Contacts of the helix formed by residues 351 - 366 (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 PHE 351 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269D GLU* 3.6 24.7 - - + -
270D VAL* 4.0 7.4 - - + -
273D PHE* 5.3 2.2 - + - -
344D LEU 4.8 0.4 - - - -
347D LEU* 3.9 24.0 - - + +
348D ARG* 3.7 38.4 - - + -
349D LYS* 3.2 19.8 - - - +
350D PRO* 1.3 78.7 - - + +
352D CYS* 1.3 54.2 + - - +
353D ASP 2.3 21.4 + - - -
354D ILE* 2.3 38.1 + - + +
355D MET 3.9 1.9 + - - -
447D ILE* 4.2 22.9 - - + -
451D GLU* 5.4 2.5 - - + -
778D 471 3.1 33.9 - + - -
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Residues in contact with CYS 352 (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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344D LEU* 3.8 5.2 + - - +
345D LYS* 2.8 49.0 + - + +
347D LEU 2.8 26.7 + - - -
349D LYS* 3.1 34.1 - - - -
351D PHE* 1.3 72.4 - - - +
353D ASP* 1.3 61.9 + - - +
355D MET* 4.8 2.1 - - - +
356D GLU* 3.5 24.1 + - - +
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Residues in contact with ASP 353 (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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349D LYS* 3.1 31.8 + - - +
350D PRO* 2.3 27.4 - - - +
351D PHE 2.3 13.1 + - - -
352D CYS* 1.3 79.8 - - - +
354D ILE* 1.3 52.4 + - - -
356D GLU* 4.7 2.0 - - - -
357D PRO* 2.6 38.3 - - - +
443D LEU* 4.0 20.7 - - + +
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Residues in contact with ILE 354 (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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273D PHE* 5.1 4.0 - - + -
351D PHE* 2.3 62.4 + - + +
353D ASP* 1.3 67.4 - - - +
355D MET* 1.3 57.4 + - + +
357D PRO* 3.1 8.0 - - - +
358D LYS* 2.6 31.2 + - - +
440D HIS* 4.3 20.4 - - + +
443D LEU* 3.9 30.7 - - + -
444D VAL* 5.9 4.0 - - + -
447D ILE* 4.7 11.0 - - + -
778D 471 3.8 42.8 - - + +
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Residues in contact with MET 355 (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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318D PHE* 6.5 0.4 - - - -
321D LEU* 4.5 5.6 - - + -
325D MET* 3.3 34.1 - - + -
330D MET* 3.7 15.0 - - + -
344D LEU* 3.8 34.8 - - + -
351D PHE 3.9 3.0 + - - +
352D CYS 4.5 1.1 + - - +
354D ILE* 1.3 78.5 - - - +
356D GLU* 1.3 65.8 + - - +
357D PRO* 3.0 3.6 - - - -
358D LYS* 2.8 30.8 + - + +
359D PHE* 3.3 15.7 + - + -
778D 471 3.9 53.2 - - + +
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Residues in contact with GLU 356 (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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341D ARG* 2.6 57.6 + - - +
344D LEU* 5.8 1.2 - - - +
345D LYS* 3.7 33.1 + - - +
352D CYS 3.5 19.5 + - - +
353D ASP* 4.7 2.2 - - - +
355D MET* 1.3 74.4 - - - +
357D PRO* 1.3 68.7 - - + +
358D LYS 3.2 0.2 + - - -
359D PHE* 3.2 6.5 + - - +
360D ASP* 3.1 23.6 + - - +
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Residues in contact with PRO 357 (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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353D ASP 2.6 30.7 - - - +
354D ILE 3.1 8.5 - - - +
355D MET 3.0 5.6 - - - -
356D GLU* 1.3 92.4 - - + +
358D LYS* 1.3 64.9 + - - +
360D ASP* 3.5 8.1 - - + +
361D PHE* 3.4 15.4 + - - +
436D LEU* 3.9 29.1 - - + +
439D GLU* 5.7 1.6 - - - +
443D LEU* 5.6 2.5 - - + -
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Residues in contact with LYS 358 (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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318D PHE* 3.9 37.7 - - + -
321D LEU* 4.0 20.2 - - + -
325D MET* 4.2 6.3 - - + -
354D ILE* 2.6 28.6 + - - +
355D MET* 2.8 18.1 + - + +
357D PRO* 1.3 84.1 - - - +
359D PHE* 1.3 60.0 + - - +
360D ASP 3.0 2.0 - - - -
361D PHE* 3.0 4.4 + - + +
362D ALA* 2.8 31.3 + - - +
436D LEU* 4.3 23.7 + - + +
440D HIS* 3.1 37.3 + - - +
443D LEU* 6.2 0.6 - - - +
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Residues in contact with PHE 359 (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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325D MET* 3.6 32.3 - - + -
326D ASN 4.0 10.3 - - - -
329D GLY* 3.4 44.4 - - - -
330D MET* 4.0 9.4 - - + -
341D ARG* 3.5 51.2 + - + +
344D LEU* 3.8 25.4 - - + -
355D MET* 3.3 18.0 + - + -
356D GLU* 3.2 11.3 + - - +
358D LYS* 1.3 77.9 - - - +
360D ASP* 1.3 62.1 + - - +
362D ALA* 3.4 4.8 - - - +
363D MET* 3.1 30.6 + - - +
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Residues in contact with ASP 360 (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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341D ARG* 4.2 8.3 + - - +
356D GLU 3.1 12.4 + - - +
357D PRO* 3.5 12.9 - - + +
359D PHE* 1.3 79.6 - - - +
361D PHE* 1.3 62.8 + - - +
363D MET* 3.8 3.5 + - - +
364D LYS* 3.3 49.4 + - - +
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Residues in contact with PHE 361 (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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318D PHE 4.3 7.6 - - - -
319D ALA* 4.4 2.5 - - - -
322D SER* 3.7 18.8 - - - -
357D PRO 3.4 4.7 + - - +
358D LYS* 3.0 8.6 + - - +
360D ASP* 1.3 78.5 + - - +
362D ALA* 1.3 61.9 + - - +
364D LYS* 3.3 8.2 + - + +
365D PHE* 2.9 57.2 + + - +
429D LYS* 4.2 17.0 + - + -
432D ASP* 4.2 25.1 - - + -
433D LEU* 3.4 41.7 - - + -
436D LEU* 3.8 29.8 - - + -
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Residues in contact with ALA 362 (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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322D SER* 3.6 25.6 - - - +
325D MET* 3.8 24.7 - - + -
358D LYS 2.8 15.9 + - - +
359D PHE* 3.4 5.8 - - - +
361D PHE* 1.3 77.2 - - - +
363D MET* 1.3 66.3 + - + +
365D PHE* 2.8 4.0 + - - +
366D ASN* 2.8 38.4 + - - +
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Residues in contact with MET 363 (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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226D ARG* 5.3 0.9 - - - +
325D MET 4.2 0.7 - - - +
326D ASN* 3.6 30.3 - - - +
327D LYS* 3.7 30.1 - - + +
341D ARG* 4.6 10.5 - - - +
359D PHE* 3.1 21.7 + - - +
360D ASP* 4.3 4.3 - - - +
361D PHE 3.5 0.2 - - - -
362D ALA* 1.3 84.4 - - + +
364D LYS* 1.3 61.1 + - + +
366D ASN* 3.4 25.2 - - + +
367D ALA* 3.6 19.2 + - - +
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Residues in contact with LYS 364 (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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360D ASP* 3.3 42.9 + - - +
361D PHE* 3.3 8.4 + - - +
362D ALA 3.1 0.6 - - - -
363D MET* 1.3 78.1 - - + +
365D PHE* 1.3 65.8 + - - +
367D ALA* 3.5 16.4 + - - +
368D LEU* 4.0 9.2 - - - +
429D LYS* 4.0 18.8 + - - +
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Residues in contact with PHE 365 (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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222D LYS* 5.5 2.4 + - - -
319D ALA* 3.8 20.0 - - + -
322D SER* 3.6 27.6 - - - +
323D SER* 6.0 0.4 - - - -
361D PHE* 2.9 36.5 + + + +
362D ALA 2.8 5.6 + - - +
364D LYS* 1.3 77.9 - - - +
366D ASN* 1.3 59.3 + - - +
368D LEU* 3.0 37.8 + - + +
369D GLU 4.1 1.0 + - - -
370D LEU* 3.7 27.0 + - + +
375D ILE* 5.4 11.7 - - + -
378D PHE* 3.7 26.9 - + - -
426D LEU* 3.8 22.4 - - + -
429D LYS* 4.1 16.5 - - + +
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Residues in contact with ASN 366 (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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222D LYS* 3.9 26.2 + - - +
226D ARG* 3.7 12.9 + - - +
322D SER* 3.3 37.6 + - - +
323D SER* 5.4 0.4 + - - -
362D ALA* 2.8 23.1 + - - +
363D MET* 3.4 25.8 - - + +
365D PHE* 1.3 70.7 - - - +
367D ALA* 1.3 56.5 + - - +
368D LEU 3.0 5.8 - - - -
369D GLU* 2.9 27.4 + - - +
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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
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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