Contacts of the helix formed by residues 359 - 368 (chain E) in PDB entry 1NBF
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 359 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358E LYS* 1.3 86.1 - - - +
360E ILE* 1.3 64.9 + - + +
361E PHE* 3.3 20.5 - - + +
362E GLU* 3.1 44.6 + - - +
363E SER* 3.5 4.9 + - - -
425E PHE* 3.1 18.8 - - - -
426E GLU* 3.2 23.8 - - + +
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Residues in contact with ILE 360 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352E LEU* 3.4 29.4 - - + -
359E ASN* 1.3 74.1 - - + +
361E PHE* 1.3 72.0 + - + +
363E SER* 3.1 12.1 + - - -
364E PHE* 3.2 34.5 + - + -
404E LEU* 4.6 2.9 - - + -
406E LEU* 4.2 5.2 - - + -
425E PHE* 3.5 21.1 - - + -
426E GLU 3.0 7.8 + - - +
427E PHE* 4.4 0.9 - - + -
428E PRO* 3.3 35.4 - - + -
431E LEU* 3.7 27.8 - - + -
516E LEU* 4.3 15.5 - - + -
518E TYR* 5.5 0.4 - - - +
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Residues in contact with PHE 361 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359E ASN* 3.3 15.4 - - + +
360E ILE* 1.3 86.9 - - + +
362E GLU* 1.3 64.6 + - + +
364E PHE* 3.4 8.2 + - - +
365E VAL* 3.1 44.1 + - + +
431E LEU* 5.8 3.4 - - + -
432E PRO 5.4 3.8 - - - -
435E GLU* 3.4 31.2 - - - -
436E PHE* 3.5 25.8 - + - -
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Residues in contact with GLU 362 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356E GLY 3.6 15.3 - - - +
357E LYS* 3.6 23.6 - - + +
358E LYS* 3.1 32.9 + - - +
359E ASN* 3.1 28.4 - - - +
360E ILE 3.2 0.4 - - - -
361E PHE* 1.3 81.2 - - + +
363E SER* 1.3 57.7 + - - +
365E VAL* 3.5 6.6 + - + +
366E ASP* 3.2 25.6 + - - +
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Residues in contact with SER 363 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352E LEU* 4.0 22.0 - - - +
353E SER 2.7 29.7 + - - -
357E LYS* 3.9 4.7 - - - +
359E ASN 3.7 0.4 + - - -
360E ILE 3.1 9.8 + - - -
362E GLU* 1.3 75.5 - - - +
364E PHE* 1.3 60.1 + - - +
366E ASP* 3.1 7.7 + - - +
367E TYR* 2.9 26.7 + - - +
425E PHE* 2.8 32.6 - - - -
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Residues in contact with PHE 364 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350E ILE* 4.5 5.6 - - + -
352E LEU* 3.8 19.7 - - + -
360E ILE* 3.2 42.9 + - + +
361E PHE* 3.4 4.2 + - - +
363E SER* 1.3 78.7 - - - +
365E VAL* 1.3 57.7 + - - +
367E TYR* 3.2 6.7 + - + +
368E VAL* 3.1 32.7 + - - +
395E PHE* 4.3 30.1 - + - -
398E LEU* 5.4 2.7 - - + -
404E LEU* 3.8 22.4 - - + -
431E LEU* 4.2 3.1 - - + -
433E LEU* 3.6 45.1 - - + -
436E PHE* 3.3 30.7 - + + -
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Residues in contact with VAL 365 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361E PHE* 3.1 48.9 + - + +
362E GLU* 3.9 8.3 - - + +
363E SER 3.3 0.2 - - - -
364E PHE* 1.3 75.6 - - - +
366E ASP* 1.3 61.3 + - - +
368E VAL* 3.8 12.3 - - + +
369E ALA* 3.4 20.4 + - - +
436E PHE* 3.9 9.0 - - + -
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Residues in contact with ASP 366 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353E SER* 3.2 23.6 + - - -
357E LYS* 3.3 31.1 + - - -
362E GLU 3.2 13.3 + - - +
363E SER* 3.1 11.3 + - - +
365E VAL* 1.3 78.0 - - - +
367E TYR* 1.3 62.1 + - - +
369E ALA* 3.1 22.7 - - - +
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Residues in contact with TYR 367 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328E MET* 4.3 16.7 - - - +
349E ASP 5.7 0.5 + - - -
350E ILE* 4.6 16.0 - - + +
351E GLN* 3.8 27.3 + - + -
352E LEU* 4.9 5.2 - - + -
353E SER 6.1 0.7 - - - -
363E SER 2.9 12.0 + - - +
364E PHE* 3.2 13.0 + - + +
366E ASP* 1.3 78.3 - - - +
368E VAL* 1.3 57.8 + - + +
369E ALA 3.0 12.3 + - - +
393E VAL* 3.7 41.5 + - + +
395E PHE* 3.4 39.7 - + + -
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Residues in contact with VAL 368 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331E TYR* 6.1 0.3 - - - -
364E PHE 3.1 16.8 + - - +
365E VAL* 3.8 15.7 - - + +
367E TYR* 1.3 74.3 - - - +
369E ALA* 1.3 65.6 + - - +
370E VAL* 3.4 11.1 + - - +
393E VAL 3.4 28.0 + - - +
394E LYS* 5.1 2.5 - - - -
395E PHE* 4.1 24.9 - - + -
436E PHE* 4.1 22.4 - - + +
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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