Contacts of the helix formed by residues 251 - 261 (chain A) in PDB entry 2YTC
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 THR 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A LEU* 5.8 0.4 - - - -
248A ASP 4.2 9.4 - - - +
249A THR 4.5 4.0 - - - +
250A ILE* 1.3 84.5 - - - +
252A GLU* 1.3 63.7 + - - +
253A THR* 3.8 7.7 + - - -
254A ASP* 3.5 30.0 + - - +
255A LEU* 3.3 21.5 - - - +
270A VAL* 5.2 4.7 - - - -
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Residues in contact with GLU 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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251A THR* 1.3 74.7 - - - +
253A THR* 1.3 58.6 + - - +
255A LEU* 2.6 28.8 + - - +
256A ARG* 2.8 18.4 + - + -
268A ILE* 3.3 37.3 - - + +
270A VAL* 3.2 40.1 + - + +
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Residues in contact with THR 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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251A THR* 3.8 7.7 + - - -
252A GLU* 1.3 77.6 - - - +
254A ASP* 1.3 67.4 + - - +
255A LEU 2.9 1.2 + - - -
256A ARG* 3.0 10.7 + - + +
257A ASN* 2.9 43.4 + - - +
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Residues in contact with ASP 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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249A THR 4.5 2.1 - - - +
250A ILE* 4.4 7.6 - - + -
251A THR* 3.5 31.5 + - - +
253A THR* 1.3 79.7 - - - +
255A LEU* 1.3 58.2 + - - +
257A ASN* 4.3 3.9 - - - +
258A HIS* 3.2 27.7 + - - +
300A VAL* 4.4 12.9 - - + +
301A ASN* 3.4 25.6 + - - +
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Residues in contact with LEU 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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243A VAL* 4.7 3.6 - - + -
246A LEU* 3.8 28.9 - - + -
250A ILE* 3.9 11.4 - - + -
251A THR 3.3 17.0 - - - +
252A GLU* 2.6 13.1 + - - +
254A ASP* 1.3 70.3 - - - +
256A ARG* 1.3 66.5 + - - +
257A ASN 3.0 1.8 - - - -
258A HIS* 2.8 3.6 + - - -
259A PHE* 2.7 52.6 + - + -
268A ILE* 4.7 0.9 - - + -
270A VAL* 4.3 7.0 - - + -
277A ALA* 3.6 30.5 - - + -
279A ILE* 4.1 10.1 - - + -
298A LEU* 4.9 0.9 - - + -
300A VAL* 4.9 8.1 - - + -
305A LEU* 4.5 12.1 - - + -
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Residues in contact with ARG 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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252A GLU* 2.8 22.8 + - + +
253A THR* 3.6 13.7 - - + +
255A LEU* 1.3 71.6 - - - +
257A ASN* 1.3 56.4 + - - +
260A TYR* 2.6 43.2 + - + +
265A ILE* 2.9 16.2 + - + +
268A ILE* 3.3 32.1 - - + +
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Residues in contact with ASN 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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253A THR* 2.9 40.6 + - - +
254A ASP* 4.3 3.5 - - - +
256A ARG* 1.3 81.2 + - - +
258A HIS* 1.3 66.6 + - - +
259A PHE 3.1 2.4 + - - -
260A TYR* 3.7 20.7 - - - +
261A GLN* 3.3 21.3 + - - +
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Residues in contact with HIS 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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254A ASP 3.2 18.7 + - - +
255A LEU* 2.8 11.8 + - - +
257A ASN* 1.3 75.7 - - - +
259A PHE* 1.3 61.9 + - + +
261A GLN* 2.8 41.9 + - - +
262A PHE* 3.5 12.8 - + - -
293A LYS 5.6 3.1 - - - -
294A SER* 5.8 0.2 - - - -
298A LEU* 2.8 35.0 - - + +
299A ILE 5.1 4.8 + - - -
300A VAL* 3.4 25.0 - - + +
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Residues in contact with PHE 259 (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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241A LEU* 5.0 6.3 - - + -
243A VAL* 3.7 26.5 - - + -
255A LEU* 2.7 48.5 + - + +
258A HIS* 1.3 76.9 - - + +
260A TYR* 1.3 54.5 + - - +
261A GLN 2.9 2.9 - - - -
262A PHE* 2.6 42.1 + + - +
263A GLY 3.5 2.8 + - - +
265A ILE* 3.9 4.3 - - + -
279A ILE* 3.5 37.2 - - + -
281A PHE* 3.7 28.1 - + + -
290A ALA* 3.8 13.0 - - + -
294A SER* 3.3 21.5 - - - -
298A LEU* 3.8 18.2 - - + -
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Residues in contact with TYR 260 (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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256A ARG* 2.6 31.7 + - + +
257A ASN* 3.7 22.2 - - - +
259A PHE* 1.3 72.2 - - - +
261A GLN* 1.3 68.7 + - + +
263A GLY* 3.0 22.8 + - - +
264A GLU* 5.4 8.3 - - - -
265A ILE* 3.2 15.8 - - + +
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Residues in contact with GLN 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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257A ASN 3.3 8.4 + - - +
258A HIS* 2.8 41.6 + - - +
259A PHE 2.8 1.2 + - - +
260A TYR* 1.3 89.8 - - + +
262A PHE* 1.3 89.1 + - + +
263A GLY* 4.5 0.2 - - - -
293A LYS* 5.2 4.2 + - - -
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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