Contacts of the helix formed by residues 348 - 359 (chain A) in PDB entry 3KHU
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 SER 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A GLY* 4.5 0.4 - - - -
311A ARG* 4.0 0.2 - - - -
336A PHE 2.8 27.5 + - - -
337A ALA 3.3 9.0 + - - -
338A PHE* 3.6 22.9 - - - -
345A THR* 3.0 16.7 + - - -
346A ARG 3.0 1.8 + - - -
347A GLU* 1.3 79.7 - - - +
349A SER* 1.3 66.1 + - - +
350A SER* 3.1 10.0 + - - -
351A ILE* 2.9 27.3 + - - +
352A TYR* 3.4 4.7 - - - -
442A ARG* 5.8 0.3 + - - -
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Residues in contact with SER 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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270A VAL* 3.8 28.5 - - - -
271A GLY* 2.6 32.1 + - - -
273A GLY* 5.0 1.0 - - - -
311A ARG* 2.9 32.1 + - - +
338A PHE* 5.1 2.2 + - - +
347A GLU 3.5 1.8 + - - -
348A SER* 1.3 73.2 + - - +
350A SER* 1.3 63.2 + - - +
352A TYR* 3.1 3.0 + - - +
353A ILE* 2.9 27.8 + - - +
414A CYS* 5.2 1.3 - - - -
442A ARG* 5.3 3.7 - - - +
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Residues in contact with SER 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ILE* 4.9 2.0 - - - -
335A GLY 2.8 27.1 + - - -
336A PHE* 3.5 21.2 - - - -
337A ALA 4.1 0.2 + - - -
348A SER* 3.1 13.2 + - - -
349A SER* 1.3 78.6 - - - +
351A ILE* 1.3 61.5 + - - +
353A ILE* 4.1 0.4 - - - +
354A SER* 2.8 31.4 + - - -
414A CYS* 3.1 26.8 + - - +
415A THR* 3.4 8.0 + - - -
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Residues in contact with ILE 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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336A PHE* 3.8 28.3 - - + -
345A THR 3.3 25.1 - - - +
346A ARG* 5.1 0.4 - - - -
347A GLU* 4.3 8.1 - - - +
348A SER* 2.9 18.3 + - - +
350A SER* 1.3 76.7 - - - +
352A TYR* 1.3 72.2 + - + +
354A SER* 3.6 2.1 - - - -
355A LYS* 2.9 42.8 + - + +
379A ASP* 4.0 37.5 - - + +
380A LEU* 3.9 6.9 - - + +
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Residues in contact with TYR 352 (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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278A GLN* 4.7 6.7 + - - -
311A ARG* 3.4 46.0 - - + -
347A GLU* 2.5 35.1 + - - -
348A SER 3.4 17.3 - - - -
349A SER 3.1 5.0 + - - +
351A ILE* 1.3 89.0 - - + +
353A ILE* 1.3 64.8 + - - +
355A LYS* 3.3 11.9 + - + +
356A TYR* 3.0 41.8 + + + -
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Residues in contact with ILE 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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270A VAL* 3.8 27.1 - - + -
311A ARG* 3.2 36.3 - - + +
314A PHE* 4.0 8.5 - - + -
315A ALA* 4.3 8.7 - - + +
318A ILE* 4.4 16.2 - - + -
333A ILE* 4.9 2.2 - - + -
349A SER 2.9 20.9 + - - +
350A SER 4.1 2.0 - - - +
352A TYR* 1.3 76.1 - - - +
354A SER* 1.3 64.3 + - - +
356A TYR* 3.2 7.6 + - + +
357A LEU* 3.1 38.8 + - + +
412A VAL* 4.4 3.6 - - + -
414A CYS* 4.3 20.9 - - - -
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Residues in contact with SER 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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333A ILE* 4.0 17.3 - - - +
336A PHE* 4.0 8.7 - - - -
350A SER 2.8 23.2 + - - -
351A ILE 3.6 3.6 - - - -
353A ILE* 1.3 76.2 - - - +
355A LYS* 1.3 58.6 + - - +
357A LEU* 3.2 4.4 + - - -
358A MET* 2.9 32.4 + - - +
364A LEU* 3.6 26.2 - - - +
366A ILE* 4.4 1.4 - - - +
380A LEU* 3.8 19.1 - - - -
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Residues in contact with LYS 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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351A ILE* 2.9 30.9 + - + +
352A TYR* 3.3 13.7 + - + +
353A ILE 3.2 0.2 - - - -
354A SER* 1.3 77.4 - - - +
356A TYR* 1.3 62.1 + - - +
358A MET* 3.2 13.2 + - + +
359A ASP* 2.9 31.9 + - - +
379A ASP 3.9 21.6 + - - -
380A LEU* 4.2 21.3 - - + +
381A SER 4.6 8.6 + - - -
382A HIS* 5.9 8.0 - - - +
383A PRO* 5.6 4.2 - - - +
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Residues in contact with TYR 356 (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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308A ASP* 4.7 4.3 + - - +
311A ARG* 4.4 8.5 - - + -
312A ARG* 3.9 43.5 + - + +
315A ALA* 3.7 28.0 - - + -
319A ILE* 4.4 2.6 - - + +
352A TYR* 3.0 35.2 + + + -
353A ILE* 3.2 6.9 + - - +
355A LYS* 1.3 78.0 - - + +
357A LEU* 1.3 61.9 + - - +
359A ASP* 3.4 21.0 + - + +
360A GLU* 3.4 19.0 - - - +
98C MET* 4.0 21.2 - - + +
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Residues in contact with LEU 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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315A ALA* 4.8 2.5 - - + +
318A ILE* 4.2 25.4 - - + -
319A ILE* 3.9 28.7 - - + -
326A VAL* 4.9 5.4 - - + -
331A ILE* 4.3 18.4 - - + -
333A ILE* 4.1 26.5 - - + -
353A ILE* 3.1 23.6 + - + +
354A SER* 3.6 6.3 - - - +
356A TYR* 1.3 75.0 - - + +
358A MET* 1.3 64.6 + - - +
360A GLU* 3.0 13.5 + - - +
361A GLY 3.2 0.2 + - - -
362A ALA* 3.1 23.6 + - + +
364A LEU* 3.9 18.4 - - + -
412A VAL* 4.9 0.2 - - + -
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Residues in contact with MET 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 SER 2.9 24.3 + - - +
355A LYS* 3.6 11.4 - - + +
357A LEU* 1.3 76.6 - - - +
359A ASP* 1.3 57.2 + - - +
360A GLU 3.0 0.2 - - - -
361A GLY* 2.8 17.0 + - - -
362A ALA 4.5 2.2 - - - +
364A LEU* 3.8 14.6 - - + -
380A LEU* 3.9 39.0 - - - +
390A GLN* 3.5 43.2 + - + +
391A VAL 4.3 4.5 - - - +
394A LEU* 3.4 27.3 - - + +
395A VAL* 3.8 28.3 - - + -
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Residues in contact with ASP 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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355A LYS* 2.9 21.0 + - - +
356A TYR* 3.5 21.0 - - + +
357A LEU 3.2 0.4 - - - -
358A MET* 1.3 74.9 - - - +
360A GLU* 1.3 58.3 + - + +
361A GLY 3.4 0.4 - - - -
390A GLN* 4.0 16.2 + - - +
96C TYR* 3.1 24.8 - - - +
97C GLY* 3.4 20.0 + - - +
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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