Contacts of the strand formed by residues 251 - 258 (chain A) in PDB entry 1NNC
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 GLU 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A TRP* 3.2 34.0 + - - +
219A ALA* 3.5 23.6 - - + +
242A THR* 3.7 1.1 - - - -
243A ASP 2.9 38.3 + - - +
250A ALA* 1.3 74.1 - - - +
252A THR* 1.3 61.1 + - - +
253A ARG* 4.7 8.1 + - + +
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Residues in contact with THR 252 (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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240A VAL* 3.7 23.1 - - + -
241A PHE 3.3 13.0 - - - +
242A THR* 3.0 23.8 + - - +
250A ALA* 3.7 6.1 + - - +
251A GLU* 1.3 72.0 - - - +
253A ARG* 1.3 66.8 + - - +
254A ILE* 5.0 1.6 - - + -
267A PRO* 3.6 5.7 - - - +
268A LEU* 3.0 53.4 + - + +
275A ILE* 3.8 21.3 + - + +
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Residues in contact with ARG 253 (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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215A ILE* 5.4 0.6 - - - +
218A TRP* 3.5 64.2 - - + +
239A VAL 3.7 0.7 - - - +
240A VAL* 3.6 3.6 - - - +
241A PHE* 3.0 32.4 + - - +
251A GLU* 4.1 7.3 + - + +
252A THR* 1.3 79.9 - - - +
254A ILE* 1.3 65.4 + - - +
255A TYR* 2.9 39.7 + - + -
265A TRP* 3.4 52.8 - - + +
266A GLU 3.2 7.0 - - - +
267A PRO* 4.7 1.3 - - + -
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Residues in contact with ILE 254 (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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238A PRO* 4.2 17.0 - - + -
239A VAL 3.5 7.2 - - - +
240A VAL* 3.5 33.4 - - + -
252A THR* 5.0 2.9 - - + -
253A ARG* 1.3 74.3 - - - +
255A TYR* 1.3 61.3 + - - +
256A TYR* 3.7 31.5 - - + +
265A TRP* 3.1 4.2 - - - -
266A GLU* 2.8 35.4 + - - +
268A LEU* 5.3 2.9 - - + -
303A ILE* 4.2 22.9 - - + -
305A ILE* 4.3 9.0 - - + -
312A HIS* 3.9 28.3 - - + +
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Residues in contact with TYR 255 (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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215A ILE* 3.8 36.1 - - + +
218A TRP* 3.9 11.8 - + - -
237A CYS 3.8 1.4 - - - +
238A PRO* 3.1 5.2 - - - +
239A VAL 2.9 33.8 + - - +
241A PHE* 3.5 21.1 - + + -
253A ARG* 2.9 51.2 + - + -
254A ILE* 1.3 75.9 - - - +
256A TYR* 1.3 60.6 + - - +
257A PHE* 3.5 20.8 - - + -
262A ILE* 4.0 27.8 - - + -
264A LYS 3.7 1.6 - - - -
265A TRP* 3.6 32.9 + + + -
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Residues in contact with TYR 256 (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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236A VAL* 4.1 10.8 - - + -
237A CYS 4.1 2.5 - - - -
238A PRO* 3.8 19.5 - - + -
254A ILE* 3.7 24.5 - - + +
255A TYR* 1.3 72.5 - - - +
257A PHE* 1.3 62.6 + - - +
262A ILE* 3.8 1.7 - - - -
263A LEU* 2.8 30.7 + - + +
264A LYS* 2.9 31.4 + - + +
266A GLU* 2.7 34.5 + - + -
305A ILE* 3.5 23.0 - - + +
306A ASP 4.4 0.9 - - - -
307A PRO* 4.8 1.1 - - + -
310A MET* 3.3 59.9 - - + -
311A THR 3.3 10.4 + - - -
312A HIS* 4.2 0.9 - - - +
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Residues in contact with PHE 257 (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 MET* 3.8 22.0 - - + -
192A ILE* 3.8 15.0 - - + -
205A ILE* 3.7 31.0 - - + -
213A THR* 5.1 0.4 - - + -
215A ILE* 4.0 6.7 - - + -
235A GLY 3.5 0.5 - - - +
236A VAL* 3.3 5.7 - - - -
237A CYS* 2.8 47.9 + - - +
239A VAL* 3.9 15.9 - - + -
241A PHE* 4.0 11.2 - + - -
255A TYR* 3.5 28.5 - - + -
256A TYR* 1.3 75.4 - - - +
258A LYS* 1.3 60.1 + - - +
260A GLY 4.1 12.3 - - - +
261A LYS 3.1 17.0 - - - +
262A ILE* 3.6 25.6 - - + -
263A LEU* 4.5 1.1 - - - -
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Residues in contact with LYS 258 (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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84A PHE* 3.7 28.3 - - - -
234A ASN* 3.2 27.3 + - - +
235A GLY* 3.4 18.8 - - - +
236A VAL* 4.3 10.1 - - + +
237A CYS* 5.9 0.2 - - - -
257A PHE* 1.3 74.7 - - - +
259A GLU* 1.3 84.2 + - + +
261A LYS* 2.9 26.0 + - - +
263A LEU* 3.7 28.4 - - + +
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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