Contacts of the strand formed by residues 277 - 283 (chain A) in PDB entry 2NZ2
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 LYS 277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269A VAL* 4.1 20.9 - - + -
270A GLU 3.2 6.3 - - - +
271A ASN* 2.9 42.0 + - - +
272A ARG* 5.8 0.2 + - - -
275A GLY 3.9 2.5 + - - +
276A MET* 1.3 79.8 - - - +
278A SER* 1.3 60.4 + - - +
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Residues in contact with SER 278 (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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191A GLU* 3.7 14.3 + - - +
268A ILE 4.0 0.3 - - - +
269A VAL* 3.3 5.4 - - - -
270A GLU* 2.7 47.1 + - - +
272A ARG* 3.3 46.8 + - - -
277A LYS* 1.3 75.2 - - - +
279A ARG* 1.3 63.2 + - - +
280A GLY 4.0 0.2 + - - -
502A CIR 5.8 0.2 - - - -
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Residues in contact with ARG 279 (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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190A TYR 4.4 0.2 - - - +
191A GLU* 3.4 27.6 - - - +
195A LEU* 3.0 48.3 + - - +
196A GLU* 5.1 4.6 - - - +
197A ASN 3.2 12.7 + - - -
198A PRO* 3.6 28.0 + - + +
200A ASN 2.8 30.7 + - - -
201A GLN* 4.3 5.7 - - - +
202A ALA 4.5 2.2 - - - +
267A ASP* 2.6 40.4 + - - +
268A ILE 3.5 8.5 - - - +
269A VAL* 3.9 17.9 - - + +
270A GLU* 5.4 0.2 - - - -
278A SER* 1.3 76.1 + - - +
280A GLY* 1.3 66.1 + - - +
281A ILE* 4.3 4.1 - - - +
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Residues in contact with GLY 280 (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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190A TYR 3.7 8.7 - - - -
191A GLU* 4.2 5.8 - - - -
195A LEU* 5.9 0.2 - - - -
267A ASP* 3.7 0.7 - - - +
268A ILE* 2.8 39.4 + - - +
270A GLU* 4.7 2.7 + - - -
278A SER 4.0 1.4 + - - -
279A ARG* 1.3 75.9 - - - +
281A ILE* 1.3 65.5 + - - +
282A TYR* 3.8 20.2 - - - -
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Residues in contact with ILE 281 (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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189A SER* 3.5 1.0 + - - -
190A TYR* 3.1 68.7 + - + -
195A LEU* 4.2 25.1 - - + -
202A ALA* 4.8 6.1 - - + -
206A LEU* 3.5 22.0 - - + -
207A TYR* 3.8 25.1 - - + +
266A ILE 3.1 15.9 - - - +
267A ASP* 4.1 20.9 - - + +
279A ARG* 4.3 3.4 - - - +
280A GLY* 1.3 76.7 - - - +
282A TYR* 1.3 70.6 + - - +
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Residues in contact with TYR 282 (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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87A TYR* 3.4 24.9 - + + -
187A HIS* 3.6 13.7 - + - +
188A ILE 3.4 2.2 - - - +
189A SER* 3.4 34.5 - - - -
191A GLU* 3.8 3.6 + - - -
264A GLY 3.3 3.7 - - - +
265A ARG* 3.4 3.6 - - - +
266A ILE* 3.0 62.4 + - + +
268A ILE* 3.7 20.2 - - + -
270A GLU* 2.4 32.1 + - - -
280A GLY* 3.8 16.4 - - - -
281A ILE* 1.3 77.4 - - - +
283A GLU* 1.3 66.2 + - - +
284A THR* 4.3 9.4 - - - +
502A CIR 2.8 22.3 + - + +
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Residues in contact with GLU 283 (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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187A HIS* 3.0 5.9 - - - -
188A ILE* 2.9 48.3 + - + +
190A TYR* 2.8 29.9 + - + -
207A TYR* 3.4 32.6 - - + +
208A THR 4.0 0.7 - - - -
209A LYS* 3.1 18.1 + - + +
210A THR* 2.7 42.7 + - + +
264A GLY 3.2 5.2 - - - -
265A ARG* 4.4 3.1 - - + -
282A TYR* 1.3 76.0 - - - +
284A THR* 1.3 59.6 + - - +
285A PRO* 3.6 5.9 - - - +
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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