Contacts of the helix formed by residues 395 - 416 (chain C) in PDB entry 1KKQ
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 GLY 395 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393C ASN 2.3 18.0 + - - -
394C VAL* 1.3 67.2 - - - +
396C HIS* 1.3 61.9 + - - -
397C ILE 3.2 1.3 - - - -
398C GLU* 3.1 4.3 + - - +
399C LYS* 2.8 34.0 + - - +
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Residues in contact with HIS 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299C ASN* 6.5 0.4 - - + -
300C LEU* 6.1 5.4 - - + -
393C ASN* 3.1 39.8 + - + +
395C GLY* 1.3 75.3 - - - +
397C ILE* 1.3 53.2 + - + +
399C LYS* 3.7 26.5 + - - +
400C MET* 2.6 47.2 + - + +
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Residues in contact with ILE 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C LEU* 4.2 14.1 - - + -
304C ASP* 4.1 17.9 - - + -
308C LEU* 3.7 22.2 - - + -
384C CYS* 3.7 7.2 - - + +
385C CYS 3.4 26.7 - - - +
386C GLY* 4.0 5.5 + - - -
391C LEU* 3.4 41.5 - - + -
393C ASN* 3.8 15.3 - - + +
394C VAL* 4.6 3.1 - - - +
395C GLY 3.2 0.2 - - - -
396C HIS* 1.3 78.6 - - + +
398C GLU* 1.3 57.5 + - - +
400C MET* 3.8 8.0 - - - +
401C GLN* 3.1 26.7 + - - +
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Residues in contact with GLU 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C GLY* 3.1 36.7 - - - +
387C ASP* 5.4 1.4 - - - +
394C VAL* 3.3 24.5 + - - +
395C GLY* 3.1 5.7 + - - +
397C ILE* 1.3 78.0 - - - +
399C LYS* 1.3 56.6 + - - +
400C MET 3.1 4.9 - - - -
401C GLN* 3.3 11.8 + - - +
402C GLU* 3.0 23.7 + - - +
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Residues in contact with LYS 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C GLY 2.8 19.8 + - - +
396C HIS* 3.7 28.9 + - - +
398C GLU* 1.3 71.3 - - - +
400C MET* 1.3 64.1 + - - +
402C GLU* 3.2 33.1 - - - +
403C GLY* 3.5 4.7 + - - -
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Residues in contact with MET 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C LEU* 5.5 0.5 - - - +
295C PRO 3.5 8.7 - - - +
296C GLY* 3.0 45.8 - - - +
297C PHE* 3.4 9.4 - - + +
300C LEU* 4.2 19.7 - - + -
384C CYS* 4.3 26.0 - - - -
396C HIS* 2.6 24.9 + - + +
397C ILE* 3.8 4.7 - - - +
399C LYS* 1.3 77.9 - - + +
401C GLN* 1.3 65.7 + - - +
402C GLU 3.0 1.1 - - - -
403C GLY* 2.9 13.5 + - - -
404C ILE* 3.3 19.6 + - + +
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Residues in contact with GLN 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381C ALA* 3.3 25.0 + - + +
384C CYS 3.0 20.0 - - - +
385C CYS* 3.5 16.6 - - - +
386C GLY* 3.5 14.4 + - - -
387C ASP* 4.5 3.6 - - - +
397C ILE 3.1 12.2 + - - +
398C GLU* 3.4 11.5 - - - +
400C MET* 1.3 80.0 - - - +
402C GLU* 1.3 59.3 + - - +
404C ILE* 3.1 10.2 + - - +
405C VAL* 2.8 46.2 + - + +
430C MET* 5.5 2.6 - - - +
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Residues in contact with GLU 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C GLU 3.0 11.0 + - - +
399C LYS* 3.2 27.8 - - - +
401C GLN* 1.3 79.5 - - - +
403C GLY* 1.3 57.0 + - - +
405C VAL* 3.8 5.8 - - - +
406C HIS* 2.9 33.0 + - + +
409C ARG* 5.4 0.2 + - - -
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Residues in contact with GLY 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C LEU* 3.4 26.7 - - - +
206C LEU* 2.9 23.2 - - - +
399C LYS 3.5 4.5 + - - -
400C MET 2.9 9.6 + - - -
402C GLU* 1.3 81.3 - - - +
404C ILE* 1.3 58.1 + - - +
406C HIS* 3.9 3.4 - - - -
407C VAL* 3.4 10.9 + - - +
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Residues in contact with ILE 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C LEU* 4.1 14.8 - - + -
210C ILE* 4.5 9.9 - - + -
294C ILE* 4.2 15.3 - - + -
295C PRO 5.7 0.2 - - - +
377C LEU* 3.8 12.8 - - + +
380C ALA* 3.9 13.0 - - + +
381C ALA* 3.8 30.5 - - + +
384C CYS* 4.0 34.3 - - + -
400C MET* 3.7 20.0 - - + +
401C GLN* 3.1 7.4 + - - +
403C GLY* 1.3 76.6 - - - +
405C VAL* 1.3 62.6 + - - +
406C HIS 3.2 1.6 - - - -
407C VAL* 3.6 3.8 + - - +
408C LEU* 2.9 26.9 + - - +
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Residues in contact with VAL 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C ALA* 4.4 14.1 - - + -
401C GLN* 2.8 43.5 + - + +
402C GLU* 3.9 5.2 - - - +
404C ILE* 1.3 77.1 - - - +
406C HIS* 1.3 63.9 + - - +
408C LEU* 3.8 8.0 - - + +
409C ARG* 3.3 30.2 + - - +
423C PHE* 3.8 22.1 - - + -
427C LEU* 5.3 5.4 - - + -
430C MET* 5.6 3.8 - - + -
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Residues in contact with HIS 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C LEU* 3.5 31.6 - - + +
402C GLU* 2.9 19.9 + - + +
403C GLY* 4.0 7.4 - - - +
405C VAL* 1.3 80.3 - - - +
407C VAL* 1.3 66.8 + - + +
409C ARG* 3.0 44.5 + - - +
410C LEU* 3.1 44.8 + - + +
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Residues in contact with VAL 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C LEU* 3.4 31.2 - - + +
204C LYS* 5.6 1.3 - - + -
206C LEU* 4.0 11.7 - - + -
207C ALA* 3.2 39.0 - - + +
377C LEU* 3.8 15.5 - - + -
403C GLY 3.4 19.1 + - - +
404C ILE* 3.6 3.3 + - - +
406C HIS* 1.3 81.8 - - + +
408C LEU* 1.3 70.2 + - - +
410C LEU* 3.3 4.5 + - - +
411C HIS* 2.9 19.3 + - + +
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Residues in contact with LEU 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374C ASP* 3.9 12.1 - - - +
377C LEU* 3.8 40.8 - - + +
378C PHE* 4.3 11.2 - - + +
381C ALA* 5.2 7.2 - - + -
404C ILE 2.9 19.3 + - - +
405C VAL* 3.8 7.4 - - + +
407C VAL* 1.3 79.3 - - - +
409C ARG* 1.3 58.2 + - - +
412C LEU* 2.7 54.5 + - + +
423C PHE* 3.5 26.0 - - + -
426C LEU* 4.5 16.4 - - + -
427C LEU* 5.0 6.1 - - + -
430C MET* 5.4 3.1 - - + -
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Residues in contact with ARG 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402C GLU 5.4 0.4 + - - -
405C VAL* 3.3 19.3 + - - +
406C HIS* 3.0 52.4 + - - +
408C LEU* 1.3 79.1 - - - +
410C LEU* 1.3 54.7 + - - +
412C LEU* 4.0 2.1 - - - +
413C GLN* 2.6 55.0 + - - +
423C PHE* 3.6 47.0 - - + +
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Residues in contact with LEU 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C LYS* 5.1 14.8 - - - +
406C HIS* 3.1 43.1 + - + +
407C VAL* 4.0 4.7 - - - +
408C LEU 2.8 5.5 + - - -
409C ARG* 1.3 80.7 - - - +
411C HIS* 1.3 62.5 + - - +
413C GLN* 3.1 30.2 + - + +
414C SER* 3.6 17.3 + - - -
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Residues in contact with HIS 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C ALA* 5.2 10.1 - - + -
373C SER* 3.1 33.5 + - - -
374C ASP* 2.8 29.2 + - - -
377C LEU* 3.9 21.3 - - + +
407C VAL* 2.9 18.6 + - + +
408C LEU* 2.9 2.5 + - - +
410C LEU* 1.3 72.4 - - - +
412C LEU* 1.3 59.6 + - - +
413C GLN 3.0 4.3 - - - -
414C SER* 3.1 7.1 + - - -
415C ASN* 2.9 55.1 + - - +
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Residues in contact with LEU 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370C LEU* 4.0 5.2 - - + -
374C ASP* 3.2 39.7 - - + +
408C LEU* 2.7 28.1 + - + +
409C ARG* 4.2 4.5 - - - +
411C HIS* 1.3 79.9 + - - +
413C GLN* 1.3 56.5 + - - +
414C SER 3.4 0.2 - - - -
415C ASN 4.1 0.4 - - - -
416C HIS* 3.4 38.9 + - - +
419C ASP 5.2 0.2 - - - +
422C LEU* 3.2 53.6 - - + +
423C PHE* 4.2 7.0 - - + +
426C LEU* 3.7 17.5 - - + -
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Residues in contact with GLN 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409C ARG* 2.6 35.3 + - - +
410C LEU* 3.1 29.9 - - + +
411C HIS 3.0 1.2 - - - -
412C LEU* 1.3 78.8 - - - +
414C SER* 1.3 59.5 + - - +
416C HIS 4.6 3.1 - - - -
417C PRO* 4.3 13.5 - - - +
419C ASP 6.1 0.4 - - - -
420C ILE* 5.5 7.5 + - - +
423C PHE* 6.1 2.6 - - + +
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Residues in contact with SER 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410C LEU 3.6 11.8 + - - -
411C HIS* 3.1 9.3 + - - -
413C GLN* 1.3 78.6 - - - +
415C ASN* 1.3 66.4 + - - +
416C HIS 3.4 1.3 - - - -
417C PRO* 3.7 15.8 - - - +
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Residues in contact with ASN 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371C ASP* 3.5 19.2 - - - +
373C SER* 3.6 2.9 + - - -
411C HIS* 2.9 44.5 + - + +
414C SER* 1.3 82.2 + - - +
416C HIS* 1.3 79.1 + - - +
417C PRO* 3.3 6.2 - - - +
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Residues in contact with HIS 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C LEU 4.4 6.5 - - - -
369C GLU* 3.4 26.1 + - + -
370C LEU* 4.3 1.8 - - + -
371C ASP* 3.4 10.1 + - - -
374C ASP* 2.8 39.7 + - - -
412C LEU* 3.4 17.0 + - + +
413C GLN* 4.8 1.8 - - - -
415C ASN* 1.3 107.6 + - - +
417C PRO* 1.3 59.1 - - - +
418C ASP 3.2 4.2 + - - -
419C ASP* 3.1 26.5 + - + +
422C LEU* 3.4 29.4 - - + -
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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
------------------------------------------------------------
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