAL* 3.7 33.2 - - + -
498A PHE* 4.0 22.9 - - + -
500A ILE* 4.3 11.7 - - + -
518A LEU* 3.8 29.4 - - + -
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Residues in contact with LEU 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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311A LEU* 5.7 7.6 - - + -
317A TRP* 5.0 27.6 - - + -
318A LYS 6.2 0.4 - - - +
338A TRP* 2.9 56.7 + - + +
339A GLU* 3.8 7.9 - - + +
341A LEU* 1.3 77.4 - - - +
343A GLU* 1.3 63.3 + - - +
345A ILE* 3.8 8.5 + - + +
346A LYS* 3.7 31.7 + - + +
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Residues in contact with GLU 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 GLU 3.0 18.0 + - - +
340A GLN* 3.6 7.2 - - - +
341A LEU 3.3 0.2 - - - -
342A LEU* 1.3 76.2 - - - +
344A SER* 1.3 65.8 + - - +
345A ILE 3.3 1.0 + - - -
346A LYS* 3.4 14.2 + - - +
347A GLU* 3.8 20.6 + - - +
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Residues in contact with SER 344 (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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340A GLN* 2.9 23.5 + - - +
341A LEU 3.3 1.5 + - - -
343A GLU* 1.3 76.7 - - - +
345A ILE* 1.3 65.4 + - - +
347A GLU* 3.8 12.6 + - - +
348A MET 4.0 4.3 + - - -
353A LEU* 3.7 23.6 - - - +
355A LEU* 3.9 26.8 - - - +
356A LYS* 5.8 4.2 + - - +
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Residues in contact with ILE 345 (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 MET* 4.5 14.1 - - + -
308A LYS* 4.7 17.7 - - + -
311A LEU* 3.9 20.6 - - + -
338A TRP* 6.2 0.9 - - + -
341A LEU* 3.0 42.1 + - + +
342A LEU* 4.3 9.0 - - + +
343A GLU 3.2 0.4 - - - -
344A SER* 1.3 77.3 - - - +
346A LYS* 1.3 74.2 + - + +
347A GLU 3.1 1.4 + - - -
348A MET* 3.3 24.8 - - - +
353A LEU* 4.1 12.3 - - + -
477A VAL* 5.4 0.2 - - + -
498A PHE* 3.6 37.7 - - + -
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Residues in contact with LYS 346 (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 LYS* 4.3 24.0 + - - +
311A LEU* 4.8 16.5 + - - +
312A ASP* 3.2 25.7 + - - +
317A TRP* 5.4 10.2 - - - +
342A LEU* 3.7 26.5 - - + +
343A GLU* 3.4 9.2 + - - +
345A ILE* 1.3 86.2 - - + +
347A GLU* 1.3 57.1 + - - +
348A MET 3.5 1.0 - - - +
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Residues in contact with GLU 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A GLU* 3.8 21.9 + - - +
344A SER* 3.8 9.0 + - - +
345A ILE 3.1 1.4 + - - -
346A LYS* 1.3 78.1 - - + +
348A MET* 1.3 60.5 + - - +
349A GLU* 3.8 9.6 + - + +
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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
------------------------------------------------------------
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