Contacts of the helix formed by residues 395 - 413 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393D ASN 2.5 11.1 + - - -
394D VAL* 1.3 76.3 - - - +
396D HIS* 1.3 61.4 + - - -
397D ILE 3.3 0.4 - - - -
398D GLU* 3.8 6.9 - - - +
399D LYS* 3.3 21.5 + - - +
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Residues in contact with HIS 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299D ASN 5.4 4.0 + - - -
300D LEU* 5.4 14.4 - - + -
393D ASN* 3.2 44.5 + - + +
395D GLY* 1.3 73.9 - - - +
397D ILE* 1.3 61.9 + - + +
399D LYS* 3.0 10.7 + - - +
400D MET* 2.4 46.3 + - + +
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Residues in contact with ILE 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300D LEU* 3.3 33.0 - - + -
304D ASP* 4.4 4.9 - - + +
308D LEU* 3.7 11.4 - - + -
384D CYS* 3.8 16.4 - - + +
385D CYS 3.8 4.7 - - - +
386D GLY* 3.5 28.5 - - - +
391D LEU* 2.9 33.2 - - + -
393D ASN* 3.4 17.9 - - + +
394D VAL* 4.7 2.9 - - - -
396D HIS* 1.3 82.5 - - + +
398D GLU* 1.3 67.3 + - - +
400D MET* 3.3 9.2 - - + +
401D GLN* 2.8 23.6 + - - +
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Residues in contact with GLU 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386D GLY* 3.4 28.2 - - - +
387D ASP* 5.4 1.2 - - - +
394D VAL* 3.2 27.4 + - - +
395D GLY* 3.8 7.4 - - - +
396D HIS 3.2 0.8 - - - -
397D ILE* 1.3 80.9 - - - +
399D LYS* 1.3 58.3 + - - +
401D GLN* 3.0 9.2 + - - +
402D GLU* 2.8 27.5 + - - +
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Residues in contact with LYS 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395D GLY 3.3 15.8 + - - +
396D HIS* 3.0 8.1 + - - +
398D GLU* 1.3 78.8 - - - +
400D MET* 1.3 63.4 + - - +
402D GLU* 3.3 46.8 + - - +
403D GLY* 3.4 5.7 + - - -
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Residues in contact with MET 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D LEU* 5.6 0.3 - - - +
294D ILE* 4.6 4.9 - - + -
295D PRO 5.0 4.3 - - - +
296D GLY* 3.7 34.8 - - - +
297D PHE* 4.5 14.1 - - + +
300D LEU* 4.6 12.8 - - + -
308D LEU* 5.3 0.2 - - + -
384D CYS* 3.0 44.2 - - + -
396D HIS* 2.4 32.8 + - + +
397D ILE* 3.0 14.3 + - + +
399D LYS* 1.3 69.1 - - - +
401D GLN* 1.3 60.8 + - - +
403D GLY* 3.0 15.4 + - - -
404D ILE* 3.0 19.9 + - + +
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Residues in contact with GLN 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381D ALA* 2.8 30.6 - - - +
384D CYS* 3.1 24.4 + - - +
385D CYS* 3.8 10.9 - - - +
386D GLY* 3.7 18.4 - - - +
387D ASP* 5.4 2.2 + - - -
397D ILE 2.8 5.9 + - - +
398D GLU* 3.4 10.9 + - - +
400D MET* 1.3 73.7 - - - +
402D GLU* 1.3 53.7 + - - +
403D GLY 2.8 6.9 + - - -
404D ILE* 2.8 7.0 + - - +
405D VAL* 2.6 46.3 + - + +
430D MET* 4.2 11.3 - - - +
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Residues in contact with GLU 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398D GLU 2.8 12.1 + - - +
399D LYS* 3.3 45.6 + - - +
401D GLN* 1.3 75.7 - - - +
403D GLY* 1.3 57.9 + - - +
405D VAL* 4.6 9.4 - - - +
406D HIS* 3.1 26.7 + - - +
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Residues in contact with GLY 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D LEU* 4.3 17.8 - - - +
206D LEU* 3.6 15.8 - - - +
399D LYS 3.4 5.3 + - - -
400D MET 3.0 9.0 + - - -
401D GLN 2.8 2.6 + - - -
402D GLU* 1.3 83.5 - - - +
404D ILE* 1.3 61.5 + - - -
406D HIS* 3.4 4.6 + - - +
407D VAL* 3.2 19.6 + - - +
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Residues in contact with ILE 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D LEU* 4.2 13.0 - - + -
210D ILE* 4.1 21.5 - - + -
294D ILE* 3.8 16.6 - - + -
377D LEU* 3.5 29.0 - - + +
380D ALA* 4.1 11.2 - - + -
381D ALA* 3.8 11.4 - - + +
384D CYS* 3.7 36.6 - - + -
400D MET* 3.0 14.5 + - + +
401D GLN* 2.8 6.6 + - - +
403D GLY* 1.3 74.2 - - - +
405D VAL* 1.3 60.8 + - - +
407D VAL* 3.3 5.0 + - - +
408D LEU* 2.9 26.2 + - - +
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Residues in contact with VAL 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381D ALA* 4.1 18.8 - - + -
401D GLN* 2.6 30.6 + - + +
402D GLU* 4.6 7.6 - - - +
404D ILE* 1.3 73.3 - - - +
406D HIS* 1.3 63.9 + - - +
408D LEU* 3.3 10.3 + - + +
409D ARG* 3.3 23.5 + - - +
423D PHE* 4.0 29.1 - - + -
427D LEU* 5.0 4.9 - - + -
430D MET* 4.9 9.6 - - + -
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Residues in contact with HIS 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D LEU* 3.4 31.3 - - + +
402D GLU 3.1 20.4 + - - +
403D GLY* 3.5 5.4 - - - +
404D ILE 3.2 0.2 - - - -
405D VAL* 1.3 83.9 - - - +
407D VAL* 1.3 66.1 + - + +
408D LEU 3.3 0.2 + - - -
409D ARG* 3.5 21.6 + - - +
410D LEU* 3.6 38.2 + - + +
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Residues in contact with VAL 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D LEU* 3.2 45.1 - - + +
206D LEU* 4.1 9.2 - - + -
207D ALA* 3.5 36.6 - - + +
377D LEU* 4.0 8.3 - - + -
403D GLY 3.2 10.1 + - - +
404D ILE* 3.8 3.8 - - - +
406D HIS* 1.3 83.9 - - + +
408D LEU* 1.3 64.4 + - - +
410D LEU* 3.8 9.4 + - + +
411D HIS* 3.3 21.2 + - + +
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Residues in contact with LEU 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374D ASP* 4.4 11.7 - - - +
377D LEU* 4.1 42.0 - - + +
378D PHE* 4.5 17.0 - - + -
381D ALA* 4.7 9.6 - - + -
404D ILE 2.9 16.7 + - - +
405D VAL* 3.4 9.6 - - + +
406D HIS 3.1 0.4 - - - -
407D VAL* 1.3 76.6 - - - +
409D ARG* 1.3 65.6 + - - +
411D HIS* 3.3 3.3 + - - +
412D LEU* 3.0 43.7 + - + +
423D PHE* 4.1 20.6 - - + -
426D LEU* 4.8 6.7 - - + -
427D LEU* 5.9 0.4 - - + -
430D MET* 5.9 2.9 - - - -
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Residues in contact with ARG 409 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405D VAL* 3.3 9.9 + - - +
406D HIS* 3.8 17.0 + - - +
407D VAL 3.4 0.2 - - - -
408D LEU* 1.3 79.0 - - - +
410D LEU* 1.3 77.7 + - + +
412D LEU* 2.8 25.4 + - - -
413D GLN* 2.8 43.5 + - - +
423D PHE* 2.9 52.9 - - + +
424D PRO* 5.6 2.4 - - - +
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Residues in contact with LEU 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406D HIS* 3.6 36.0 + - + +
407D VAL* 4.1 8.7 - - + +
408D LEU 3.4 0.4 - - - -
409D ARG* 1.3 102.1 - - + +
411D HIS* 1.3 59.3 + - - +
413D GLN* 3.4 13.4 + - - +
414D SER* 3.4 26.7 + - - -
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Residues in contact with HIS 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B LEU* 3.0 29.2 + - + +
393B ASN* 3.1 25.3 + - - -
207D ALA* 5.2 3.6 - - + -
371D ASP* 4.6 0.4 - - - -
373D SER* 2.5 39.4 + - - -
374D ASP* 2.9 24.1 + - - +
377D LEU* 4.3 14.1 - - + +
407D VAL* 3.3 17.2 + - + +
408D LEU* 3.6 4.2 + - - +
409D ARG 3.1 0.4 - - - -
410D LEU* 1.3 79.7 - - - +
412D LEU* 1.3 59.4 + - - +
413D GLN 3.4 0.2 - - - -
414D SER* 4.2 2.2 - - - -
415D ASN* 3.4 31.9 + - - +
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Residues in contact with LEU 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370D LEU* 4.5 1.1 - - + -
374D ASP* 3.6 36.1 - - + +
408D LEU* 3.0 34.5 + - + +
409D ARG* 2.8 7.9 + - - +
411D HIS* 1.3 77.4 - - - +
413D GLN* 1.3 61.9 + - + +
414D SER 3.4 1.1 - - - -
415D ASN 4.2 1.1 - - - -
416D HIS* 3.4 33.6 + - - +
419D ASP 4.8 1.2 - - - +
422D LEU* 3.9 24.3 - - + +
423D PHE* 3.9 27.8 - - + +
426D LEU* 3.2 32.5 - - + -
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Residues in contact with GLN 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409D ARG* 2.8 56.0 + - + +
410D LEU* 3.4 12.4 + - - +
412D LEU* 1.3 81.3 - - + +
414D SER* 1.3 58.4 + - - +
415D ASN 3.5 0.4 - - - -
416D HIS 4.5 4.7 - - - -
417D PRO* 4.0 17.2 - - - +
420D ILE* 5.2 11.8 + - - +
423D PHE* 5.6 6.5 - - + +
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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