Contacts of the helix formed by residues 345 - 363 (chain B) in PDB entry 3NA0
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 ASN 345 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B GLU* 3.0 27.9 + - - +
342B MET 3.4 6.7 - - - +
344B ARG* 1.3 102.9 + - - +
346B LEU* 1.3 64.4 + - - +
347B LYS 3.2 3.1 - - - -
348B VAL* 3.1 31.0 + - + +
349B GLN 3.1 9.5 + - - -
434B ASN* 4.2 13.9 - - - +
435B PHE* 3.5 30.0 + - + +
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Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B MET 3.9 2.2 - - - +
343B ALA 3.8 20.0 - - - +
344B ARG 3.9 1.4 + - - -
345B ASN* 1.3 73.8 - - - +
347B LYS* 1.3 60.7 + - + +
349B GLN* 3.4 25.8 + - - +
350B ASP* 3.1 35.1 + - - +
485B VAL 4.0 8.7 - - - +
486B GLU* 4.7 18.4 - - + +
490B LEU* 6.6 0.4 - - + -
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Residues in contact with LYS 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B ASN 3.2 1.0 - - - -
346B LEU* 1.3 77.3 - - + +
348B VAL* 1.3 68.5 + - + +
350B ASP* 3.4 11.8 + - + +
351B MET* 3.1 29.6 + - - +
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Residues in contact with VAL 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B MET* 5.8 0.9 - - + -
345B ASN* 3.1 21.6 + - + +
347B LYS* 1.3 76.8 - - + +
349B GLN* 1.3 65.3 + - - +
351B MET* 3.2 15.8 + - + +
352B LEU* 3.0 31.5 + - + +
376B LEU* 5.7 1.8 - - + -
435B PHE* 3.9 32.8 - - + +
436B ASP* 5.5 0.9 - - - +
437B PRO* 3.8 31.4 - - + -
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Residues in contact with GLN 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B MET* 3.0 52.2 - - + +
345B ASN 3.1 5.9 + - - -
346B LEU* 3.5 17.8 - - - +
348B VAL* 1.3 75.6 - - - +
350B ASP* 1.3 56.5 + - - +
352B LEU* 3.3 3.4 + - - +
353B ARG* 2.9 63.2 + - - +
480B LEU* 4.2 2.4 - - + +
483B PHE 4.1 0.2 + - - -
484B ARG* 3.5 4.4 - - - +
485B VAL* 2.9 52.1 - - - +
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Residues in contact with ASP 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU* 3.1 21.4 + - - +
347B LYS* 3.5 14.8 - - - +
348B VAL 3.2 0.2 - - - -
349B GLN* 1.3 75.9 - - - +
351B MET* 1.3 57.9 + - + +
353B ARG* 3.2 19.3 + - - +
354B ALA* 2.9 31.2 + - - +
484B ARG* 4.7 12.6 + - - -
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Residues in contact with MET 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LYS* 3.1 19.4 + - - +
348B VAL* 3.2 17.2 + - + +
350B ASP* 1.3 75.3 - - + +
352B LEU* 1.3 61.6 + - - +
354B ALA* 3.4 7.1 + - - +
355B GLU* 3.1 23.2 + - - +
376B LEU* 3.7 27.9 - - + +
438B THR* 4.2 21.3 - - + -
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Residues in contact with LEU 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B HIS* 4.2 5.2 - - - +
342B MET* 3.9 24.7 - - + -
348B VAL* 3.0 32.7 + - + +
349B GLN* 3.6 4.5 - - - +
351B MET* 1.3 73.7 - - - +
353B ARG* 1.3 65.4 + - - +
355B GLU* 3.4 4.6 + - - +
356B VAL* 3.1 27.5 + - - +
376B LEU* 3.4 49.4 - - + +
377B LEU* 3.6 14.7 - - + +
380B SER* 3.9 20.2 - - - +
435B PHE* 5.0 1.1 - - + -
437B PRO* 5.1 0.7 - - + -
480B LEU* 3.8 14.1 - - + -
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Residues in contact with ARG 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B GLN* 2.9 44.7 + - - +
350B ASP* 3.7 23.3 + - - +
352B LEU* 1.3 74.3 - - - +
354B ALA* 1.3 65.6 + - - +
356B VAL* 3.1 2.9 + - - +
357B LEU* 3.0 37.3 + - + +
480B LEU* 2.8 48.2 + - + +
483B PHE 2.5 30.9 + - - -
484B ARG* 3.5 18.2 - - - +
514B PHE* 3.5 33.8 - - - -
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Residues in contact with ALA 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B ASP 2.9 17.4 + - - +
351B MET* 3.7 8.1 - - - +
353B ARG* 1.3 75.9 - - - +
355B GLU* 1.3 62.4 + - - +
357B LEU* 3.6 8.6 + - - +
358B ALA* 3.1 23.9 + - - +
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Residues in contact with GLU 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B MET 3.1 16.9 + - - +
352B LEU* 3.7 6.8 - - - +
353B ARG 3.2 0.2 - - - -
354B ALA* 1.3 77.0 - - - +
356B VAL* 1.3 56.9 + - - +
358B ALA* 3.3 6.6 + - + +
359B ALA* 2.9 27.6 + - - +
373B LEU 3.8 10.3 - - - +
374B VAL* 3.1 24.9 - - - +
375B PRO* 3.2 14.9 - - + +
376B LEU* 3.1 42.3 + - + +
377B LEU* 3.2 10.7 + - - +
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Residues in contact with VAL 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B LEU 3.1 16.2 + - - +
353B ARG* 3.1 7.2 + - - +
355B GLU* 1.3 76.8 - - + +
357B LEU* 1.3 57.7 + - + +
359B ALA 3.2 0.7 + - - -
360B ARG* 2.9 28.6 + - - +
370B MET* 3.5 15.8 - - + +
374B VAL* 4.0 15.5 - - + -
377B LEU* 4.0 28.7 - - + -
477B ILE* 3.8 26.7 - - + +
480B LEU* 4.1 14.6 - - + -
481B GLU* 3.8 16.2 - - + +
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Residues in contact with LEU 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ARG* 3.0 27.1 + - + +
354B ALA* 3.9 7.9 - - - +
356B VAL* 1.3 73.2 - - + +
358B ALA* 1.3 65.4 + - - +
360B ARG* 3.5 5.8 + - + +
361B HIS* 3.2 23.2 + - - +
481B GLU* 4.2 28.3 - - + +
514B PHE* 3.9 35.4 - - + -
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Residues in contact with ALA 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B ALA 3.1 18.4 + - - +
355B GLU* 3.6 7.4 - - + +
356B VAL 3.3 0.2 - - - -
357B LEU* 1.3 75.0 - - - +
359B ALA* 1.3 52.3 + - - +
361B HIS* 3.3 6.8 + - - +
362B GLN* 2.7 37.4 + - + +
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Residues in contact with ALA 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B GLU 2.9 17.5 + - - +
356B VAL 3.2 3.8 + - - +
358B ALA* 1.3 75.3 - - - +
360B ARG* 1.3 59.1 + - - +
362B GLN* 3.8 4.2 - - - +
363B ALA* 2.9 34.1 + - - +
370B MET* 3.7 9.8 - - + +
373B LEU* 3.5 38.3 - - + +
374B VAL* 3.9 12.1 - - + -
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Residues in contact with ARG 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B ASP* 5.2 3.6 + - - -
176B ARG* 5.3 10.7 - - - +
356B VAL 2.9 14.2 + - - +
357B LEU* 3.9 7.0 - - + +
358B ALA 3.4 0.2 - - - -
359B ALA* 1.3 75.9 - - - +
361B HIS* 1.3 59.2 + - - +
364B GLN 3.4 2.1 + - - -
365B GLY* 2.9 61.3 + - - -
367B MET* 3.8 16.8 - - - +
370B MET* 3.3 24.6 - - + +
477B ILE* 3.6 14.8 - - - +
478B ASN* 4.4 8.7 + - - +
481B GLU* 2.6 44.9 + - - +
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Residues in contact with HIS 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357B LEU 3.2 16.7 + - - +
358B ALA* 3.5 5.3 + - - +
359B ALA 3.2 0.2 - - - -
360B ARG* 1.3 74.2 - - - +
362B GLN* 1.3 71.9 + - - +
363B ALA 3.0 1.8 - - - -
364B GLN* 2.9 20.1 + - - +
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Residues in contact with GLN 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B ALA 2.7 21.5 + - - +
359B ALA* 3.9 1.1 - - - +
361B HIS* 1.3 80.8 + - - +
363B ALA* 1.3 56.8 + - - +
364B GLN* 3.3 5.1 + - - +
369B THR* 5.1 1.7 - - - +
373B LEU* 3.8 30.6 - - + +
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Residues in contact with ALA 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B ALA 2.9 18.8 + - - +
360B ARG 3.6 1.8 + - - +
361B HIS 3.0 0.2 - - - -
362B GLN* 1.3 76.0 - - - +
364B GLN* 1.3 70.1 + - - +
365B GLY 2.9 1.4 + - - +
366B ASP* 3.0 23.9 + - - +
369B THR* 3.6 30.7 + - + -
370B MET* 3.7 20.9 - - + +
373B LEU* 4.2 1.8 - - + -
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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
------------------------------------------------------------
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