Contacts of the helix formed by residues 305 - 317 (chain A) in PDB entry 3KMR
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 LEU 305 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A EQN 4.2 18.2 - - + -
270A ILE* 5.5 4.0 - - + -
302A PHE* 2.9 28.2 + - + +
304A PRO* 1.3 82.1 - - + +
306A THR* 1.3 64.3 + - - +
307A ASP 3.5 0.4 - - - -
308A LEU* 3.3 10.9 + - + +
309A VAL* 3.0 29.5 + - + +
387A ILE* 4.1 9.9 - - + +
390A LYS* 3.5 44.2 - - + +
391A GLY* 3.5 20.6 - - - +
394A ARG* 3.7 21.5 - - + -
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Residues in contact with THR 306 (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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217A ARG* 4.3 8.7 - - - +
294A ARG* 3.6 42.8 - - + +
297A MET* 4.5 1.6 - - + -
298A HIS* 3.2 27.1 - - + +
302A PHE* 3.4 11.9 - - + +
303A GLY 2.7 21.2 + - - -
304A PRO 3.3 0.8 - - - -
305A LEU* 1.3 79.4 - - - +
307A ASP* 1.3 59.8 + - - +
309A VAL* 3.3 3.1 + - - +
310A PHE* 2.9 44.8 + - + -
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Residues in contact with ASP 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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217A ARG* 3.7 19.5 + - - -
294A ARG* 2.9 35.4 + - - +
304A PRO 4.7 3.1 + - - +
305A LEU 3.5 0.2 - - - -
306A THR* 1.3 75.2 - - - +
308A LEU* 1.3 60.0 + - + +
310A PHE* 3.5 1.0 + - - +
311A ALA* 2.8 30.9 + - - +
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Residues in contact with LEU 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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304A PRO 4.9 9.4 + - - +
305A LEU* 3.3 11.8 + - + +
306A THR 3.3 0.4 - - - -
307A ASP* 1.3 79.9 - - + +
309A VAL* 1.3 56.9 + - - +
311A ALA* 3.4 8.7 + - + +
312A PHE* 2.9 28.2 + - - +
386A SER* 6.0 1.6 - - - +
387A ILE* 3.9 27.9 - - + +
390A LYS* 3.7 37.7 - - + +
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Residues in contact with VAL 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ILE* 4.3 12.1 - - + -
273A ILE* 4.9 2.0 - - + -
274A CYS* 3.5 24.8 - - - -
284A MET* 4.0 13.9 - - + -
297A MET* 5.4 0.2 - - + -
302A PHE* 4.1 33.4 - - + -
305A LEU* 3.0 22.2 + - + +
306A THR* 3.7 4.0 - - - +
308A LEU* 1.3 73.5 - - - +
310A PHE* 1.3 61.2 + - + +
312A PHE* 3.2 8.8 + - - +
313A ALA 3.0 23.0 + - - -
387A ILE* 3.9 24.2 - - + -
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Residues in contact with PHE 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A TYR* 3.6 19.3 - + - -
282A ASP* 3.3 40.8 - - - -
283A THR 4.5 0.4 - - - -
284A MET* 3.7 26.2 - - + -
293A ASN 4.3 0.7 - - - -
294A ARG* 3.3 50.5 - - + +
297A MET* 3.8 33.7 - - + -
302A PHE* 6.3 0.9 - + - -
306A THR* 2.9 36.7 + - + +
309A VAL* 1.3 75.2 - - + +
311A ALA* 1.3 60.8 + - - +
313A ALA* 3.3 1.7 + - - +
314A ASN* 3.0 36.3 + - - -
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Residues in contact with ALA 311 (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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294A ARG* 5.2 0.4 - - - +
307A ASP 2.8 19.6 + - - +
308A LEU* 3.5 11.4 - - + +
310A PHE* 1.3 74.8 - - - +
312A PHE* 1.3 63.1 + - - +
314A ASN* 3.3 7.4 + - - +
315A GLN* 3.1 41.3 + - - +
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Residues in contact with PHE 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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270A ILE* 4.8 1.3 - - + -
271A LEU* 4.2 9.6 - - + -
274A CYS* 3.8 19.1 - - + -
308A LEU 2.9 12.9 + - - +
309A VAL* 3.3 9.0 - - - +
311A ALA* 1.3 76.5 - - - +
313A ALA* 1.3 56.9 + - - +
315A GLN* 3.2 12.4 + - - +
316A LEU* 2.9 56.7 + - + +
380A LYS* 3.5 50.0 - - + -
383A ASP* 3.9 18.4 - - + -
384A LEU* 3.8 31.6 - - + -
387A ILE* 3.7 17.7 - - + -
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Residues in contact with ALA 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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274A CYS* 3.8 19.7 - - + +
277A TYR* 3.7 25.4 - - + +
284A MET* 3.7 28.3 - - + -
309A VAL 3.0 7.3 + - - +
310A PHE 3.3 7.8 + - - +
312A PHE* 1.3 75.1 - - - +
314A ASN* 1.3 58.6 + - - +
316A LEU* 3.2 5.6 + - - +
317A LEU* 3.0 31.2 + - - +
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Residues in contact with ASN 314 (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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277A TYR* 3.1 38.8 + - - -
279A PRO* 4.7 7.1 - - - +
294A ARG* 4.4 9.1 - - - +
310A PHE 3.0 27.5 + - - +
311A ALA* 3.7 7.7 - - - +
312A PHE 3.3 0.2 - - - -
313A ALA* 1.3 76.0 - - - +
315A GLN* 1.3 58.7 + - + +
317A LEU* 4.0 5.5 + - - +
318A PRO* 3.0 22.2 - - - +
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Residues in contact with GLN 315 (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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311A ALA* 3.1 29.4 + - - +
312A PHE* 3.7 12.2 - - - +
314A ASN* 1.3 77.4 - - + +
316A LEU* 1.3 63.9 + - - +
318A PRO* 3.6 11.3 - - - +
319A LEU* 3.6 12.5 - - - +
380A LYS* 3.3 30.7 + - - +
383A ASP* 4.5 9.7 - - - +
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Residues in contact with LEU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU* 3.8 31.9 - - + -
274A CYS* 4.1 18.8 - - + +
275A THR* 4.1 15.0 - - + +
312A PHE* 2.9 37.7 + - + +
313A ALA 3.5 4.7 - - - +
315A GLN* 1.3 78.1 - - - +
317A LEU* 1.3 66.1 + - - +
319A LEU* 3.0 26.2 + - + +
320A GLU 4.2 0.7 + - - -
321A MET* 4.0 27.1 + - + +
329A LEU* 5.3 0.4 - - + -
380A LYS* 4.3 16.8 - - + +
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Residues in contact with LEU 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A TYR* 4.0 22.4 - - + +
279A PRO* 3.9 31.2 - - + -
313A ALA 3.0 15.3 + - - +
314A ASN* 4.2 6.3 - - - +
316A LEU* 1.3 77.4 - - - +
318A PRO* 1.4 70.5 - - + +
319A LEU 3.1 5.2 + - - -
320A GLU* 3.1 19.8 + - - +
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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