Contacts of the strand formed by residues 267 - 271 (chain C) in PDB entry 2CNW
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 ILE 267 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C LEU* 4.2 15.4 + - + +
91C ARG* 4.3 5.8 + - - +
242C LEU* 3.6 34.3 - - + +
244C LEU* 4.4 11.9 - - + -
256C ALA* 3.9 31.6 - - + +
260C ARG* 4.2 10.6 - - + +
265C LYS 3.6 3.3 + - - +
266C PRO* 1.3 73.0 - - - +
268C TYR* 1.3 62.3 + - - +
269C PHE 4.0 8.5 - - - +
282C PHE* 3.3 65.6 - - + +
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Residues in contact with TYR 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C ARG* 3.3 35.8 + - - +
92C LEU* 3.8 7.7 - - - +
93C PRO* 3.5 41.4 - - + +
213C GLU* 3.0 33.1 + - - -
215C LEU* 3.8 26.2 - - + -
240C THR* 3.5 8.0 + - - -
241C GLY* 3.8 13.5 - - - -
242C LEU 3.1 8.7 + - - +
243C VAL* 5.9 0.2 - - + -
266C PRO* 3.6 24.2 - - + +
267C ILE* 1.3 73.1 - - - +
269C PHE* 1.3 85.9 + + + +
281C PRO* 3.7 3.1 - - - +
282C PHE* 3.1 17.0 + - - +
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Residues in contact with PHE 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C LEU* 3.5 25.6 - - + -
93C PRO* 3.8 21.8 - - + -
101C TRP* 4.9 2.9 - + - -
118C LEU* 3.7 22.9 - - + -
121C TYR* 4.0 23.3 - + - -
122C TYR* 3.6 23.8 - + - -
215C LEU* 5.4 1.8 - - + -
242C LEU 3.6 3.2 + - - -
243C VAL* 3.6 18.5 - - + -
244C LEU* 3.1 24.4 + - - +
267C ILE* 3.5 6.5 - - - +
268C TYR* 1.3 89.7 - + + +
270C ALA* 1.3 59.8 + - - +
279C LEU* 3.8 32.1 - - + -
280C GLU 3.4 16.6 - - - +
281C PRO* 4.8 1.1 - - + -
282C PHE* 3.9 5.8 - - - +
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Residues in contact with ALA 270 (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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243C VAL* 5.1 0.2 - - - -
244C LEU 3.4 4.5 - - - -
247C LEU* 3.6 23.1 - - + -
269C PHE* 1.3 74.1 - - - +
271C GLY* 1.3 60.1 + - - +
272C VAL* 4.0 12.9 + - + -
279C LEU* 3.4 11.0 - - - +
280C GLU* 2.8 42.9 + - + +
281C PRO 4.3 9.9 - - - +
282C PHE* 4.1 10.2 - - + +
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Residues in contact with GLY 271 (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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114C THR* 6.1 0.2 - - - -
117C LYS* 3.7 5.4 - - - -
243C VAL* 4.9 2.7 - - - +
244C LEU 2.7 15.7 + - - -
245C THR* 3.9 6.9 - - - -
246C LYS 3.3 1.2 + - - -
247C LEU* 3.0 28.2 + - - +
270C ALA* 1.3 73.0 - - - +
272C VAL* 1.3 62.7 + - - +
278C GLY 3.6 6.5 - - - -
279C LEU* 4.7 4.3 - - - -
1001C GDP 3.1 17.3 - - - -
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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