Contacts of the helix formed by residues 302 - 314 (chain A) in PDB entry 2CHR
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 302 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A SER* 1.3 72.7 + - - +
303A ILE* 1.3 64.8 + - - +
305A THR* 4.4 0.9 - - - -
306A SER* 2.8 37.2 + - - -
327A PRO* 3.7 30.0 - - + +
333A THR* 4.3 17.9 - - + +
334A LEU 4.5 8.7 + - - -
335A SER* 3.1 29.2 + - - +
337A GLU 4.5 7.2 - - - +
338A PRO* 5.3 0.4 - - + -
339A LEU* 4.5 12.9 - - + +
356A MET* 3.9 13.0 - - - -
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Residues in contact with ILE 303 (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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33A ILE* 3.8 19.5 - - + -
44A VAL* 3.6 21.3 - - + +
45A GLY* 3.8 31.0 - - - -
46A GLU* 3.0 15.3 - - - +
106A MET* 5.3 0.9 - - - -
301A SER* 3.3 4.2 - - - +
302A THR* 1.3 82.9 + - - +
304A GLY* 1.3 60.2 - - - +
306A SER* 4.8 0.2 - - - -
307A VAL* 3.3 23.1 + - + +
334A LEU* 4.6 7.2 - - + +
335A SER* 5.5 2.0 - - - -
354A HIS* 4.0 21.6 + - + -
356A MET* 5.0 6.3 - - + -
358A LEU* 3.5 33.4 - - + +
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Residues in contact with GLY 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLU* 3.3 18.7 + - - -
106A MET* 4.7 14.4 - - - -
270A LEU* 5.4 1.2 - - - +
300A ASP* 3.2 15.7 - - - -
301A SER 3.5 1.8 + - - -
302A THR 3.1 0.6 - - - -
303A ILE* 1.3 76.0 - - - +
305A THR* 1.3 65.0 + - - +
306A SER 2.9 3.6 + - - -
307A VAL* 2.9 14.6 + - - +
308A ALA* 3.0 14.0 + - - +
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Residues in contact with THR 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A THR* 4.6 1.9 + - - -
300A ASP* 2.9 19.9 + - - -
301A SER 2.9 18.3 + - - -
302A THR 3.9 0.4 - - - -
304A GLY* 1.3 72.6 - - - +
306A SER* 1.3 56.9 + - - +
308A ALA* 3.6 6.0 + - - -
309A LEU* 3.0 28.6 + - + +
324A LEU* 3.5 41.2 - - + +
326A GLY* 4.2 3.1 + - - -
327A PRO* 3.4 12.1 - - + +
339A LEU* 3.4 26.2 - - + -
346A LEU* 4.2 4.5 - - + -
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Residues in contact with SER 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A THR 2.8 18.9 + - - -
303A ILE 4.0 2.0 - - - -
305A THR* 1.3 74.3 - - - +
307A VAL* 1.3 62.6 + - - +
309A LEU* 3.2 8.5 + - - +
310A GLN* 3.0 29.9 + - - +
339A LEU* 4.2 10.7 - - - +
349A PRO* 3.7 15.2 - - - +
354A HIS* 2.8 36.3 + - - -
356A MET* 3.8 10.8 - - - +
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Residues in contact with VAL 307 (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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44A VAL 5.4 1.8 - - - +
106A MET* 4.1 31.2 - - + +
109A LEU* 5.8 0.9 - - + -
120A ILE* 3.8 19.4 - - + +
270A LEU* 3.9 6.7 - - + -
276A VAL* 3.6 27.6 - - + -
303A ILE* 3.3 17.0 + - + +
304A GLY 2.9 6.7 + - - +
306A SER* 1.3 73.0 - - - +
308A ALA* 1.3 65.8 + - - +
310A GLN* 3.2 11.7 + - - +
311A LEU* 3.2 20.6 + - - +
354A HIS* 3.8 21.8 - - + +
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Residues in contact with ALA 308 (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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270A LEU* 4.2 19.5 - - + +
296A GLY 5.3 0.7 - - - +
300A ASP* 5.6 1.1 - - - +
304A GLY 3.0 15.3 + - - +
305A THR* 3.9 5.6 - - - +
307A VAL* 1.3 76.3 - - - +
309A LEU* 1.3 56.9 + - - +
311A LEU* 3.3 3.6 + - - +
312A TYR* 2.9 63.8 + - + +
324A LEU* 4.3 9.6 - - + -
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Residues in contact with LEU 309 (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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132A ILE* 4.0 22.4 - - + -
305A THR 3.0 22.6 + - - +
306A SER* 3.3 6.3 - - - +
308A ALA* 1.3 74.0 - - - +
310A GLN* 1.3 66.0 + - - +
312A TYR* 3.3 3.0 + - - +
313A SER* 3.1 26.3 + - - -
322A CYS* 5.3 0.2 - - - -
324A LEU* 3.6 20.2 - - + +
339A LEU* 4.2 14.8 - - + -
346A LEU* 3.8 30.5 - - + +
347A GLN 3.7 20.6 - - - +
348A VAL* 4.3 12.9 - - + +
349A PRO* 4.0 17.0 - - + -
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Residues in contact with GLN 310 (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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119A SER* 2.9 25.2 + - - -
120A ILE* 3.6 27.4 - - + -
121A ALA* 3.2 24.2 + - - +
124A LEU* 4.7 0.2 - - - -
306A SER* 3.0 18.9 + - - +
307A VAL* 3.3 10.3 - - - +
309A LEU* 1.3 76.9 - - - +
311A LEU* 1.3 57.4 + - - +
313A SER* 2.7 22.7 + - - -
314A THR* 3.6 10.9 - - - +
348A VAL* 4.5 5.8 - - - +
349A PRO* 3.9 33.2 + - - +
351A GLY 5.5 1.0 + - - +
354A HIS* 3.6 22.1 - - - +
355A GLY 4.6 0.4 - - - +
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Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ILE* 5.8 0.4 - - + -
124A LEU* 3.7 25.5 - - + +
270A LEU* 3.5 32.8 - - + -
276A VAL* 3.8 15.0 - - + -
279A THR* 3.6 22.9 - - + -
280A GLN* 3.5 30.5 - - + +
307A VAL 3.2 8.8 + - - +
308A ALA* 3.7 5.8 - - - +
310A GLN* 1.3 77.5 - - - +
312A TYR* 1.3 71.7 + - + +
313A SER 3.2 0.2 - - - -
314A THR* 2.4 27.7 + - - +
315A VAL* 3.6 9.6 + - + +
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Residues in contact with TYR 312 (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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129A ARG* 2.6 29.6 + - - -
132A ILE* 3.6 18.4 - - + -
268A LEU* 2.9 54.5 + - + -
269A LYS* 4.4 3.1 + - - -
270A LEU* 4.7 4.8 + - + +
279A THR* 4.9 0.9 - - + -
294A TYR 4.9 0.9 - - - -
295A GLY* 3.7 20.6 - - - -
296A GLY 3.2 9.7 + - - -
308A ALA* 2.9 44.9 + - + +
309A LEU* 3.3 1.3 + - - +
311A LEU* 1.3 86.6 - - + +
313A SER* 1.3 54.4 + - - +
314A THR 3.0 6.7 + - - -
315A VAL* 3.2 13.8 + - + +
318A LEU* 3.7 10.0 - - + +
322A CYS* 4.6 7.2 - - + -
324A LEU* 3.9 24.9 - - + -
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Residues in contact with SER 313 (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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121A ALA* 4.0 6.8 - - - +
127A PRO* 3.7 13.1 - - - +
128A LEU* 2.9 33.2 + - - +
129A ARG* 3.7 35.9 + - - +
132A ILE* 4.1 1.5 - - - +
309A LEU 3.1 11.6 + - - -
310A GLN* 2.7 23.0 + - - -
312A TYR* 1.3 77.0 - - - +
314A THR* 1.3 57.6 + - - +
315A VAL 3.4 0.2 - - - -
348A VAL* 4.0 16.1 - - - +
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Residues in contact with THR 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ALA* 3.9 15.7 - - - +
124A LEU* 4.1 20.9 - - + +
126A GLY 3.5 24.9 - - - +
128A LEU* 3.9 11.8 - - - +
280A GLN* 5.3 2.3 + - - -
310A GLN 3.6 15.9 - - - +
311A LEU* 2.4 33.6 + - - +
313A SER* 1.3 81.0 - - - +
315A VAL* 1.3 63.4 + - - +
316A PRO* 3.6 4.3 - - - +
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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