Contacts of the helix formed by residues 335 - 349 (chain A) in PDB entry 3N9Y
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 335 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A GLU* 3.3 13.9 - - - +
317A VAL* 4.3 22.4 - - + -
320A ALA* 3.7 19.1 - - + -
331A MET* 3.8 13.5 - - + +
332A LEU* 4.0 15.5 + - - +
333A GLN 3.6 1.4 - - - -
334A LEU* 1.3 84.0 - - - +
336A PRO* 1.4 64.1 - - - +
337A LEU 3.3 3.1 - - - -
338A LEU* 3.2 10.5 + - + -
339A LYS* 3.2 23.3 + - + +
434A THR* 4.1 24.7 - - + -
438A ILE* 4.7 9.4 - - + -
72C ASP* 5.6 0.4 - - - -
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Residues in contact with PRO 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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316A GLU* 3.2 15.3 - - - +
333A GLN 4.9 3.1 - - - +
334A LEU* 3.3 10.3 - - - +
335A VAL* 1.4 88.3 - - - +
337A LEU* 1.3 54.8 + - + +
339A LYS* 3.5 9.1 + - + +
340A ALA* 3.0 27.0 + - - +
402A LEU* 4.3 24.0 - - + +
72C ASP* 5.4 10.1 - - - +
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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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309A VAL* 5.8 1.3 - - + -
312A MET* 3.9 43.5 - - + +
313A LEU* 3.7 20.4 - - + -
316A GLU* 2.9 20.5 + - + +
336A PRO* 1.3 75.9 - - - +
338A LEU* 1.3 60.4 + - - +
340A ALA* 3.3 4.7 + - - +
341A SER* 2.8 27.4 + - - -
398A PRO* 3.9 18.2 - - + +
399A THR* 3.8 28.5 - - + +
402A LEU* 3.9 19.3 - - + -
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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
----------------------------------------------------------
299A HIS* 4.3 3.8 - - - +
313A LEU* 3.7 9.4 - - + +
316A GLU* 2.9 12.5 + - - +
317A VAL* 4.0 13.5 - - + -
335A VAL* 3.2 14.1 + - + +
337A LEU* 1.3 76.1 - - - +
339A LYS* 1.3 57.3 + - - +
341A SER* 2.5 35.4 + - - +
342A ILE* 3.2 11.3 + - + +
434A THR* 3.8 24.9 - - + +
437A LEU* 4.0 25.1 - - + -
438A ILE* 3.7 33.9 - - + +
441A LEU* 4.1 15.5 - - + -
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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
----------------------------------------------------------
332A LEU* 2.9 29.2 + - - +
333A GLN* 3.8 4.9 + - - -
335A VAL* 3.2 13.9 + - - +
336A PRO* 3.8 9.4 - - + +
338A LEU* 1.3 73.3 - - - +
340A ALA* 1.3 64.2 + - - +
342A ILE* 3.3 11.5 + - + +
343A LYS* 3.3 28.9 + - - +
431A LEU* 6.1 3.0 - - - +
434A THR* 4.4 28.0 - - + +
72C ASP* 2.8 36.7 + - + +
73C GLU* 3.2 22.8 + - - +
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Residues in contact with ALA 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 PRO 3.0 15.1 + - - +
337A LEU* 3.5 12.1 - - - +
338A LEU 3.2 0.2 - - - -
339A LYS* 1.3 74.6 - - - +
341A SER* 1.3 60.0 + - - +
343A LYS* 3.1 9.7 + - - +
344A GLU* 2.9 28.2 + - - +
398A PRO* 3.2 26.9 - - - +
401A TRP* 3.6 19.5 - - + -
402A LEU* 4.4 10.1 - - + -
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Residues in contact with SER 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A HIS* 2.8 27.9 + - - -
313A LEU* 3.9 11.2 - - - -
337A LEU 2.8 13.6 + - - -
338A LEU* 2.5 28.2 + - - +
340A ALA* 1.3 76.3 - - - +
342A ILE* 1.3 55.9 + - - +
344A GLU* 3.7 3.7 - - - +
345A THR* 2.9 31.0 + - - -
396A PHE* 3.7 5.2 - - - -
398A PRO* 3.7 24.9 - - - -
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Residues in contact with ILE 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A THR* 5.4 2.0 - - + -
299A HIS* 4.3 3.4 - - - +
338A LEU* 3.2 15.7 + - + +
339A LYS* 3.6 12.3 - - - +
340A ALA 3.1 0.6 - - - -
341A SER* 1.3 76.6 - - - +
343A LYS* 1.3 64.7 + - + +
345A THR* 3.1 7.3 + - - +
346A LEU* 3.0 33.0 + - + +
416A PHE* 5.5 3.6 - - + -
430A GLU* 4.6 7.6 - - + +
433A MET* 4.0 33.7 - - + -
434A THR* 3.4 40.8 - - + +
437A LEU* 4.2 18.8 - - + -
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Residues in contact with LYS 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LYS* 3.3 17.9 + - - +
340A ALA* 3.1 9.5 + - - +
342A ILE* 1.3 76.3 - - + +
344A GLU* 1.3 58.1 + - - +
346A LEU* 3.4 7.5 + - - +
347A ARG* 2.9 27.9 + - - +
401A TRP* 3.8 49.8 + - + +
413A ASN* 3.6 31.6 - - - +
76C ASP* 2.6 41.1 + - - +
79C ASP* 5.3 4.8 + - - -
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Residues in contact with GLU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A ALA 2.9 16.3 + - - +
341A SER* 3.7 9.2 - - - +
343A LYS* 1.3 78.3 - - - +
345A THR* 1.3 63.0 + - - +
347A ARG* 2.8 45.2 + - - +
348A LEU* 3.4 21.1 + - - +
395A ASN 3.3 0.2 - - - +
396A PHE* 3.5 23.6 - - + -
397A ASP 2.9 31.8 + - - +
398A PRO* 4.1 3.4 - - + -
400A ARG* 3.0 13.1 + - - -
401A TRP* 2.7 29.9 + - + +
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Residues in contact with THR 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A THR* 3.5 34.8 - - + +
298A TRP* 3.8 12.8 - - + +
299A HIS* 3.2 33.0 + - + +
302A GLU* 4.9 0.4 - - + +
341A SER 2.9 23.4 + - - -
342A ILE* 3.1 7.1 + - - -
344A GLU* 1.3 76.7 - - - +
346A LEU* 1.3 50.6 + - - +
348A LEU 3.4 1.4 + - - -
349A HIS* 2.7 42.0 + - + +
396A PHE* 3.5 14.5 - - - -
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Residues in contact with LEU 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A THR* 3.9 25.1 - - + +
342A ILE* 3.0 26.9 + - + +
343A LYS* 3.9 6.1 - - - +
345A THR* 1.3 73.4 - - - +
347A ARG* 1.3 65.6 + - - +
349A HIS 3.8 15.5 - - - +
350A PRO* 3.1 24.5 - - + +
351A ILE 4.2 7.6 - - - +
380A ILE* 5.1 2.6 - - - +
413A ASN* 5.8 3.8 - - - +
415A GLY* 4.6 16.2 - - - +
416A PHE* 3.5 38.8 - - + -
433A MET* 4.9 0.9 - - + -
601A HEM 3.7 22.7 - - + -
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Residues in contact with ARG 347 (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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343A LYS 2.9 14.2 + - - +
344A GLU* 2.8 48.2 + - - +
345A THR 3.3 0.4 - - - -
346A LEU* 1.3 78.7 - - - +
348A LEU* 1.3 77.6 + - - +
350A PRO* 3.7 7.6 - - - +
380A ILE* 4.7 4.0 - - - +
381A TYR 4.9 1.4 - - - +
384A GLY* 2.8 55.4 + - - -
385A ARG* 5.0 0.5 + - - -
390A PHE* 3.5 39.4 - - + +
393A PRO* 2.9 34.6 + - - +
395A ASN 3.0 11.3 + - - -
400A ARG* 3.6 11.5 - - - +
401A TRP* 4.1 9.4 - - + -
412A ARG 5.7 2.2 - - - +
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Residues in contact with LEU 348 (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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302A GLU* 3.9 25.8 - - + +
305A ARG* 5.2 0.7 - - - +
344A GLU 3.4 10.7 + - - +
345A THR 3.4 1.4 + - - -
347A ARG* 1.3 106.4 - - - +
349A HIS* 1.3 71.9 + - + +
350A PRO* 3.4 6.6 - - - +
381A TYR* 4.2 1.9 - - - -
385A ARG* 2.7 57.4 + - - +
393A PRO 3.3 23.6 - - - +
394A GLU* 4.6 10.5 - - - +
396A PHE* 4.3 17.0 - - + +
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Residues in contact with HIS 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A THR* 5.0 3.3 + - - +
298A TRP* 3.3 81.6 - + + +
301A TYR* 4.9 2.2 - + - -
302A GLU* 2.7 35.0 + - + -
345A THR* 2.7 22.9 + - + +
346A LEU* 3.5 14.7 - - - +
348A LEU* 1.3 87.0 + - + +
350A PRO* 1.4 67.4 - - - +
351A ILE* 3.5 2.1 + - - +
385A ARG* 3.8 18.7 + - - -
454A VAL 5.2 2.0 - - - -
456A THR* 4.5 2.8 + - - -
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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