Contacts of the helix formed by residues 359 - 369 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357B LYS* 3.4 1.4 - - - +
358B LYS* 1.3 83.4 - - - +
360B ILE* 1.3 65.1 + - - +
361B PHE* 2.8 26.5 - - + +
362B GLU* 2.8 39.7 + - - +
363B SER 3.1 15.1 + - - -
425B PHE* 3.2 13.1 - - - -
426B GLU* 3.1 34.0 - - + +
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Residues in contact with ILE 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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352B LEU* 3.5 26.9 - - + -
359B ASN* 1.3 73.2 - - - +
361B PHE* 1.3 58.2 + - + +
363B SER* 3.2 3.5 + - - -
364B PHE* 2.9 40.7 + - + -
404B LEU* 4.1 5.8 - - + -
425B PHE* 3.5 17.9 - - + -
426B GLU 2.8 9.3 + - - +
427B PHE* 3.4 28.5 - - + -
428B PRO* 4.2 10.5 - - + -
431B LEU* 3.4 31.6 - - + -
516B LEU* 3.9 18.2 - - + -
518B TYR* 4.6 1.8 - - - +
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Residues in contact with PHE 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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359B ASN* 2.8 22.5 - - + +
360B ILE* 1.3 79.9 - - + +
362B GLU* 1.3 56.1 + - + +
364B PHE* 3.3 6.6 + - - +
365B VAL* 3.0 34.6 + - + +
428B PRO* 3.7 39.3 - - + -
430B GLN 4.5 0.7 - - - -
431B LEU* 3.7 15.3 - - + -
432B PRO* 3.6 34.8 - - + -
436B PHE* 4.2 13.1 - + + -
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Residues in contact with GLU 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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356B GLY 4.1 4.2 - - - +
357B LYS* 3.7 20.0 - - + +
358B LYS* 3.1 46.3 + - - +
359B ASN* 2.8 28.3 - - - +
361B PHE* 1.3 74.1 - - + +
363B SER* 1.3 57.7 + - - +
365B VAL* 3.7 9.4 - - + +
366B ASP* 3.0 27.4 + - - +
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Residues in contact with SER 363 (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 27.9 - - - +
353B SER* 2.9 32.6 + - - -
357B LYS* 4.3 5.6 - - - +
359B ASN 3.1 12.5 + - - -
360B ILE* 3.3 10.1 - - - -
361B PHE 3.1 0.2 - - - -
362B GLU* 1.3 76.4 - - - +
364B PHE* 1.3 59.3 + - - +
366B ASP* 3.3 5.3 + - - +
367B TYR* 2.9 26.2 + - - +
425B PHE* 3.8 12.1 - - - -
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Residues in contact with PHE 364 (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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350B ILE* 4.1 21.1 - - + -
352B LEU* 3.9 26.0 - - + -
360B ILE* 2.9 40.3 + - + +
361B PHE* 3.9 0.7 - - - +
363B SER* 1.3 74.4 - - - +
365B VAL* 1.3 66.6 + - - +
367B TYR* 3.0 15.9 + - + +
368B VAL* 3.1 19.4 + - - +
395B PHE* 3.8 28.9 - + - -
398B LEU* 5.2 2.0 - - + -
402B LEU* 5.0 0.2 - - + -
404B LEU* 4.2 13.7 - - + -
431B LEU* 4.5 0.9 - - + -
433B LEU* 3.9 32.5 - - + -
436B PHE* 3.5 42.0 - + + -
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Residues in contact with VAL 365 (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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361B PHE* 3.0 24.8 + - + +
362B GLU* 3.7 9.9 - - + +
363B SER 3.3 0.2 - - - -
364B PHE* 1.3 77.0 - - - +
366B ASP* 1.3 63.7 + - - +
368B VAL* 3.4 7.4 - - + +
369B ALA* 3.1 23.1 + - + +
435B GLU* 6.2 0.4 - - + -
436B PHE* 4.0 17.9 - - + -
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Residues in contact with ASP 366 (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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353B SER* 3.9 19.2 + - - -
357B LYS* 3.5 29.3 + - + -
362B GLU 3.0 18.4 + - - +
363B SER* 3.5 6.5 - - - +
364B PHE 3.1 0.2 - - - -
365B VAL* 1.3 79.8 - - - +
367B TYR* 1.3 64.0 + - - +
369B ALA* 3.2 22.9 + - - +
306C LYS* 4.8 7.8 + - - -
309C THR 5.6 0.5 - - - +
310C GLY* 4.9 7.6 - - - +
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Residues in contact with TYR 367 (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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328B MET* 3.5 20.1 - - - +
350B ILE* 3.9 17.0 - - + +
351B GLN* 3.4 29.1 + - + -
352B LEU* 4.7 4.5 - - + -
353B SER 5.8 0.9 - - - -
363B SER 2.9 15.3 + - - +
364B PHE* 3.0 16.8 + + + +
366B ASP* 1.3 79.4 - - - +
368B VAL* 1.3 63.0 + - + +
369B ALA 3.7 2.6 + - - +
393B VAL* 3.9 33.6 + - + +
395B PHE* 3.7 33.4 - + - -
306C LYS* 3.4 32.9 + - + +
368C HIS* 3.5 20.7 - + - -
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Residues in contact with VAL 368 (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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331B TYR* 4.5 7.8 + - - -
364B PHE 3.1 16.5 + - - +
365B VAL* 3.4 11.9 - - + +
367B TYR* 1.3 85.5 - - + +
369B ALA* 1.3 65.9 + - - +
370B VAL* 3.6 2.3 + - - +
393B VAL 3.2 34.0 + - - +
394B LYS* 4.1 22.5 - - + -
395B PHE* 4.5 7.9 - - + -
436B PHE* 4.0 34.1 - - + +
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Residues in contact with ALA 369 (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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365B VAL* 3.1 15.7 + - + +
366B ASP* 3.2 24.6 + - - +
367B TYR 4.5 2.6 - - - +
368B VAL* 1.3 79.1 - - - +
370B VAL* 1.3 69.2 + - - +
371B GLU* 3.5 9.5 + - + +
391B LYS 4.0 4.0 - - - +
392B GLY* 4.3 3.0 - - - -
393B VAL 4.9 0.2 + - - -
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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