Contacts of the strand formed by residues 182 - 188 (chain C) in PDB entry 5NC5
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 TYR 182 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150C THR* 4.4 1.2 + - - -
152C GLU* 3.5 31.5 - - + +
153C ASP* 2.8 39.6 + - - -
156C ASP* 2.8 42.7 + - + +
180C SER 3.9 1.5 + - - -
181C GLN* 1.3 82.8 + - - +
183C ALA* 1.3 63.3 + - - +
270C LEU* 3.8 38.1 - - + -
271C GLY* 3.2 31.0 - - - -
272C GLY* 4.3 0.9 - - - -
273C GLU* 4.0 3.2 - - - +
762C PHE* 5.7 0.2 - - - -
764C ASP* 4.8 0.7 - - - +
765C ARG* 4.7 6.1 - - - -
769C LYS* 3.6 29.0 - - + +
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Residues in contact with ALA 183 (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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182C TYR* 1.3 73.7 - - - +
184C MET* 1.3 63.8 + - - +
185C ARG* 3.3 8.4 + - - +
270C LEU* 3.4 7.6 - - - +
271C GLY 2.5 39.9 + - - +
272C GLY 4.0 5.4 - - - +
273C GLU* 4.4 3.1 - - + -
762C PHE* 4.2 4.3 - - - -
770C LYS* 3.2 17.5 - - + +
772C TYR* 3.6 31.4 - - + -
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Residues in contact with MET 184 (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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183C ALA* 1.3 70.1 - - - +
185C ARG* 1.3 62.4 + - - +
186C ILE* 3.9 4.7 + - + -
242C SER* 4.2 3.1 - - - +
243C THR* 3.6 40.4 - - - +
246C PHE* 3.9 31.6 - - + -
268C ILE* 3.7 15.9 - - + -
269C GLU 4.2 2.7 - - - +
270C LEU* 3.9 11.7 - - + -
762C PHE* 3.3 45.3 - - + -
770C LYS 2.9 8.1 + - - -
771C VAL* 3.6 15.7 - - + +
772C TYR 2.9 28.2 + - - +
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Residues in contact with ARG 185 (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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223B PRO* 5.9 0.2 - - - +
183C ALA* 3.5 13.9 - - - +
184C MET* 1.3 74.4 - - - +
186C ILE* 1.3 63.1 + - - +
187C TRP* 3.6 39.2 - - + +
267C LYS 3.7 0.7 - - - +
268C ILE* 3.4 6.2 - - - +
269C GLU 2.8 40.2 + - - +
271C GLY* 3.5 28.5 - - - +
272C GLY 2.5 36.7 + - - +
273C GLU* 3.2 22.8 + - - +
275C TYR* 4.3 5.3 - - - -
756C GLY* 5.4 0.6 - - - -
772C TYR* 3.6 26.0 + - - +
774C MET* 3.5 39.0 - - - +
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Residues in contact with ILE 186 (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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184C MET* 4.8 11.2 - - + +
185C ARG* 1.3 75.4 + - - +
187C TRP* 1.3 61.5 + - - +
188C MET* 3.9 5.8 - - + -
203C VAL* 4.3 9.4 - - + -
207C ILE* 3.3 33.2 - - + -
246C PHE* 4.7 8.3 - - + -
262C LEU* 3.6 23.6 - - + -
266C ALA* 3.6 27.8 - - + -
267C LYS 3.5 3.8 - - - +
268C ILE* 4.8 7.2 - - + -
771C VAL* 4.9 4.0 - - + -
772C TYR 3.0 9.5 + - - +
773C VAL* 3.4 18.2 - - + +
774C MET* 3.0 27.4 + - - +
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Residues in contact with TRP 187 (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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223B PRO* 3.9 26.0 - - + -
185C ARG* 3.6 40.6 - - + +
186C ILE* 1.3 72.3 - - - +
188C MET* 1.3 63.3 - - - +
189C ASN* 4.0 0.5 + - - +
266C ALA* 3.6 3.6 - - - -
267C LYS* 2.8 53.4 + - + +
269C GLU* 3.1 34.0 + - + -
275C TYR* 3.9 21.5 - + - -
774C MET* 3.3 20.6 - - + -
775C SER 3.4 26.0 - - - -
776C GLU* 4.1 24.5 - - + +
777C ALA 4.9 0.9 - - - -
780C ARG* 4.2 11.2 - - - -
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Residues in contact with MET 188 (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 ILE* 4.6 16.2 - - + +
187C TRP* 1.3 74.6 - - - +
189C ASN* 1.3 59.5 - - - +
190C PRO* 4.1 0.7 - - - +
193C LEU* 4.1 18.6 - - + -
200C PRO* 3.6 46.2 - - + -
203C VAL* 4.7 9.6 - - + -
266C ALA* 4.8 6.7 - - + -
752C ALA 4.3 3.4 - - - +
753C ALA* 4.2 11.4 - - - -
773C VAL* 4.4 11.2 - - + -
774C MET* 2.9 37.6 + - - +
775C SER* 3.5 11.9 + - - +
776C GLU* 2.9 25.2 + - - +
789C TRP* 4.4 8.7 - - + -
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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