Contacts of the strand formed by residues 260 - 266 (chain A) in PDB entry 1NYR
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 GLY 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A ASN* 5.3 4.0 - - - +
256A SER 3.2 18.4 + - - +
257A GLN* 3.8 5.8 + - - -
259A VAL* 1.3 85.2 - - - +
261A ALA* 1.3 64.4 + - - -
262A GLY 3.9 0.5 + - - -
263A LEU* 4.0 14.9 + - - +
300B ASN* 5.3 1.3 - - - -
329B MET* 3.7 15.5 - - - -
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Residues in contact with ALA 261 (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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260A GLY* 1.3 70.6 - - - -
262A GLY* 1.3 67.8 + - - +
263A LEU* 3.1 10.6 + - - +
369A SER* 6.2 1.8 - - - -
372A VAL* 4.8 12.1 - - + -
379A ARG* 3.6 25.1 - - - +
325B GLU* 4.1 26.7 - - - +
329B MET* 4.1 6.7 - - + +
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Residues in contact with GLY 262 (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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255A ASN* 6.3 1.2 - - - +
260A GLY 3.9 0.6 + - - -
261A ALA* 1.3 73.7 - - - +
263A LEU* 1.3 65.0 + - - +
264A PRO* 3.5 7.6 - - - +
372A VAL* 3.8 22.9 - - - +
374A GLY 5.5 1.6 - - - -
378A VAL* 3.1 19.1 - - - +
379A ARG 2.7 32.0 + - - -
380A GLY 3.2 0.7 + - - +
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Residues in contact with LEU 263 (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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255A ASN* 5.3 3.0 - - - +
256A SER 5.4 0.3 + - - -
259A VAL* 3.8 11.3 - - + +
260A GLY* 4.0 25.4 + - - +
261A ALA 3.1 9.8 - - - +
262A GLY* 1.3 90.0 - - - +
264A PRO* 1.3 70.3 - - - +
265A LEU* 3.6 7.6 - - - +
318A PHE* 6.1 0.7 - - + -
364A HIS* 4.6 6.7 - - + +
379A ARG* 4.1 5.6 - - + -
380A GLY* 3.2 28.9 - - - +
296B PRO* 2.9 30.4 - - + +
298B LEU* 3.9 33.2 - - + -
329B MET* 4.4 10.5 - - + -
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Residues in contact with PRO 264 (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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253A PHE* 4.1 11.7 - - + -
254A THR 3.1 16.6 - - - +
255A ASN* 4.4 10.2 - - - +
262A GLY* 3.5 7.9 - - - +
263A LEU* 1.3 92.6 - - - +
265A LEU* 1.3 62.3 + - - +
266A TRP* 4.0 12.2 + - - +
374A GLY 4.3 5.8 - - - +
375A LEU* 3.4 33.9 - - + -
378A VAL* 4.0 14.8 - - + -
380A GLY 5.2 2.5 - - - +
525A GLU* 5.3 3.4 - - - +
294B TYR 4.6 0.2 - - - +
295B THR* 4.7 0.3 - - - -
296B PRO* 3.4 11.8 - - - +
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Residues in contact with LEU 265 (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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253A PHE* 3.6 2.2 - - - +
254A THR* 2.7 42.9 + - - +
256A SER* 4.7 10.3 - - - +
259A VAL* 3.8 23.3 - - + -
263A LEU 3.6 9.0 - - - +
264A PRO* 1.3 73.1 - - + +
266A TRP* 1.3 61.8 + - - +
267A LEU* 3.5 1.4 + - - +
294B TYR 3.7 4.9 - - - -
295B THR* 4.2 6.3 - - + -
296B PRO* 3.3 24.5 - - + -
338B HIS* 3.8 13.7 - - - +
341B MET* 3.7 32.5 - - + +
342B ILE* 4.0 22.7 - - + +
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Residues in contact with TRP 266 (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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252A LEU 4.0 5.8 - - - -
253A PHE* 4.4 3.1 - - + -
264A PRO* 4.3 10.3 + - - +
265A LEU* 1.3 72.6 - - - +
267A LEU* 1.3 67.1 + - - +
270A GLY* 3.5 32.8 - - - -
271A ALA 4.2 4.0 - - - +
274A ARG* 3.0 43.6 - - + +
375A LEU* 4.4 20.3 - - + +
524A MET* 3.3 22.7 - - + -
525A GLU* 3.3 41.3 + - + -
528A VAL* 3.7 28.3 - - + -
293B VAL* 3.4 22.5 - - - +
294B TYR* 2.7 32.7 + - + +
295B THR 6.2 0.2 - - - -
342B ILE* 4.1 1.9 - - - +
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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