Contacts of the helix formed by residues 252 - 261 (chain M) in PDB entry 6CNB
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 PHE 252 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249M GLU 5.1 10.1 - - - -
250M GLY* 4.1 3.9 + - - -
251M THR* 1.3 95.2 - - - +
253M GLU* 1.3 76.6 + - + +
254M GLN* 3.4 4.4 - - - +
255M PHE* 4.0 3.2 + - - +
256M LYS* 3.5 26.8 + - - +
407N GLU* 4.6 18.9 + - - +
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Residues in contact with GLU 253 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82M GLU* 3.2 25.1 - - + +
83M GLU* 3.6 20.3 - - - +
252M PHE* 1.3 87.5 + - - +
254M GLN* 1.3 64.9 + - - +
255M PHE 3.0 3.1 - - - -
256M LYS* 2.6 12.0 + - + +
257M ASP* 2.3 51.9 + - + +
407N GLU* 4.8 9.3 - - - +
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Residues in contact with GLN 254 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82M GLU* 4.0 12.8 - - - +
162M PHE* 3.2 20.3 - - + -
250M GLY 3.6 6.7 + - - +
251M THR* 2.4 49.7 + - + +
252M PHE 4.1 1.3 - - - +
253M GLU* 1.3 81.3 - - + +
255M PHE* 1.3 63.2 + - + +
258M THR* 2.8 22.7 + - - +
302N GLU* 2.8 26.6 + - - -
304N PHE* 4.9 3.4 - - + -
407N GLU* 5.0 1.2 - - - +
409N LEU* 3.1 38.7 - - + +
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Residues in contact with PHE 255 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162M PHE* 4.7 10.3 - + - -
164M LYS* 3.1 31.1 - - - +
251M THR* 3.4 28.9 - - + -
252M PHE 4.0 2.6 + - - +
253M GLU 3.0 3.8 - - - -
254M GLN* 1.3 79.1 - - + +
256M LYS* 1.3 87.0 + - + +
258M THR* 2.2 23.6 + - - -
259M ILE* 2.9 18.1 + - + +
300N LYS* 3.7 43.3 - - + -
301N PRO 5.1 2.2 - - - -
302N GLU* 4.3 10.1 - - - -
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Residues in contact with LYS 256 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164M LYS* 5.7 0.2 - - - +
252M PHE 3.5 18.8 + - - +
253M GLU* 2.6 11.7 + - + -
255M PHE* 1.3 99.1 - - + +
257M ASP* 1.3 56.6 + - - +
259M ILE* 2.9 14.2 + - + +
260M VAL* 2.7 45.1 + - + +
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Residues in contact with ASP 257 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79M SER* 5.9 0.3 - - - -
80M GLY 5.1 1.4 + - - -
82M GLU* 2.9 37.6 - - - +
253M GLU* 2.3 47.5 + - + +
256M LYS* 1.3 67.7 - - - +
258M THR* 1.3 60.7 + - - +
260M VAL* 3.2 9.8 - - - +
261M LYS* 3.1 59.9 + - - +
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Residues in contact with THR 258 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78M ILE 6.1 0.7 - - - -
79M SER* 4.3 20.2 - - - +
82M GLU* 4.6 12.3 - - - +
162M PHE* 3.6 19.6 - - + -
164M LYS* 4.4 0.2 - - - -
169M TYR* 3.8 28.1 - - + -
171M VAL* 5.0 2.5 - - + -
253M GLU 3.5 0.4 + - - +
254M GLN* 2.8 22.1 + - - +
255M PHE* 2.2 29.5 + - - -
257M ASP* 1.3 77.8 - - - +
259M ILE* 1.3 60.6 + - - +
261M LYS* 4.2 4.4 - - - +
262M GLU* 3.7 17.7 + - - +
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Residues in contact with ILE 259 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164M LYS* 3.6 31.4 - - + +
167M GLN* 5.1 2.0 - - - +
169M TYR* 4.3 12.8 - - + +
255M PHE* 2.9 30.1 + - + +
256M LYS* 2.9 17.4 + - + +
258M THR* 1.3 75.8 - - - +
260M VAL* 1.3 67.9 + - + +
262M GLU* 3.2 32.7 - - - +
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Residues in contact with VAL 260 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256M LYS* 2.7 26.6 + - + +
257M ASP* 3.2 24.9 - - - +
259M ILE* 1.3 79.3 - - + +
261M LYS* 1.3 66.8 + - + +
262M GLU 3.4 2.5 + - - -
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Residues in contact with LYS 261 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77M LYS* 5.3 0.3 - - - -
78M ILE* 5.5 5.7 - - - +
79M SER* 4.5 4.0 - - - -
80M GLY* 3.5 36.4 - - - +
81M GLU 5.0 0.6 - - - +
82M GLU 6.2 0.2 - - - +
257M ASP* 3.1 45.8 + - - +
258M THR* 3.7 6.0 + - - +
259M ILE 3.2 0.2 - - - -
260M VAL* 1.3 84.3 - - + +
262M GLU* 1.3 65.1 + - - +
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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