Contacts of the strand formed by residues 272 - 278 (chain C) in PDB entry 2NYM
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 GLN 272 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416A LYS* 5.9 3.4 - - - +
244C VAL 4.1 0.2 - - - +
245C MET 3.0 11.5 + - - +
246C GLU* 3.7 22.2 - - - +
247C GLY* 3.4 14.3 + - - -
260C PHE* 5.6 0.3 - - - +
263C PRO* 5.2 0.2 - - - -
271C ASN* 1.3 91.2 + - - +
273C ALA* 1.3 60.3 + - - +
288C GLN* 2.7 39.9 + - + +
289C PHE 4.2 9.4 - - - +
290C ASP* 4.1 23.3 + - - +
291C PRO* 5.9 0.4 - - - -
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Residues in contact with ALA 273 (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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247C GLY* 3.7 3.6 - - - -
260C PHE 3.4 15.9 - - - +
261C SER* 3.5 24.9 - - - +
262C ALA 3.9 1.8 - - - +
263C PRO* 3.5 23.5 - - + +
271C ASN* 3.8 0.6 + - - +
272C GLN* 1.3 75.4 - - - +
274C ALA* 1.3 56.6 + - - +
288C GLN* 3.5 1.0 - - - -
289C PHE* 2.7 44.5 + - + +
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Residues in contact with ALA 274 (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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247C GLY 3.6 17.2 + - - +
248C TYR* 4.1 10.3 - - + -
259C ILE* 3.2 12.1 - - - +
260C PHE 3.1 17.9 + - - +
261C SER* 3.5 3.1 + - - -
273C ALA* 1.3 74.4 - - - +
275C ILE* 1.3 74.9 + - - +
286C PHE* 5.3 0.7 - - + -
287C LEU 2.9 17.9 - - - +
288C GLN* 3.4 21.5 - - + -
289C PHE* 4.7 1.6 - - - -
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Residues in contact with ILE 275 (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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53C THR* 3.5 24.5 - - + -
54C VAL 3.5 11.9 - - - +
55C CYS* 4.0 5.2 - - - -
68C LEU* 3.8 36.1 - - + -
71C ILE* 4.2 20.6 - - + -
72C GLY* 4.2 11.4 - - - -
259C ILE* 4.0 4.3 - - - -
261C SER* 4.1 7.2 - - - +
274C ALA* 1.3 80.6 - - - +
276C MET* 1.3 61.7 + - - +
277C GLU* 4.2 0.4 + - + -
286C PHE* 3.7 6.9 - - - -
287C LEU* 2.7 46.5 + - + +
289C PHE* 3.9 11.7 - - + -
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Residues in contact with MET 276 (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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53C THR* 3.6 1.8 - - - -
54C VAL* 2.7 57.1 + - + +
163C ILE* 4.8 2.7 - - + -
236C LEU* 4.8 17.7 - - + -
238C SER* 4.4 16.8 - - - +
257C VAL* 4.8 1.6 - - - -
259C ILE* 3.9 15.6 - - + +
275C ILE* 1.3 72.4 - - - +
277C GLU* 1.3 68.7 + - - +
278C LEU* 3.2 38.1 + - + -
284C TYR* 5.2 4.0 - - - -
285C SER 3.7 8.1 - - - +
286C PHE* 3.1 43.3 - - + -
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Residues in contact with GLU 277 (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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454A HIS* 4.8 6.8 - - - +
459A ARG* 5.8 0.2 + - - -
494A ASN* 5.1 6.8 + - - +
496A LEU* 3.1 33.2 - - + +
52C VAL 3.6 5.6 - - - +
53C THR* 4.2 14.5 + - + +
71C ILE 4.9 0.5 - - - +
72C GLY* 4.2 13.7 - - - +
275C ILE* 5.1 1.3 - - + -
276C MET* 1.3 76.4 - - - +
278C LEU* 1.3 69.1 + - - +
279C ASP 3.9 1.3 - - - +
283C LYS 3.0 17.0 - - - +
285C SER* 3.0 33.2 + - - +
287C LEU* 3.3 41.2 - - + +
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Residues in contact with LEU 278 (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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495A TYR* 5.5 0.4 - - - -
51C PRO* 3.0 2.5 - - + +
52C VAL* 2.7 53.1 + - + +
54C VAL* 4.6 4.7 - - + -
159C VAL* 3.7 24.7 - - + -
163C ILE* 3.7 18.6 - - + -
276C MET* 3.2 36.6 - - + -
277C GLU* 1.3 81.7 - - - +
279C ASP* 1.3 67.0 + - - +
282C LEU* 3.6 31.4 - - + -
283C LYS 3.8 13.5 - - - +
284C TYR* 4.9 5.6 - - + -
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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