Contacts of the helix formed by residues 348 - 364 (chain A) in PDB entry 3KA0
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 ARG 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261A PRO* 5.6 0.9 - - - -
264A TYR* 3.1 39.8 + - - -
345A ASP* 3.3 42.2 + - - +
346A LYS 3.2 4.0 - - - -
347A GLU* 1.3 75.3 - - - +
349A TRP* 1.3 55.7 + - - +
350A GLU 3.2 1.1 - - - -
351A ASP* 2.8 34.9 + - + +
352A VAL* 3.0 28.8 + - + +
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Residues in contact with TRP 349 (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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145A GLU* 4.7 6.0 + - - -
147A PHE* 3.6 49.7 - + + +
148A SER* 5.5 3.8 + - - +
151A GLN* 5.3 12.1 - - - +
189A PRO* 3.8 23.1 - - + -
255A ILE* 4.3 15.9 - - + -
259A GLY 5.4 0.9 - - - -
261A PRO* 6.0 2.2 - - + -
342A LEU* 4.0 25.6 - - + +
345A ASP 3.9 3.0 + - - +
346A LYS* 4.6 10.1 - - + -
347A GLU 3.2 10.1 - - - +
348A ARG* 1.3 78.3 - - - +
350A GLU* 1.3 68.8 + - + +
352A VAL* 3.2 27.8 - - + +
353A LYS* 3.0 61.7 + - + +
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Residues in contact with GLU 350 (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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347A GLU* 4.0 12.5 + - - +
348A ARG 3.2 0.6 - - - -
349A TRP* 1.3 81.6 - - + +
351A ASP* 1.3 68.1 + - - +
353A LYS* 2.7 38.6 + - - +
354A GLU* 3.3 22.2 + - - +
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Residues in contact with ASP 351 (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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347A GLU 4.0 12.0 - - - +
348A ARG* 2.8 24.7 + - + +
350A GLU* 1.3 77.9 - - - +
352A VAL* 1.3 59.5 + - + +
354A GLU* 3.3 10.9 + - - +
355A GLU* 2.9 37.3 + - + +
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Residues in contact with VAL 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A PRO* 6.2 0.9 - - + -
255A ILE* 5.9 2.0 - - + -
261A PRO* 3.5 37.9 - - + -
264A TYR* 6.2 0.2 - - + -
348A ARG* 3.0 29.9 + - + +
349A TRP* 3.2 47.8 - - + +
351A ASP* 1.3 74.9 - - + +
353A LYS* 1.3 70.3 + - - +
354A GLU 3.0 1.3 - - - -
355A GLU* 3.9 6.6 - - + +
356A MET* 2.9 27.4 + - - +
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Residues in contact with LYS 353 (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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145A GLU* 4.2 16.6 - - - +
189A PRO* 4.6 17.8 - - + +
190A GLU* 3.6 28.1 - - + +
349A TRP* 3.0 54.0 + - + +
350A GLU* 2.7 45.6 + - - +
352A VAL* 1.3 75.7 - - - +
354A GLU* 1.3 57.3 + - - +
356A MET* 3.8 4.4 + - - +
357A THR* 3.1 31.5 + - - -
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Residues in contact with GLU 354 (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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350A GLU 3.3 17.1 + - - +
351A ASP* 3.5 10.8 - - - +
352A VAL 3.0 0.6 - - - -
353A LYS* 1.3 77.9 - - - +
355A GLU* 1.3 74.2 + - + +
357A THR* 3.3 14.0 + - - +
358A SER* 3.3 14.0 + - - -
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Residues in contact with GLU 355 (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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275A MET* 4.3 42.8 - - + +
351A ASP* 2.9 24.8 + - + +
352A VAL* 4.0 7.0 - - + +
354A GLU* 1.3 82.4 - - + +
356A MET* 1.3 57.7 + - - +
358A SER* 3.0 14.8 + - - -
359A ALA* 2.8 28.1 + - - +
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Residues in contact with MET 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A VAL 3.8 20.0 - - - +
188A LYS* 4.1 3.6 - - + -
189A PRO* 3.7 29.2 - - + -
247A TRP* 4.2 13.5 - - + -
248A SER* 4.0 13.5 - - - +
251A VAL* 3.4 41.3 - - + -
252A ILE* 4.0 12.6 - - + -
255A ILE* 5.4 2.5 - - - -
352A VAL 2.9 18.5 + - - +
353A LYS* 4.2 4.3 - - - +
355A GLU* 1.3 75.8 - - - +
357A THR* 1.3 62.6 + - - +
359A ALA* 3.7 5.7 - - - +
360A LEU* 3.1 30.2 + - + +
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Residues in contact with THR 357 (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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186A ASP* 4.7 2.0 - - - +
188A LYS* 2.6 41.1 + - - +
190A GLU* 4.3 4.7 + - - -
353A LYS 3.1 20.3 + - - -
354A GLU* 3.7 7.6 - - - +
355A GLU 3.2 0.4 - - - -
356A MET* 1.3 77.6 - - - +
358A SER* 1.3 60.3 + - - +
360A LEU* 3.6 3.9 + - - +
361A ALA* 3.0 24.9 + - + +
364A ARG* 5.0 2.1 + - - +
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Residues in contact with SER 358 (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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354A GLU* 3.3 10.5 + - - -
355A GLU* 3.0 18.7 + - - -
357A THR* 1.3 76.1 - - - +
359A ALA* 1.3 70.0 + - - +
360A LEU 3.2 0.9 - - - -
361A ALA* 3.6 9.3 - - - +
362A THR* 2.8 30.0 + - - -
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Residues in contact with ALA 359 (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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247A TRP* 3.8 25.1 - - + -
279A ILE* 4.0 21.8 - - + -
355A GLU 2.8 16.5 + - - +
356A MET* 3.7 7.6 - - - +
358A SER* 1.3 75.9 + - - +
360A LEU* 1.3 65.3 + - - +
362A THR* 2.9 19.4 + - - +
363A MET* 3.0 17.4 + - - +
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Residues in contact with LEU 360 (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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185A ARG 4.2 9.3 - - - +
186A ASP* 3.4 23.8 - - - +
187A VAL 3.7 14.4 - - - +
188A LYS* 3.7 21.3 - - + -
244A CYS* 5.0 2.9 - - + +
247A TRP* 3.8 21.5 - - + -
248A SER* 3.3 22.0 - - - +
356A MET* 3.1 20.5 + - + +
357A THR 3.7 3.6 - - - +
359A ALA* 1.3 78.6 - - - +
361A ALA* 1.3 62.5 + - - +
363A MET* 3.1 25.0 + - + +
364A ARG* 3.2 31.2 + - - +
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Residues in contact with ALA 361 (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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357A THR* 3.0 20.4 + - + +
358A SER* 3.6 11.7 - - - +
359A ALA 3.2 0.2 - - - -
360A LEU* 1.3 74.8 - - - +
362A THR* 1.3 62.0 + - - +
363A MET 3.5 0.2 + - - -
364A ARG* 3.6 35.8 + - - +
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Residues in contact with THR 362 (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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276A LYS* 5.4 16.6 - - + +
358A SER* 2.8 21.9 + - - -
359A ALA* 2.9 9.4 + - - +
361A ALA* 1.3 80.2 - - - +
363A MET* 1.3 60.5 + - + +
364A ARG 3.5 3.1 + - - -
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Residues in contact with MET 363 (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 TYR* 2.7 45.0 + - - +
244A CYS* 3.3 55.6 - - + +
247A TRP* 3.9 44.4 - - + -
279A ILE* 6.3 1.6 - - - -
313A ARG* 4.7 7.2 - - - +
359A ALA* 3.2 15.3 - - - +
360A LEU* 3.1 17.0 + - + +
362A THR* 1.3 75.2 - - + +
364A ARG* 1.3 62.3 + - - +
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Residues in contact with ARG 364 (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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185A ARG* 2.8 90.1 + - - +
186A ASP* 3.0 21.6 + - - +
210A PHE* 3.4 46.8 - - - -
240A TYR* 5.1 3.5 - - - -
244A CYS* 5.7 1.3 - - - -
357A THR* 5.0 2.0 + - - +
360A LEU* 3.2 19.5 + - - +
361A ALA* 3.7 37.3 - - - +
362A THR 3.3 3.9 - - - -
363A MET* 1.3 84.3 - - - +
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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