Contacts of the helix formed by residues 464 - 482 (chain A) 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 GLY 464 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A VAL* 4.8 1.3 - - - -
462A CYS* 3.2 10.5 - - - -
463A LEU* 1.3 78.1 - - - +
465A ARG* 1.3 57.0 + - - +
466A ARG 3.4 2.7 - - - -
467A ILE* 3.3 9.3 + - - +
468A ALA* 2.8 31.9 + - - +
601A HEM 3.5 37.2 - - - +
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Residues in contact with ARG 465 (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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159A MET* 4.2 4.9 - - - -
452A ASN* 3.6 32.1 + - - +
455A PHE* 3.6 48.8 - - + +
456A GLY 4.3 10.9 + - - -
461A GLN* 2.9 30.4 - - - +
462A CYS* 3.6 16.9 - - + +
463A LEU 3.2 3.4 + - - -
464A GLY* 1.3 77.4 - - - +
466A ARG* 1.3 77.9 + - - +
468A ALA* 3.4 1.0 + - - +
469A GLU* 2.8 56.6 + - - +
76C ASP* 4.2 11.7 + - - +
77C MET* 3.4 17.7 - - - +
80C LEU* 6.0 1.2 - - - +
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Residues in contact with ARG 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A VAL 3.8 12.8 - - - +
159A MET* 3.7 45.5 + - - +
164A THR* 3.9 17.0 - - + -
461A GLN* 4.8 1.6 - - - +
463A LEU 4.8 0.4 + - - -
464A GLY 3.4 0.2 - - - -
465A ARG* 1.3 101.8 - - - +
467A ILE* 1.3 61.0 + - - +
469A GLU* 2.8 33.1 + - - -
470A LEU* 2.9 42.2 + - + +
50C LEU* 3.4 26.4 + - - +
73C GLU* 3.7 37.2 + - - +
76C ASP* 4.7 2.4 + - - +
77C MET* 5.3 5.1 - - - +
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Residues in contact with ILE 467 (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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158A VAL* 3.9 26.7 + - + +
167A PHE* 3.5 26.7 - - + -
171A LEU* 4.4 8.2 - - + +
210A ILE* 4.1 23.6 - - + -
213A VAL* 4.0 14.8 - - + -
301A ILE* 4.0 23.3 - - + -
323A MET* 4.0 9.6 - - + -
464A GLY* 3.3 9.5 + - - +
466A ARG* 1.3 75.8 - - - +
468A ALA* 1.3 59.0 + - - +
470A LEU* 4.1 2.0 - - - +
471A GLU* 2.8 46.3 + - + +
601A HEM 4.5 11.0 - - + -
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Residues in contact with ALA 468 (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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331A THR* 3.7 27.6 - - + -
455A PHE* 3.8 9.6 - - + -
464A GLY 2.8 18.1 + - - +
465A ARG 3.8 2.7 - - - +
467A ILE* 1.3 76.4 - - - +
469A GLU* 1.3 59.6 + - - +
471A GLU* 3.3 0.5 + - - +
472A MET* 2.9 40.0 + - + +
601A HEM 3.8 24.5 - - + -
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Residues in contact with GLU 469 (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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378A LYS* 6.3 0.4 - - - +
381A ILE* 5.6 6.7 - - + -
455A PHE* 4.0 18.1 - - + -
465A ARG* 2.8 50.0 + - - +
466A ARG* 2.8 38.3 + - - +
468A ALA* 1.3 72.7 - - - +
470A LEU* 1.3 58.1 + - + +
472A MET* 3.8 7.1 - - + +
473A THR* 2.7 40.5 + - - +
73C GLU* 4.4 7.5 - - - +
76C ASP* 4.3 7.7 - - - +
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Residues in contact with LEU 470 (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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164A THR* 3.7 39.7 - - - +
167A PHE* 4.2 11.9 - - + -
168A LEU* 3.7 24.5 - - + -
171A LEU* 3.9 14.1 - - + -
371A LEU* 4.1 16.6 - - + -
378A LYS* 5.8 5.6 - - - +
466A ARG* 2.9 29.2 + - + +
469A GLU* 1.3 77.8 - - + +
471A GLU* 1.3 57.1 + - - +
473A THR* 4.1 3.3 - - - -
474A ILE* 3.0 36.7 + - - +
73C GLU* 6.0 2.7 - - - +
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Residues in contact with GLU 471 (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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171A LEU* 3.8 20.3 - - + +
175A SER* 4.4 1.2 + - - -
205A PHE* 3.3 33.4 - - + -
206A ALA* 3.7 11.1 - - - +
209A SER* 3.6 21.1 - - - -
210A ILE* 4.8 2.4 + - - +
327A GLY 5.0 1.9 - - - +
331A THR* 2.8 39.2 + - - +
467A ILE* 2.8 32.8 + - - +
468A ALA 3.7 2.0 - - - +
470A LEU* 1.3 72.8 - - - +
472A MET* 1.3 58.5 + - - +
474A ILE* 3.9 1.0 - - - +
475A PHE* 2.9 29.3 + - - +
601A HEM 5.3 1.0 - - - +
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Residues in contact with MET 472 (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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331A THR* 4.2 15.7 - - - +
334A THR* 3.5 34.5 - - + -
335A LEU* 3.7 29.8 - - + -
381A ILE* 3.9 33.2 - - + -
385A LEU* 5.0 0.2 - - + -
455A PHE* 4.0 10.1 - - + -
468A ALA* 2.9 30.6 + - + +
469A GLU* 4.0 3.1 - - - +
471A GLU* 1.3 73.1 - - - +
473A THR* 1.3 61.4 + - - +
475A PHE* 3.3 1.5 + - - +
476A LEU* 2.9 34.8 + - - +
601A HEM 3.8 21.1 - - + -
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Residues in contact with THR 473 (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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371A LEU* 3.7 25.1 - - + -
374A VAL* 4.2 11.4 - - + -
377A LEU* 3.8 24.8 - - + +
378A LYS* 4.5 19.8 + - + +
381A ILE* 3.3 18.9 - - + +
469A GLU* 2.7 25.7 + - - +
470A LEU* 4.2 2.5 - - - -
472A MET* 1.3 75.1 - - - +
474A ILE* 1.3 57.6 + - - +
476A LEU 3.3 1.0 + - - -
477A ILE* 3.0 34.3 + - + +
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Residues in contact with ILE 474 (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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168A LEU* 3.9 42.0 - - + +
171A LEU* 4.1 12.6 - - + -
172A ASP* 3.4 39.5 - - - +
175A SER* 3.8 5.8 - - - +
367A MET* 4.0 23.1 - - + -
371A LEU* 4.3 9.2 - - + -
470A LEU 3.0 23.8 + - - +
471A GLU* 4.1 3.1 - - - +
473A THR* 1.3 72.2 - - - +
475A PHE* 1.3 67.1 + - - +
477A ILE* 3.5 6.7 + - - +
478A ASN* 3.0 32.9 + - - +
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Residues in contact with PHE 475 (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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175A SER* 3.3 15.3 + - - +
178A PHE* 3.5 40.6 - + + -
202A LEU* 3.8 19.7 - - + -
205A PHE* 3.3 31.0 - + + -
335A LEU* 3.5 32.1 - - + -
339A LEU* 4.3 13.5 - - + -
471A GLU 2.9 20.3 + - - +
472A MET 3.6 4.0 - - - +
474A ILE* 1.3 78.0 - - - +
476A LEU* 1.3 68.2 + - + +
478A ASN* 3.4 3.3 + - - +
479A MET* 3.0 52.6 + - + +
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Residues in contact with LEU 476 (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 LEU* 3.9 15.3 - - + -
338A HIS* 3.6 52.0 - - + +
339A LEU* 4.4 7.2 - - + -
342A MET* 3.9 14.4 - - + -
377A LEU* 4.1 16.4 - - + -
381A ILE* 4.1 16.4 - - + -
472A MET 2.9 19.2 + - - +
473A THR 3.9 3.1 - - - +
475A PHE* 1.3 93.2 - - + +
477A ILE* 1.3 64.7 + - - +
479A MET* 4.0 3.8 - - + +
480A LEU* 2.9 32.6 + - + +
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Residues in contact with ILE 477 (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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356A VAL* 3.8 15.2 - - + +
360A ARG* 3.8 10.8 - - - +
367A MET* 3.8 26.2 - - + -
370A MET* 3.7 37.0 - - + -
371A LEU* 4.0 16.6 - - + -
374A VAL* 4.7 6.5 - - + -
377A LEU* 3.7 14.5 - - + +
473A THR* 3.0 25.0 + - + +
474A ILE* 3.7 5.2 - - - +
476A LEU* 1.3 77.2 - - - +
478A ASN* 1.3 63.2 + - - +
480A LEU 3.4 0.2 + - - -
481A GLU* 3.1 40.0 + - - +
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Residues in contact with ASN 478 (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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172A ASP* 2.8 26.8 + - - +
175A SER* 3.5 19.3 - - - +
176A ARG* 3.7 22.3 + - - +
179A VAL* 3.8 17.2 - - + +
360A ARG* 4.1 8.1 + - - -
367A MET* 4.5 3.6 - - - +
474A ILE* 3.0 23.8 + - - +
475A PHE 3.7 4.0 - - - +
477A ILE* 1.3 76.6 - - - +
479A MET* 1.3 63.7 + - - +
481A GLU* 3.5 14.2 + - - +
482A ASN* 2.8 33.3 + - - +
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Residues in contact with MET 479 (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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178A PHE* 3.9 17.7 - - + -
179A VAL* 4.2 6.3 - - + -
182A LEU* 3.6 17.9 - - + -
339A LEU* 4.3 19.1 - - + -
342A MET* 5.9 1.3 - - + -
475A PHE* 3.0 45.6 + - + +
476A LEU* 4.0 7.2 - - + +
477A ILE 3.4 0.2 - - - -
478A ASN* 1.3 75.3 - - - +
480A LEU* 1.3 59.3 + - + +
482A ASN* 2.9 2.9 + - - -
483A PHE* 2.9 58.6 + - + +
485A VAL* 5.0 4.0 - - + -
511A PHE* 3.6 32.8 - - + -
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Residues in contact with LEU 480 (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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342A MET* 3.8 34.3 - - + -
349A GLN* 4.2 5.4 - - + +
352A LEU* 3.9 30.1 - - + +
353A ARG* 2.8 72.8 + - - +
356A VAL* 4.3 11.7 - - + -
377A LEU* 3.9 20.4 - - + -
476A LEU* 2.9 22.1 + - + +
477A ILE 3.8 3.1 - - - +
479A MET* 1.3 76.7 - - - +
481A GLU* 1.3 60.1 + - - +
482A ASN 3.4 0.3 + - - -
483A PHE 4.0 1.2 + - - +
485A VAL* 6.1 0.7 - - + -
514A PHE* 4.4 0.5 - - - -
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Residues in contact with GLU 481 (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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356A VAL* 3.7 14.0 - - + +
357A LEU* 4.4 22.0 - - + +
360A ARG* 2.7 59.0 + - - +
477A ILE* 3.1 28.4 + - - +
478A ASN* 3.8 13.1 - - - +
479A MET 3.2 0.2 - - - -
480A LEU* 1.3 76.2 - - - +
482A ASN* 1.3 65.7 + - - +
514A PHE* 3.6 19.5 - - - +
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Residues in contact with ASN 482 (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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179A VAL* 3.5 20.3 - - - +
183A HIS* 3.1 20.4 + - - +
478A ASN* 2.8 30.0 + - - +
479A MET 2.9 2.2 + - - -
481A GLU* 1.3 91.9 + - - +
483A PHE* 1.3 89.9 + - + +
513A PRO* 3.5 2.6 - - - +
514A PHE* 3.0 23.4 + - - +
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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