Contacts of the helix formed by residues 422 - 442 (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 LEU 422 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368C LEU* 4.2 38.8 - - + +
370C LEU* 4.3 5.8 - - + -
412C LEU* 3.2 28.8 - - + +
416C HIS* 3.4 41.5 - - + -
419C ASP* 3.2 38.1 + - + +
420C ILE 3.3 2.8 - - - -
421C PHE* 1.3 75.7 - - - +
423C PHE* 1.3 62.3 + - - +
425C LYS* 3.5 6.1 - - + -
426C LEU* 3.3 19.3 + - + +
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Residues in contact with PHE 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C VAL* 3.8 23.8 - - + -
408C LEU* 3.5 30.7 - - + -
409C ARG* 3.6 53.4 - - + +
412C LEU* 4.2 9.1 - - + +
413C GLN* 6.1 2.2 - - + +
420C ILE 4.8 1.9 + - - +
422C LEU* 1.3 75.9 - - - +
424C PRO* 1.3 68.3 - - + +
425C LYS 2.8 4.5 - - - -
426C LEU* 2.8 20.8 + - + +
427C LEU* 3.0 49.6 + - + +
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Residues in contact with PRO 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420C ILE 4.7 2.9 - - - +
421C PHE* 3.6 34.3 - - + +
423C PHE* 1.3 100.1 - - + +
425C LYS* 1.3 59.3 + - - +
427C LEU* 4.0 15.3 - - + +
428C GLN* 3.7 17.3 + - - +
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Residues in contact with LYS 425 (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 17.4 - - + +
419C ASP* 3.2 34.0 + - - +
421C PHE* 2.8 27.6 + - - +
422C LEU* 3.5 18.2 - - + +
423C PHE 2.8 0.2 - - - -
424C PRO* 1.3 80.9 - - - +
426C LEU* 1.3 61.7 + - - +
428C GLN* 3.4 16.2 - - - +
429C LYS* 3.6 13.1 + - - +
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Residues in contact with LEU 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C PHE* 3.9 13.9 - - + -
368C LEU* 3.4 29.4 - - + -
370C LEU* 3.7 26.0 - - + -
374C ASP* 5.7 0.7 - - + -
378C PHE* 4.2 21.1 - - + -
408C LEU* 4.5 17.0 - - + -
412C LEU* 3.7 31.9 - - + -
422C LEU* 3.3 9.1 + - + +
423C PHE* 2.8 9.5 + - - +
425C LYS* 1.3 76.7 - - - +
427C LEU* 1.3 54.0 + - + +
428C GLN 2.7 7.4 + - - -
429C LYS* 2.5 28.2 + - + +
430C MET* 2.9 14.5 + - - +
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Residues in contact with LEU 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C VAL* 5.3 6.1 - - + -
408C LEU* 5.0 4.0 - - + -
423C PHE* 3.0 61.2 + - + +
424C PRO* 4.0 11.4 + - + +
425C LYS 3.6 0.2 - - - -
426C LEU* 1.3 74.8 - - - +
428C GLN* 1.3 59.2 + - - +
430C MET* 3.8 27.5 + - - +
431C ALA* 3.6 17.2 + - - +
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Residues in contact with GLN 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C PRO 3.7 11.7 + - - +
425C LYS* 3.4 13.0 - - - +
426C LEU 2.7 1.6 + - - -
427C LEU* 1.3 78.3 - - - +
429C LYS* 1.3 57.4 + - + +
430C MET 3.2 0.2 - - - -
431C ALA* 3.1 12.8 + - - +
432C ASP* 2.7 65.9 + - - +
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Residues in contact with LYS 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C PHE* 3.8 11.9 + - + -
364C LYS* 3.6 33.0 - - - +
365C PHE* 3.8 51.1 - - + +
368C LEU* 4.0 19.7 - - + -
378C PHE* 4.1 4.9 - - + -
425C LYS 3.6 15.0 - - - +
426C LEU* 2.5 17.4 + - - +
428C GLN* 1.3 71.4 - - + +
430C MET* 1.3 61.7 + - - +
432C ASP* 3.1 27.4 + - - +
433C LEU* 3.1 19.8 + - - +
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Residues in contact with MET 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C GLU* 5.0 2.3 - - - +
378C PHE* 3.1 36.1 - - + +
381C ALA* 3.4 39.0 - - + +
382C ILE* 3.5 27.4 - - + -
401C GLN* 5.5 3.1 - - - +
405C VAL* 5.6 2.9 - - + -
408C LEU* 5.4 4.3 - - + -
426C LEU 2.9 8.4 + - - +
427C LEU* 3.9 32.1 - - - +
429C LYS* 1.3 77.5 - - - +
431C ALA* 1.3 59.0 + - - +
433C LEU* 3.8 8.0 + - - +
434C ARG* 3.6 24.3 + - - +
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Residues in contact with ALA 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C LEU 3.9 9.6 - - - +
428C GLN* 3.1 20.8 + - - +
430C MET* 1.3 76.9 - - - +
432C ASP* 1.3 64.2 + - - +
433C LEU 3.2 1.7 + - - -
434C ARG* 3.7 15.3 + - - +
435C GLN* 3.7 12.1 + - - +
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Residues in contact with ASP 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C PHE* 4.1 16.5 - - + -
428C GLN* 2.7 47.0 + - - +
429C LYS* 3.1 23.8 + - - +
431C ALA* 1.3 78.8 - - - +
433C LEU* 1.3 59.2 + - - +
434C ARG 3.4 0.2 - - - -
435C GLN* 3.5 7.9 + - - +
436C LEU* 2.9 28.4 + - - +
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Residues in contact with LEU 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C GLU* 3.5 39.1 - - + +
318C PHE* 4.2 10.1 - - + -
319C ALA* 4.0 3.8 - - + -
361C PHE* 3.3 39.9 - - + -
378C PHE* 3.9 24.7 - - + -
382C ILE* 5.4 4.0 - - + -
429C LYS 3.1 17.8 + - - +
430C MET* 4.0 7.9 - - - +
431C ALA 3.2 0.2 - - - -
432C ASP* 1.3 76.4 - - - +
434C ARG* 1.3 59.2 + - - +
435C GLN 3.1 2.0 - - - -
436C LEU* 3.7 17.8 - - + +
437C VAL* 3.0 34.8 + - - +
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Residues in contact with ARG 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C GLU* 3.0 23.6 + - - +
382C ILE 5.3 0.2 + - - -
385C CYS* 3.3 30.5 - - - +
387C ASP* 2.7 33.7 + - - -
388C ARG* 3.6 17.9 - - - +
430C MET 3.6 16.2 + - - +
431C ALA* 3.7 10.7 + - - +
432C ASP 3.4 0.4 - - - -
433C LEU* 1.3 78.0 - - - +
435C GLN* 1.3 60.5 + - - +
437C VAL* 4.1 4.5 - - - +
438C THR* 3.5 21.1 + - - -
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Residues in contact with GLN 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C ALA 3.7 11.2 + - - +
432C ASP* 3.5 10.3 + - - +
433C LEU 3.1 0.2 - - - -
434C ARG* 1.3 79.2 - - - +
436C LEU* 1.3 63.6 + - - +
437C VAL 3.2 1.6 - - - -
438C THR* 3.3 13.3 + - - +
439C GLU* 3.0 69.2 + - - +
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Residues in contact with LEU 436 (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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318C PHE* 4.1 18.8 - - + -
357C PRO* 3.6 34.8 - - + +
358C LYS* 4.3 19.0 + - + -
361C PHE* 4.0 22.0 - - + -
432C ASP 2.9 17.7 + - - +
433C LEU* 3.9 28.0 - - + +
435C GLN* 1.3 77.4 - - - +
437C VAL* 1.3 63.5 + - + +
439C GLU* 4.2 11.4 - - - +
440C HIS* 3.2 22.5 + - - +
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Residues in contact with VAL 437 (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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311C TYR 5.5 2.5 - - - +
314C TYR* 3.7 35.4 - - + +
315C GLU* 3.8 22.0 - - + +
318C PHE* 4.4 8.3 - - + -
433C LEU 3.0 22.2 + - - +
434C ARG* 4.2 5.8 - - - +
435C GLN 3.2 0.2 - - - -
436C LEU* 1.3 75.6 - - + +
438C THR* 1.3 56.9 + - - +
440C HIS* 3.0 9.1 + - - +
441C ALA* 2.7 33.5 + - + +
682G ASN* 3.6 28.9 - - + +
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Residues in contact with THR 438 (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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434C ARG 3.5 15.2 + - - -
435C GLN* 3.3 21.7 + - - +
437C VAL* 1.3 81.0 - - - +
439C GLU* 1.3 75.0 + - + +
441C ALA* 3.2 6.7 + - - +
442C GLN* 2.8 36.7 + - + +
682G ASN* 5.7 1.6 - - - -
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Residues in contact with GLU 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C PRO* 5.6 4.3 - - + +
435C GLN* 3.0 45.0 + - - +
436C LEU* 4.2 17.0 - - - +
437C VAL 3.3 0.6 - - - -
438C THR* 1.3 77.1 - - + +
440C HIS* 1.3 60.3 + - - +
442C GLN* 3.0 14.5 + - - +
443C LEU* 2.9 37.1 + - + +
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Residues in contact with HIS 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C TYR* 6.0 6.5 - + - -
318C PHE* 4.1 21.2 - + + -
354C ILE* 4.0 12.7 - - + +
358C LYS* 2.9 42.3 - - - +
436C LEU 3.2 13.8 + - - +
437C VAL* 3.0 8.2 + - - +
439C GLU* 1.3 78.3 - - - +
441C ALA* 1.3 62.4 + - - +
443C LEU* 3.9 6.3 - - - +
444C VAL* 3.0 38.4 + - + +
777C 471 3.2 42.4 + - - -
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Residues in contact with ALA 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C TYR* 6.3 0.9 - - + -
437C VAL* 2.7 12.7 + - + +
438C THR* 3.4 10.1 - - - +
440C HIS* 1.3 81.2 + - - +
442C GLN* 1.3 58.1 + - + +
443C LEU 3.2 3.3 + - - -
444C VAL* 3.7 4.6 + - - +
445C GLN* 3.4 22.3 + - - +
682G ASN* 3.9 31.9 - - + +
683G MET* 6.3 0.2 - - + -
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Residues in contact with GLN 442 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C THR* 2.8 21.9 + - + +
439C GLU* 3.0 18.7 + - - +
441C ALA* 1.3 76.3 - - + +
443C LEU* 1.3 55.8 + - - +
444C VAL 3.7 0.4 - - - -
445C GLN* 4.5 11.4 - - + -
446C ILE* 4.7 8.1 - - - +
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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
------------------------------------------------------------
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