Contacts of the helix formed by residues 357 - 369 (chain A) in PDB entry 3K2H
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 ASP 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337A TRP 3.6 0.7 - - - +
338A ARG* 2.6 62.5 + - - +
355A GLY 3.9 2.4 + - - +
356A ILE* 1.3 72.7 - - - +
358A GLN* 1.3 63.3 + - - +
359A LEU 3.3 2.8 + - - -
360A ALA* 3.0 25.7 + - + +
361A GLU* 2.9 27.1 + - + +
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Residues in contact with GLN 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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336A GLN 2.9 25.8 + - - +
337A TRP 3.0 9.5 + - - +
340A PHE* 3.6 8.0 - - + -
356A ILE* 3.1 7.2 + - + +
357A ASP* 1.3 73.6 - - - +
359A LEU* 1.3 65.3 + - - +
361A GLU* 3.2 0.3 + - - +
362A ILE* 2.9 29.1 + - - +
377A VAL* 3.4 18.0 - - + +
378A CYS 2.8 48.5 + - - +
516A EDO 3.4 28.8 - - - +
382B VAL* 3.4 29.4 - - + +
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Residues in contact with LEU 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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290A ILE* 4.0 23.6 - - + +
337A TRP* 3.1 26.6 + - + +
338A ARG* 3.9 27.1 - - - +
357A ASP* 3.2 6.5 - - - +
358A GLN* 1.3 76.4 - - - +
360A ALA* 1.3 63.9 + - - +
362A ILE* 4.1 1.3 - - + +
363A ILE* 3.1 47.1 + - + +
377A VAL* 4.4 15.7 - - + +
397A PHE* 5.3 4.9 - - + -
399A PHE* 5.9 2.5 - - + -
431A LEU* 4.7 9.2 - - + -
435A VAL* 5.0 3.1 - - + -
486A ILE* 4.0 29.8 - - + -
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Residues in contact with ALA 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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338A ARG* 4.5 5.6 - - - +
357A ASP* 3.0 33.6 + - + +
359A LEU* 1.3 77.6 - - - +
361A GLU* 1.3 62.9 + - + +
363A ILE* 4.0 6.9 - - - +
364A ASN* 3.1 25.3 + - - +
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Residues in contact with GLU 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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356A ILE* 3.8 23.0 - - - +
357A ASP* 2.9 22.8 + - + +
358A GLN 3.2 2.9 + - - +
360A ALA* 1.3 77.9 - - + +
362A ILE* 1.3 58.0 + - + +
364A ASN* 3.4 5.6 + - - +
365A ARG* 2.8 39.7 + - - +
516A EDO 3.3 23.7 + - - +
386B LYS* 4.6 19.2 + - - -
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Residues in contact with ILE 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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358A GLN 2.9 19.6 + - - +
359A LEU* 4.2 2.0 - - + +
361A GLU* 1.3 73.5 - - - +
363A ILE* 1.3 60.0 + - + +
365A ARG* 3.2 29.7 + - - +
366A ILE* 2.8 31.7 + - + +
374A ARG 3.8 1.1 - - - +
375A LEU* 3.9 20.9 - - + +
376A ILE 3.4 39.7 - - - +
377A VAL* 4.0 7.2 - - + -
399A PHE* 3.7 31.4 - - + -
516A EDO 3.9 13.0 - - - +
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Residues in contact with ILE 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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359A LEU* 3.1 36.2 + - + +
360A ALA* 4.0 5.2 - - - +
362A ILE* 1.3 76.3 - - + +
364A ASN* 1.3 63.0 + - - +
366A ILE* 3.4 4.0 + - + -
367A LYS* 3.3 36.5 + - - +
399A PHE* 6.2 0.9 - - + -
435A VAL* 3.9 21.5 - - + -
438A VAL* 3.8 24.5 - - + -
439A CYS* 3.7 11.5 - - - -
486A ILE* 3.5 42.6 - - + -
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Residues in contact with ASN 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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360A ALA 3.1 18.3 + - - +
361A GLU* 3.8 4.7 - - - +
363A ILE* 1.3 80.8 - - - +
365A ARG* 1.3 62.1 + - - +
367A LYS* 3.2 17.5 + - - +
368A THR* 3.0 44.2 + - - +
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Residues in contact with ARG 365 (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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361A GLU* 2.8 28.8 + - - +
362A ILE* 3.2 15.8 + - - +
364A ASN* 1.3 75.0 - - - +
366A ILE* 1.3 59.2 + - - +
368A THR* 3.8 6.7 - - - +
369A ASN* 2.7 52.2 + - + +
372A ASP* 3.3 33.8 + - - -
374A ARG* 2.7 36.8 + - - +
375A LEU* 3.8 10.1 - - + +
516A EDO 4.1 19.6 - - - -
380B TRP* 5.9 0.2 - - - -
385B LEU* 6.2 0.2 - - - +
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Residues in contact with ILE 366 (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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362A ILE* 2.8 26.6 + - + +
363A ILE* 3.7 5.2 - - - +
365A ARG* 1.3 72.8 - - - +
367A LYS* 1.3 62.1 + - - +
370A PRO* 3.5 23.7 - - - +
375A LEU* 4.1 24.2 - - + -
399A PHE* 3.9 18.8 - - + -
401A VAL* 4.0 8.3 - - + -
406A LEU* 3.8 15.0 - - + -
435A VAL* 3.6 28.9 - - + -
439A CYS* 3.7 12.6 - - + -
441A LEU* 3.5 31.5 - - + +
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Residues in contact with LYS 367 (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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363A ILE* 3.3 31.6 + - - +
364A ASN* 3.2 21.4 + - - +
366A ILE* 1.3 78.2 - - - +
368A THR* 1.3 65.4 + - + +
370A PRO* 4.2 4.5 - - - +
438A VAL* 3.4 26.5 + - - +
439A CYS* 4.0 16.8 - - + +
484A ARG 4.9 7.7 + - - -
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Residues in contact with THR 368 (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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364A ASN* 3.0 35.6 + - - +
365A ARG* 3.8 8.0 + - - +
367A LYS* 1.3 82.5 - - + +
369A ASN* 1.3 65.4 + - - +
370A PRO* 3.7 5.3 - - - +
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Residues in contact with ASN 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ARG* 2.7 30.5 + - + +
368A THR* 1.3 77.8 + - - +
370A PRO* 1.3 65.9 - - - +
371A ASN* 3.8 9.4 + - - +
372A ASP* 3.1 44.3 + - - +
375A LEU* 4.5 1.7 - - - +
248B ARG* 6.3 1.2 - - - +
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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