Contacts of the helix formed by residues 355 - 366 (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 MET 355 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318C PHE* 5.3 0.9 - - + -
321C LEU* 3.7 24.9 - - + -
325C MET* 4.6 3.4 - - + -
330C MET* 3.5 27.1 - - - -
344C LEU* 3.7 38.1 - - + -
351C PHE 4.6 1.6 + - - -
352C CYS 5.3 0.8 - - - -
354C ILE* 1.3 91.3 - - + +
356C GLU* 1.3 65.9 + - - +
358C LYS* 3.1 24.2 + - + +
359C PHE* 3.1 23.9 + - + -
777C 471 3.8 42.0 - - + +
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Residues in contact with GLU 356 (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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341C ARG* 2.5 58.1 + - - +
344C LEU* 6.5 0.2 - - + -
345C LYS* 4.0 31.2 - - + +
352C CYS 4.4 10.8 + - - +
353C ASP* 5.2 1.8 - - - +
354C ILE 3.5 1.4 - - - +
355C MET* 1.3 74.9 - - + +
357C PRO* 1.3 69.0 - - + +
359C PHE* 2.7 22.4 + - + +
360C ASP* 3.0 12.7 + - - +
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Residues in contact with PRO 357 (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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353C ASP* 3.5 20.0 - - - +
354C ILE 3.1 17.0 - - - +
356C GLU* 1.3 92.3 - - + +
358C LYS* 1.3 65.0 + - - +
360C ASP* 3.5 6.9 + - + +
361C PHE* 3.4 16.1 + - - +
436C LEU* 3.6 27.2 - - + +
439C GLU* 5.6 4.7 - - + +
443C LEU* 5.2 2.9 - - + -
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Residues in contact with LYS 358 (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* 3.5 43.3 - - + +
321C LEU* 4.6 12.6 - - + -
322C SER* 4.8 1.0 + - - -
325C MET* 4.0 6.8 - - + +
354C ILE* 2.7 33.6 + - - +
355C MET* 3.1 15.4 + - + +
356C GLU 3.0 1.0 - - - -
357C PRO* 1.3 82.9 - - - +
359C PHE* 1.3 65.2 + - - +
360C ASP 3.2 0.7 - - - -
361C PHE* 4.0 2.9 - - - +
362C ALA* 3.2 22.7 + - - +
436C LEU* 4.3 22.1 + - + -
440C HIS* 2.9 52.2 - - + +
443C LEU* 4.9 2.0 - - - +
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Residues in contact with PHE 359 (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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325C MET* 3.4 34.1 - - + -
326C ASN 3.4 25.8 - - - -
329C GLY* 3.6 35.4 - - - -
330C MET* 3.7 6.5 - - + -
339C ILE 5.3 0.2 - - - -
341C ARG* 3.5 52.4 + - + +
344C LEU* 4.4 7.2 - - + -
355C MET* 3.1 31.4 + - + -
356C GLU* 2.7 15.1 + - + +
358C LYS* 1.3 77.6 - - - +
360C ASP* 1.3 63.4 + - - +
362C ALA* 3.5 4.0 - - - +
363C MET* 3.2 28.2 + - - +
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Residues in contact with ASP 360 (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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341C ARG* 4.5 8.2 - - - +
356C GLU 3.0 10.0 + - - +
357C PRO* 3.8 10.3 - - + +
359C PHE* 1.3 74.4 - - - +
361C PHE* 1.3 69.7 + - - +
362C ALA 3.0 2.0 + - - -
363C MET* 3.1 15.9 + - - +
364C LYS* 2.7 43.8 + - - +
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Residues in contact with PHE 361 (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 4.0 13.7 - - - -
319C ALA* 4.6 1.8 - - - -
322C SER* 4.0 7.4 - - - -
357C PRO 3.4 13.4 + - - +
358C LYS 4.1 3.6 - - - +
360C ASP* 1.3 80.1 - - - +
362C ALA* 1.3 58.8 + - - +
364C LYS* 3.4 9.0 + - - +
365C PHE* 2.8 68.5 + + + +
429C LYS* 3.8 24.7 + - + +
432C ASP* 4.1 19.5 - - + -
433C LEU* 3.3 44.2 - - + -
436C LEU* 4.0 18.8 - - + -
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Residues in contact with ALA 362 (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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322C SER* 3.2 31.4 - - - +
325C MET* 3.8 17.5 - - + -
358C LYS 3.2 16.3 + - - +
359C PHE 3.5 6.5 - - - +
360C ASP 3.0 0.4 - - - -
361C PHE* 1.3 78.0 - - - +
363C MET* 1.3 64.5 - - + +
364C LYS 3.0 0.2 + - - -
365C PHE* 4.2 0.2 - - - -
366C ASN* 2.8 41.6 + - - +
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Residues in contact with MET 363 (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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226C ARG* 6.0 0.2 - - - +
326C ASN* 3.5 30.7 - - - +
327C LYS* 3.6 30.7 - - + +
341C ARG* 4.2 10.8 - - - +
359C PHE* 3.2 15.8 + - + +
360C ASP* 3.1 12.6 + - - +
362C ALA* 1.3 86.3 - - + +
364C LYS* 1.3 61.8 + - + +
366C ASN* 4.0 15.9 + - + +
367C ALA* 3.6 15.9 + - - +
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Residues in contact with LYS 364 (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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360C ASP* 2.7 43.5 + - - +
361C PHE* 3.4 6.5 + - - +
362C ALA 3.1 0.4 - - - -
363C MET* 1.3 77.7 - - + +
365C PHE* 1.3 68.0 + - - +
366C ASN 3.1 1.6 - - - -
367C ALA* 2.9 23.7 + - + +
368C LEU* 3.4 9.9 + - - +
429C LYS* 3.6 21.0 + - - +
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Residues in contact with PHE 365 (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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222C LYS* 6.1 1.3 - - - -
319C ALA* 4.4 19.1 - - + -
322C SER* 4.3 2.2 - - - +
361C PHE* 2.8 50.2 + + + +
362C ALA* 3.7 5.2 - - - +
364C LYS* 1.3 76.2 - - - +
366C ASN* 1.3 70.9 + - - +
368C LEU* 3.2 22.1 + - + +
370C LEU* 3.6 30.6 + - + +
375C ILE* 4.8 13.0 - - + -
378C PHE* 3.5 38.6 - + - -
426C LEU* 3.9 8.5 - - + -
429C LYS* 3.8 30.0 - - + +
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Residues in contact with ASN 366 (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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222C LYS* 4.1 21.2 + - - +
226C ARG* 3.6 19.2 + - - +
322C SER* 3.4 41.6 + - - +
325C MET 3.8 4.7 - - - +
362C ALA* 2.8 22.8 + - - +
363C MET* 4.0 13.6 - - + +
365C PHE* 1.3 79.8 - - - +
367C ALA* 1.3 58.7 + - - +
368C LEU 3.1 2.0 - - - -
369C GLU* 3.0 26.9 + - - +
370C LEU 4.7 0.2 + - - -
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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