Contacts of the strand formed by residues 222 - 234 (chain C) in PDB entry 5NXR
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 ARG 222 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174C ASP 4.5 2.6 + - - -
175C GLY* 5.0 0.2 - - - -
176C TYR* 3.6 24.0 + - - -
196C SER* 3.1 31.3 + - - +
197C SER* 3.5 20.5 + - - +
198C SER* 3.6 21.6 - - - +
199C ARG* 3.9 4.7 - - - -
220C GLY 3.2 0.8 - - - -
221C LYS* 1.3 103.0 - - + +
223C ALA* 1.3 62.4 + - - +
224C GLN* 4.2 2.5 + - + -
247C GLN* 4.0 4.2 - - - +
248C ASN* 3.0 24.8 + - - +
430C LDA 5.5 9.2 - - - -
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Residues in contact with ALA 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C PHE* 3.6 34.3 - - + -
195C SER* 4.1 1.0 + - - +
196C SER* 3.6 3.5 + - - -
197C SER* 2.8 36.0 + - - +
199C ARG* 3.8 4.8 - - + +
222C ARG* 1.3 72.7 - - - +
224C GLN* 1.3 63.0 + - - +
247C GLN 3.3 4.5 - - - -
248C ASN 3.4 21.1 - - - +
249C THR* 3.6 8.5 - - - +
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Residues in contact with GLN 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C TYR* 3.2 27.6 + - + +
195C SER* 3.4 17.5 - - - +
196C SER* 4.6 4.8 + - - +
222C ARG* 4.2 2.9 + - + +
223C ALA* 1.3 75.5 - - - +
225C ALA* 1.3 60.9 + - - +
226C TRP* 3.9 19.8 - - - +
245C GLN 5.7 0.4 + - - -
246C THR* 3.3 2.6 - - - -
247C GLN* 2.7 66.7 + - + +
249C THR* 3.3 5.9 + - - -
429C LDA 3.6 21.4 + - - +
430C LDA 3.7 22.9 + - - +
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Residues in contact with ALA 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C VAL* 3.8 14.0 - - + +
119C MET* 5.7 2.0 - - + -
125C PHE* 6.4 0.7 - - + -
127C THR* 4.1 26.0 - - + -
194C TYR* 3.5 1.7 - - - -
195C SER* 2.8 42.0 + - - +
224C GLN* 1.3 76.4 - - - +
226C TRP* 1.3 63.5 + - - +
245C GLN 3.4 6.3 - - - +
246C THR* 4.1 10.3 - - - +
249C THR* 4.6 4.5 - - + +
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Residues in contact with TRP 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C VAL* 4.5 2.9 - - - -
119C MET* 3.8 3.3 - - - +
193C GLY 3.2 15.5 - - - +
194C TYR* 3.7 12.8 - + + -
224C GLN* 3.9 16.8 - - - +
225C ALA* 1.3 75.6 - - - +
227C ASN* 1.3 74.5 + - - +
228C VAL* 4.0 21.5 - - + -
243C TYR* 3.7 32.1 - + - -
244C GLY* 3.2 3.0 - - - -
245C GLN* 2.9 78.0 + - + +
411C LDA 3.9 28.9 - - + -
413C LDA 4.2 5.6 - - + -
429C LDA 3.5 48.4 - - + +
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Residues in contact with ASN 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C VAL* 2.8 31.3 + - - +
104C THR* 3.7 10.5 + - - -
105C ASN* 3.9 8.1 - - - +
119C MET* 3.8 13.1 - - - -
192C GLY* 3.0 3.7 - - - -
193C GLY* 2.9 36.8 + - - +
226C TRP* 1.3 80.5 - - - +
228C VAL* 1.3 68.3 + - - +
242C MET* 3.7 26.5 - - + -
243C TYR 3.1 13.0 - - - +
244C GLY* 3.8 5.6 - - - -
429C LDA 4.1 0.3 - - - +
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Residues in contact with VAL 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C THR* 4.0 4.0 - - - -
191C GLY 3.5 7.9 - - - +
192C GLY* 4.1 0.2 - - - -
226C TRP* 4.0 15.7 - - + -
227C ASN* 1.3 79.0 - - - +
229C GLY* 1.3 58.0 + - - +
242C MET* 3.3 3.5 - - - +
243C TYR* 2.8 39.7 + - + +
411C LDA 4.2 17.0 - - + -
413C LDA 4.0 38.1 - - + +
429C LDA 3.7 37.7 - - + -
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Residues in contact with GLY 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C THR* 3.6 10.5 - - - +
107C TRP* 3.8 6.5 - - - -
190C LEU* 3.6 5.9 - - - +
191C GLY 2.9 30.9 + - - +
228C VAL* 1.3 77.9 - - - +
230C GLY* 1.3 58.8 + - - -
241C ALA 3.1 13.2 - - - -
242C MET* 4.1 0.4 - - - -
413C LDA 4.3 12.2 - - - +
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Residues in contact with GLY 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C TRP* 4.0 6.7 - - - +
189C THR 3.1 12.8 - - - -
190C LEU* 4.3 9.9 - - - -
229C GLY* 1.3 74.5 - - - -
231C LYS* 1.3 63.1 + - - +
240C ALA* 3.3 4.0 - - - +
241C ALA* 3.0 30.6 + - - +
413C LDA 4.1 9.1 - - - +
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Residues in contact with LYS 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C TRP* 3.4 43.9 - - + +
187C GLY 3.5 1.7 - - - +
188C VAL* 3.4 7.8 - - - +
189C THR* 3.0 52.5 + - - -
230C GLY* 1.3 76.1 - - - +
232C PHE* 1.3 58.9 + - - +
233C ASP* 4.1 15.8 + - + +
238C TYR* 3.6 27.6 + - + +
239C LEU 3.1 14.4 - - - +
240C ALA* 3.9 10.1 - - + +
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Residues in contact with PHE 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C TRP 3.2 26.7 - - - -
187C GLY 3.3 1.3 - - - -
188C VAL* 3.7 16.4 - - + +
231C LYS* 1.3 73.6 - - - +
233C ASP* 1.3 65.4 + - - +
234C ALA* 3.9 11.9 - - + -
235C ASN* 4.0 18.4 - - - -
237C VAL* 3.5 37.6 - - + +
238C TYR* 3.2 7.6 - - - -
239C LEU* 2.8 48.6 + - + +
416C LDA 4.0 16.2 - - + -
418C LDA 3.5 50.7 - - + -
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Residues in contact with ASP 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C GLY* 2.8 21.3 + - - +
231C LYS* 4.8 15.3 + - + +
232C PHE* 1.3 76.1 - - - +
234C ALA* 1.3 65.3 + - - +
237C VAL 3.5 6.9 - - - +
238C TYR* 3.4 32.3 - - + +
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Residues in contact with ALA 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C TRP 4.0 20.2 - - - +
187C GLY* 4.4 3.1 - - - -
232C PHE* 3.9 7.2 - - + -
233C ASP* 1.3 76.6 + - - +
235C ASN* 1.3 76.5 + - - +
236C ASN 3.2 3.1 - - - -
237C VAL* 2.8 34.4 + - - +
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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