Contacts of the helix formed by residues 371 - 384 (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 ASP 371 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211C TYR* 5.2 1.2 + - - -
222C LYS* 4.6 3.8 - - - -
223C VAL* 6.4 1.1 - - + -
369C GLU 4.9 1.8 - - - +
370C LEU* 1.3 75.4 - - - +
372C ASP* 1.3 67.5 + - - +
373C SER* 2.4 36.3 + - - -
374C ASP* 2.5 39.2 + - - +
375C ILE* 3.2 17.0 + - - +
415C ASN* 3.5 6.1 - - - +
416C HIS* 3.4 13.7 + - - -
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Residues in contact with ASP 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C TYR* 3.6 21.5 - - + +
214C TYR* 3.3 28.2 + - + -
215C LEU* 4.5 4.2 - - + +
221C ASN* 3.6 6.9 - - - +
222C LYS* 2.9 33.1 + - - +
223C VAL* 2.8 37.7 + - + +
371C ASP* 1.3 74.1 + - - +
373C SER* 1.3 62.5 + - - +
375C ILE* 3.4 5.4 + - - +
376C SER* 3.1 26.0 + - - -
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Residues in contact with SER 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C TYR* 3.4 31.2 - - - +
371C ASP* 2.4 29.7 + - - -
372C ASP* 1.3 78.0 - - - +
374C ASP* 1.3 59.9 + - - +
376C SER* 2.8 17.2 + - - -
377C LEU* 3.6 14.9 - - - +
411C HIS* 3.1 30.3 + - - -
415C ASN* 3.6 2.6 + - - -
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Residues in contact with ASP 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C LEU* 3.8 14.3 - - + -
371C ASP* 2.5 37.1 + - - +
373C SER* 1.3 75.7 - - - +
375C ILE* 1.3 59.2 + - - +
377C LEU* 3.1 10.2 + - - +
378C PHE* 2.9 25.3 + - - +
408C LEU* 3.9 5.7 - - + +
411C HIS* 2.8 34.7 + - - -
412C LEU* 3.2 25.1 - - + +
416C HIS* 2.8 22.8 + - - -
426C LEU* 5.7 0.7 - - + -
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Residues in contact with ILE 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C TYR* 4.1 15.9 - - - +
222C LYS* 4.2 21.3 - - + +
319C ALA* 5.4 0.7 - - + -
320C MET* 4.4 12.1 - - + +
323C SER* 4.4 10.3 - - - +
365C PHE* 4.8 11.7 - - + -
370C LEU* 4.2 24.5 - - + -
371C ASP 3.2 25.0 + - - +
372C ASP* 4.1 7.2 - - - +
374C ASP* 1.3 73.0 - - - +
376C SER* 1.3 58.7 + - - +
378C PHE* 3.7 14.1 - - + -
379C VAL* 2.6 52.5 + - + +
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Residues in contact with SER 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C ILE* 4.2 8.5 - - - -
211C TYR* 3.6 21.2 - - - +
214C TYR* 3.7 38.5 - - - -
290C PHE* 3.7 6.5 - - - -
372C ASP 3.1 13.9 + - - -
373C SER 2.8 25.1 + - - -
375C ILE* 1.3 74.5 - - - +
377C LEU* 1.3 57.3 + - - +
379C VAL* 3.7 1.0 - - - -
380C ALA* 2.7 36.0 + - - +
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Residues in contact with LEU 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C LEU* 6.0 0.2 - - + -
207C ALA* 4.1 16.8 - - - +
210C ILE* 3.9 28.0 - - + -
373C SER 3.6 15.9 - - - +
374C ASP* 3.1 7.8 + - - +
375C ILE 3.1 0.2 - - - -
376C SER* 1.3 81.8 + - - +
378C PHE* 1.3 62.0 + - - +
380C ALA* 3.7 3.4 - - - -
381C ALA* 3.1 23.9 + - - +
404C ILE* 3.8 11.0 - - + +
407C VAL* 3.8 33.9 - - + -
408C LEU* 3.8 24.1 - - + +
411C HIS* 3.9 28.9 - - + +
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Residues in contact with PHE 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C ALA* 4.1 13.5 - - + -
365C PHE* 3.5 39.0 - + + -
370C LEU* 5.3 1.6 - - + -
374C ASP 2.9 13.7 + - - +
375C ILE* 3.0 15.7 + - + +
377C LEU* 1.3 76.4 - - - +
379C VAL* 1.3 61.2 + - - +
381C ALA* 3.1 4.8 + - - +
382C ILE* 2.9 37.2 + - + +
408C LEU* 4.3 9.6 - - + +
426C LEU* 4.1 31.9 - - + -
429C LYS* 4.1 1.3 - - + -
430C MET* 3.1 48.2 - - + -
433C LEU* 3.9 22.9 - - + -
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Residues in contact with VAL 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C TYR* 5.0 1.3 - - + -
287C LEU* 4.1 12.3 - - + -
290C PHE* 3.7 19.3 - - + -
316C ALA* 3.7 24.2 - - + +
319C ALA* 4.6 9.4 - - + -
320C MET* 3.6 24.9 - - + -
375C ILE* 2.6 41.7 + - + +
376C SER* 3.9 3.8 - - - +
378C PHE* 1.3 73.8 - - + +
380C ALA* 1.3 61.3 + - - +
382C ILE* 3.6 9.9 - - - +
383C ILE* 3.6 21.9 + - + +
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Residues in contact with ALA 380 (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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210C ILE* 4.1 18.6 - - + -
290C PHE* 4.3 3.6 - - + -
294C ILE* 4.1 21.8 - - + -
376C SER 2.7 19.3 + - - +
377C LEU* 3.9 7.9 - - - +
378C PHE 3.1 0.2 - - - -
379C VAL* 1.3 78.1 - - - +
381C ALA* 1.3 61.2 + - - +
383C ILE* 3.7 1.2 + - - +
384C CYS* 3.4 30.5 + - - +
404C ILE* 3.9 16.8 - - + +
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Residues in contact with ALA 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C LEU 3.1 17.5 + - - +
378C PHE* 3.1 2.1 + - - +
380C ALA* 1.3 77.1 - - - +
382C ILE* 1.3 62.7 + - - +
383C ILE 3.3 0.7 - - - -
384C CYS 4.0 8.2 - - - +
385C CYS* 4.2 1.2 + - - +
401C GLN* 3.3 22.5 + - - +
404C ILE* 3.8 18.3 - - + +
405C VAL* 4.4 17.5 - - + -
408C LEU* 5.2 4.9 - - + -
430C MET* 3.4 21.9 - - + +
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Residues in contact with ILE 382 (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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312C GLY 3.0 28.9 - - - +
315C GLU* 3.5 35.7 - - + +
316C ALA* 3.5 17.3 - - + +
378C PHE* 2.9 32.4 + - + +
379C VAL* 3.6 13.5 - - - +
381C ALA* 1.3 76.1 - - - +
383C ILE* 1.3 62.6 + - - +
385C CYS* 4.1 5.6 - - - +
388C ARG* 2.7 30.5 + - - -
430C MET* 3.5 28.5 - - + -
433C LEU* 5.4 5.2 - - + -
434C ARG* 5.3 0.2 + - - -
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Residues in contact with ILE 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C LEU* 4.2 25.8 - - + +
290C PHE* 4.8 5.2 - - + -
291C ALA* 4.6 7.4 - - + -
294C ILE* 5.0 2.5 - - + -
297C PHE* 4.2 18.4 - - + -
308C LEU* 3.8 31.9 - - + +
309C LEU* 3.7 26.9 - - + -
312C GLY 3.7 20.0 - - - +
313C VAL* 5.8 0.2 - - - -
316C ALA* 4.8 1.8 - - + -
379C VAL* 3.6 20.3 + - + +
380C ALA* 4.0 3.4 - - - +
382C ILE* 1.3 87.3 - - + +
384C CYS* 1.3 71.7 + - - +
385C CYS 3.0 8.3 + - - -
388C ARG* 4.1 5.8 + - - +
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Residues in contact with CYS 384 (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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294C ILE* 4.1 16.6 - - - -
297C PHE* 4.2 15.3 - - - -
308C LEU* 4.4 10.3 - - + -
380C ALA 3.4 18.1 + - - +
381C ALA* 4.0 5.1 + - - +
383C ILE* 1.3 86.2 - - - +
385C CYS* 1.3 59.6 + - - +
397C ILE* 3.7 6.0 - - + +
400C MET* 4.3 19.7 - - - -
401C GLN* 3.0 26.7 + - - +
404C ILE* 4.0 22.0 - - + -
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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