Contacts of the helix formed by residues 223 - 232 (chain A) 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 ASN 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A LEU* 5.8 2.8 - - - +
177A LYS* 4.8 1.0 + - - +
221A ASP* 4.0 10.5 + - - +
222A LEU* 1.3 68.5 - - - +
224A PRO* 1.3 57.3 - - - +
225A LEU* 2.9 34.4 - - - +
226A LYS* 2.4 41.7 + - + +
227A THR 3.0 8.0 + - - -
313A MET* 4.4 8.9 - - - +
316A TRP* 2.9 32.5 - - - -
541O ILE* 5.3 2.6 - - - +
547O GLU* 6.2 1.8 - - + -
548O ILE* 4.5 29.7 - - + +
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Residues in contact with PRO 224 (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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89A PRO* 3.6 22.3 - - - +
91A PHE* 3.3 36.1 - - + +
176A LEU 5.0 5.8 - - - +
177A LYS* 4.7 10.3 - - + +
178A ILE* 5.9 1.6 - - + -
222A LEU 3.0 10.8 - - - +
223A ASN* 1.3 81.3 - - - +
225A LEU* 1.3 62.4 + - - +
227A THR* 3.1 25.4 - - + +
228A LEU 3.9 1.4 + - - -
257A ILE* 4.3 3.1 - - - +
316A TRP* 3.3 27.8 - - + -
320A GLN* 3.8 13.0 - - - +
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Residues in contact with LEU 225 (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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88A LEU* 5.6 9.9 - - + -
89A PRO* 3.4 32.7 - - + +
223A ASN* 2.8 26.9 + - - +
224A PRO* 1.3 73.1 - - - +
226A LYS* 1.3 67.2 + - + +
227A THR 3.0 1.7 + - - -
228A LEU* 3.0 30.0 + - + +
229A ASN* 3.5 22.9 + - - +
316A TRP* 4.0 8.2 - - + -
541O ILE* 3.6 32.5 - - + +
542O ARG* 4.5 17.5 - - + +
544O ASN* 5.4 2.0 - - - -
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Residues in contact with LYS 226 (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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180A HIS* 5.8 0.4 + - - -
220A ASP* 4.7 7.7 + - - -
221A ASP 3.5 17.0 + - - -
222A LEU* 3.6 33.0 - - - +
223A ASN* 2.4 28.8 + - + +
225A LEU* 1.3 77.3 - - + +
227A THR* 1.3 56.4 + - - +
229A ASN* 3.1 13.0 + - + +
230A LEU* 2.8 29.5 + - + +
544O ASN* 5.1 5.6 - - - +
547O GLU* 2.4 53.2 + - + +
548O ILE 5.3 0.6 + - - -
549O GLN* 5.6 0.4 + - - -
567O ARG* 5.0 0.4 - - - +
569O LYS* 5.9 1.4 - - - +
572O HIS* 4.3 29.0 + - + +
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Residues in contact with THR 227 (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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91A PHE* 3.9 20.1 - - + -
103A LEU* 3.3 29.4 - - - +
178A ILE* 6.2 0.7 - - - -
222A LEU* 4.4 12.5 - - - +
223A ASN 3.0 7.7 + - - -
224A PRO* 3.1 31.0 - - + +
225A LEU 3.0 0.4 + - - -
226A LYS* 1.3 77.0 - - - +
228A LEU* 1.3 58.0 + - - +
230A LEU* 3.5 7.8 - - - +
231A PHE* 2.8 38.5 + - + -
257A ILE* 4.5 9.9 - - + -
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Residues in contact with LEU 228 (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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89A PRO* 3.0 44.9 - - + -
225A LEU* 3.0 21.1 + - + +
227A THR* 1.3 77.1 - - - +
229A ASN* 1.3 100.7 + - - +
230A LEU 2.9 1.1 - - - -
231A PHE* 3.5 8.7 - - + +
232A LYS* 2.8 50.0 + - + +
254A GLU* 5.4 4.9 - - + +
257A ILE* 3.2 21.5 - - + -
259A ARG* 5.2 12.6 - - - +
316P THR 5.4 5.6 - - - +
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Residues in contact with ASN 229 (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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225A LEU* 3.5 35.2 + - - +
226A LYS* 3.1 11.4 + - + +
228A LEU* 1.3 92.2 - - - +
230A LEU* 1.3 49.6 + - - +
232A LYS* 3.7 13.4 + - - +
233A GLN* 2.4 30.5 + - - +
542O ARG 4.9 2.9 + - - +
544O ASN* 3.2 44.0 + - - +
572O HIS* 5.5 4.7 - - + -
576O PHE* 4.3 20.4 - - + +
315P TRP* 5.2 2.6 - - - -
316P THR 5.1 6.0 + - - +
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Residues in contact with LEU 230 (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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103A LEU* 5.2 6.1 - - + -
106A ILE* 4.4 21.7 - - + +
107A CYS 4.7 1.1 - - - +
108A LYS* 3.6 32.1 - - + +
111A SER* 3.1 24.6 + - - +
222A LEU* 4.4 17.7 - - + -
226A LYS* 2.8 20.7 + - - +
227A THR* 3.5 9.0 - - - +
229A ASN* 1.3 75.1 - - - +
231A PHE* 1.3 74.1 + - + +
232A LYS 3.0 4.9 - - - -
233A GLN* 2.7 25.7 + - - +
572O HIS* 4.1 17.5 - - - +
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Residues in contact with PHE 231 (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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99A THR* 3.8 27.6 - - + -
102A ILE* 4.0 28.7 - - + -
103A LEU* 4.4 16.2 - - + -
106A ILE* 5.4 5.2 - - + -
227A THR* 2.8 39.0 + - - +
228A LEU* 3.1 14.0 + - - +
230A LEU* 1.3 83.5 - - + +
232A LYS* 1.3 61.0 + - - +
233A GLN 3.2 2.4 + - - -
234A ILE* 4.2 14.4 + - - +
235A LYS* 5.1 1.0 - - - +
252A ARG* 5.6 0.5 - - - -
253A PRO* 3.1 39.5 - - + +
254A GLU* 4.4 14.5 - - + +
256A TYR* 5.3 5.6 - + + -
257A ILE* 4.3 18.2 - - + -
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Residues in contact with LYS 232 (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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228A LEU* 2.8 45.1 + - + +
229A ASN* 3.8 12.8 - - - +
230A LEU 3.0 1.4 - - - -
231A PHE* 1.3 76.8 - - + +
233A GLN* 1.3 63.7 + - - +
235A LYS* 2.3 48.2 - - - +
254A GLU* 4.9 21.9 - - + +
259A ARG* 4.0 23.4 - - - +
41O THR* 4.6 12.7 + - - +
44O PRO* 5.9 2.8 - - + +
576O PHE* 6.2 1.8 - - + -
315P TRP* 3.3 43.7 + - + -
316P THR 5.1 7.4 - - - -
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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