Contacts of the helix formed by residues 441 - 454 (chain C) in PDB entry 1KHU
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 HIS 441 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302B PRO* 3.5 42.5 + - + +
313B LEU* 5.8 2.4 - - + +
270C HIS* 3.4 35.7 + - + +
271C TRP 3.3 6.7 + - - +
272C CYS* 4.2 7.9 - - - -
273C SER* 3.2 31.7 + - - -
288C HIS* 4.5 11.9 - + - -
439C HIS* 3.5 19.0 - - + +
440C LEU* 1.3 69.3 - - - +
442C GLY* 1.3 56.6 + - - +
444C LEU* 4.2 2.2 - - + -
445C GLN* 2.7 37.6 + - - +
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Residues in contact with GLY 442 (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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270C HIS 5.3 0.4 + - - -
271C TRP* 4.4 4.8 + - - +
338C TYR* 6.1 1.3 - - - -
441C HIS* 1.3 75.1 - - - +
443C PRO* 1.3 71.0 - - - +
445C GLN* 2.9 9.2 + - - +
446C TRP* 2.9 48.4 + - - -
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Residues in contact with PRO 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C TRP 5.5 0.9 - - - +
338C TYR* 6.0 0.7 - - - +
383C PHE* 3.4 33.4 - - + -
385C ASN* 4.3 4.5 - - + +
388C PHE* 3.5 18.2 - - + -
410C CYS* 3.6 18.4 - - - -
440C LEU* 3.4 23.1 - - + +
442C GLY* 1.3 87.6 - - - +
444C LEU* 1.3 56.0 + - - +
446C TRP* 3.3 26.5 + - + +
447C LEU* 3.0 29.5 + - - +
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Residues in contact with LEU 444 (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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300B THR* 3.0 52.8 + - + +
302B PRO* 4.2 4.3 - - + -
313B LEU* 4.1 18.4 - - + -
407C THR* 4.0 17.7 - - + -
410C CYS* 3.4 27.4 - - + -
411C THR* 5.8 0.2 - - + -
439C HIS* 3.9 37.2 - - + -
440C LEU 3.0 23.3 + - - +
441C HIS* 3.6 10.1 - - + +
443C PRO* 1.3 76.9 - - - +
445C GLN* 1.3 57.2 + - - +
447C LEU* 3.4 3.2 + - + +
448C ASP* 3.0 12.5 + - - +
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Residues in contact with GLN 445 (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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301B ASP* 3.5 22.8 + - - +
302B PRO* 3.9 13.6 - - + +
303B SER* 3.8 17.0 + - - -
441C HIS 2.7 21.7 + - - +
442C GLY* 3.4 7.4 - - - +
444C LEU* 1.3 71.3 - - - +
446C TRP* 1.3 72.9 + - + +
448C ASP* 2.9 14.9 + - - +
449C LYS* 3.0 38.0 + - - +
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Residues in contact with TRP 446 (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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338C TYR* 5.3 4.7 - - - -
385C ASN* 3.2 49.6 - - + -
388C PHE* 3.9 14.1 - + - -
389C ALA* 5.1 9.4 - - + -
392C LEU* 3.8 13.9 - - + +
442C GLY* 2.9 28.0 + - - -
443C PRO* 3.3 26.2 - - + +
445C GLN* 1.3 86.6 + - + +
447C LEU* 1.3 61.9 + - - +
449C LYS* 3.2 26.0 + - + +
450C VAL* 3.5 12.5 + - - +
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Residues in contact with LEU 447 (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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300B THR* 4.0 11.4 - - - +
388C PHE* 4.4 4.3 - - + -
392C LEU* 3.5 30.5 - - + -
403C VAL* 3.6 25.4 - - + +
406C LEU* 3.9 11.9 - - + +
407C THR* 3.4 44.9 - - + +
410C CYS* 4.2 7.9 - - - -
443C PRO 3.0 17.6 + - - +
444C LEU* 3.5 5.6 - - + +
446C TRP* 1.3 78.3 - - - +
448C ASP* 1.3 58.0 + - - +
450C VAL* 3.4 1.6 + - - +
451C LEU* 3.0 33.3 + - + +
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Residues in contact with ASP 448 (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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299B PHE* 3.3 4.9 - - - +
300B THR* 3.2 29.9 + - - +
301B ASP* 3.3 22.7 + - - +
308B ARG* 2.7 42.4 + - - -
444C LEU 3.0 7.8 + - - +
445C GLN* 2.9 13.9 + - - +
447C LEU* 1.3 75.4 - - - +
449C LYS* 1.3 60.4 + - + +
451C LEU* 4.5 2.9 - - - +
452C THR* 2.8 42.6 + - - +
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Residues in contact with LYS 449 (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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301B ASP* 5.2 3.4 + - - -
445C GLN* 3.0 54.0 + - + +
446C TRP* 3.2 15.7 + - + +
448C ASP* 1.3 83.3 + - + +
450C VAL* 1.3 58.7 + - + +
452C THR* 2.8 18.4 + - - -
453C GLN* 3.2 28.2 + - - +
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Residues in contact with VAL 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C LEU* 4.0 26.7 - - + +
396C VAL* 4.8 17.7 - - + -
403C VAL* 4.0 12.1 - - + -
446C TRP 3.7 12.3 - - - +
447C LEU 3.4 5.7 + - - +
448C ASP 3.1 0.2 - - - -
449C LYS* 1.3 75.7 - - + +
451C LEU* 1.3 67.6 + - - +
452C THR 3.1 1.8 - - - -
453C GLN* 3.0 11.9 + - + +
454C MET* 2.8 47.4 + - + +
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Residues in contact with LEU 451 (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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299B PHE* 4.3 21.6 - - + -
300B THR* 4.2 23.6 - - + +
400C PHE* 3.8 22.8 - - + -
403C VAL* 3.3 38.6 - - + -
404C TYR* 3.7 33.9 - - + +
407C THR* 4.6 0.4 - - - +
447C LEU* 3.0 29.9 + - + +
448C ASP* 4.2 3.4 - - - +
450C VAL* 1.3 76.6 - - - +
452C THR* 1.3 51.4 + - - +
454C MET* 3.4 5.4 - - - -
455C GLY* 2.7 30.1 + - - -
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Residues in contact with THR 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B PHE* 4.0 19.7 - - + -
308B ARG* 3.9 15.5 - - - +
448C ASP* 2.8 41.5 + - - +
449C LYS* 2.8 16.8 + - - -
451C LEU* 1.3 74.7 - - - +
453C GLN* 1.3 61.0 + - - +
454C MET 3.1 1.8 - - - -
455C GLY* 2.9 18.9 + - - +
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Residues in contact with GLN 453 (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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449C LYS* 3.2 29.6 - - - +
450C VAL* 3.0 12.9 + - + +
452C THR* 1.3 83.6 + - - +
454C MET* 1.3 62.4 + - + +
455C GLY 3.2 0.2 - - - -
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Residues in contact with MET 454 (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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395C SER 4.4 0.4 - - - +
396C VAL* 3.3 31.4 - - + +
397C ASN* 4.7 2.0 - - - -
399C GLY* 4.0 31.4 - - - +
400C PHE* 4.2 15.7 - - + +
403C VAL* 3.9 17.0 - - + -
450C VAL* 2.8 38.0 + - + +
451C LEU 3.4 4.3 - - - +
453C GLN* 1.3 78.4 - - + +
455C GLY* 1.3 71.7 + - - +
456C SER* 3.1 4.4 + - - -
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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