Contacts of the helix formed by residues 332 - 340 (chain A) in PDB entry 3KJR
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 ILE 332 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A TRP* 3.8 24.9 - - + -
289A PHE* 5.4 0.2 - - + -
293A SER 5.3 0.4 - - - +
294A THR* 4.1 10.8 - - + +
307A TRP* 3.9 28.9 - - + -
329A LEU* 3.4 37.5 - - + +
330A GLY 2.8 17.1 + - - +
331A PRO* 1.3 74.5 - - - +
333A TYR* 1.3 77.5 + - + +
334A GLY 3.4 1.8 - - - +
335A PHE 3.1 12.6 + - - -
336A GLN* 3.1 14.1 + - - +
388A MET* 4.6 7.9 - - + -
390A LEU 3.8 21.8 - - - +
392A PRO* 4.6 10.1 - - + -
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Residues in contact with TYR 333 (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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289A PHE* 3.5 33.2 - + + -
307A TRP* 3.6 33.4 - + - -
332A ILE* 1.3 83.5 - - + +
334A GLY* 1.3 58.2 + - - +
336A GLN* 3.1 2.0 + - - +
337A TRP* 2.8 49.2 + - + +
379A SER* 4.2 11.0 - - - -
392A PRO* 3.5 23.2 - - + +
393A CYS* 2.6 30.8 + - - +
394A HIS* 3.2 60.2 - + - -
516A GOL 5.9 0.6 - - - -
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Residues in contact with GLY 334 (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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289A PHE* 3.4 28.5 - - - -
292A GLY* 3.3 29.2 - - - -
293A SER 4.0 10.1 + - - -
332A ILE* 3.2 2.6 + - - +
333A TYR* 1.3 78.3 - - - +
335A PHE* 1.3 60.0 - - - +
337A TRP* 3.9 0.8 - - - +
338A ARG* 3.2 20.4 + - - +
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Residues in contact with PHE 335 (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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292A GLY 3.8 8.0 + - - -
294A THR* 3.7 19.4 - - + +
331A PRO* 3.5 22.2 - - + -
332A ILE 3.1 8.4 + - - +
334A GLY* 1.3 73.5 - - - +
336A GLN* 1.3 65.4 + - - +
339A HIS* 2.7 62.0 + + + +
341A GLY 5.1 0.4 - - - -
342A ALA* 3.5 38.4 - - + -
344A TYR* 3.7 33.9 - + + -
351A TYR* 3.7 33.2 - + - -
384A ASP* 3.9 13.2 - - - -
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Residues in contact with GLN 336 (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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331A PRO* 3.0 30.4 + - - +
332A ILE* 3.1 12.4 + - - +
333A TYR 3.9 4.7 - - - +
335A PHE* 1.3 75.4 - - - +
337A TRP* 1.3 64.1 + - - +
338A ARG 3.4 0.3 + - - -
340A PHE* 3.3 28.0 + - - +
358A GLN* 2.9 21.0 + - - +
378A CYS 4.2 2.2 - - - +
379A SER* 3.6 37.6 + - - +
381A ASN* 3.2 32.1 + - - +
384A ASP* 2.9 29.1 + - - +
388A MET* 4.9 2.0 - - - -
392A PRO* 5.1 0.4 - - + -
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Residues in contact with TRP 337 (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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286A LEU* 3.9 14.8 - - + -
289A PHE* 3.6 49.4 - + + -
290A ILE* 4.2 9.4 - - + -
333A TYR* 2.8 36.6 + - + +
334A GLY* 3.9 4.5 - - - +
336A GLN* 1.3 76.8 - - - +
338A ARG* 1.3 66.7 + - + +
357A ASP* 3.6 0.7 - - - +
358A GLN* 3.0 23.2 + - - +
359A LEU* 3.0 32.5 + - + -
377A VAL* 3.8 20.0 - - + -
379A SER* 3.2 24.9 + - - -
394A HIS* 4.9 1.5 + + - -
397A PHE* 3.8 18.6 - + - -
428A TYR* 3.8 22.6 + + - -
431A LEU* 3.9 25.1 - - + -
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Residues in contact with ARG 338 (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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289A PHE 4.4 1.3 - - - +
290A ILE* 2.7 41.4 + - - +
291A LYS* 4.5 4.1 + - - +
292A GLY* 3.7 15.7 - - - +
334A GLY 3.2 17.2 + - - +
337A TRP* 1.3 85.7 - - - +
339A HIS* 1.3 84.2 + - + +
354A LYS 4.2 1.2 - - - +
355A GLY 4.9 0.2 - - - +
356A ILE 3.6 5.6 - - - -
357A ASP* 2.7 62.6 + - - +
359A LEU* 4.0 22.2 - - - +
360A ALA* 4.4 7.1 - - - +
486A ILE* 5.5 3.9 - - - +
487A GLU* 5.1 13.5 + - - +
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Residues in contact with HIS 339 (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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291A LYS 5.5 1.4 + - - -
292A GLY* 4.7 10.5 + - - -
335A PHE* 2.7 51.6 + + + +
338A ARG* 1.3 98.4 + - + +
340A PHE* 1.3 67.1 + - - +
341A GLY 3.2 0.3 + - - -
342A ALA* 2.9 20.6 + - + +
351A TYR* 3.2 42.6 + + + +
352A THR* 4.3 4.9 - - - -
353A GLY 5.0 2.0 + - - -
354A LYS 3.1 25.5 + - - +
355A GLY* 3.8 0.4 - - - -
356A ILE 3.7 4.5 - - - -
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Residues in contact with PHE 340 (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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335A PHE 3.6 0.2 + - - -
336A GLN* 3.3 35.5 + - - +
339A HIS* 1.3 73.5 - - - +
341A GLY* 1.3 62.3 + - - +
355A GLY* 3.2 2.9 - - - -
356A ILE* 2.7 45.7 + - + +
358A GLN* 3.5 24.9 - - + +
378A CYS* 3.6 14.8 - - - -
380A TRP 4.5 4.5 - - - -
381A ASN* 3.6 42.0 - - + -
340B PHE* 5.0 7.9 - + - -
380B TRP 4.9 3.8 - - - -
381B ASN* 4.8 3.1 - - - -
382B VAL* 3.7 41.3 - - + -
383B SER* 3.8 16.8 - - - -
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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