Contacts of the helix formed by residues 350 - 354 (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 PRO 350 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348C ARG* 5.9 0.2 - - - +
349C LYS* 1.3 96.1 - - + +
351C PHE* 1.3 77.1 + - + +
352C CYS 3.4 2.2 - - - -
353C ASP* 3.4 28.6 + - - +
354C ILE* 4.0 7.3 + - - +
443C LEU* 4.2 24.2 - - + +
446C ILE* 4.0 32.8 - - + +
447C ILE* 6.0 0.9 - - + -
450C THR* 6.3 1.1 - - + -
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Residues in contact with PHE 351 (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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269C GLU* 3.0 52.0 - - + -
270C VAL* 6.1 0.9 - - + -
273C PHE* 6.0 4.7 - + - -
344C LEU 4.2 1.0 - - - +
347C LEU* 4.4 7.6 - - + -
348C ARG* 2.9 26.5 - - - +
349C LYS 3.1 3.0 - - - -
350C PRO* 1.3 89.9 - - + +
352C CYS* 1.3 56.7 + - - +
353C ASP 2.9 9.8 + - - -
354C ILE* 3.4 17.9 + - + +
355C MET* 4.6 0.9 + - - +
446C ILE 5.3 0.2 - - - -
447C ILE* 3.3 42.2 - - + -
451C GLU* 4.6 18.2 - - + -
777C 471 3.3 40.2 - + - -
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Residues in contact with CYS 352 (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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344C LEU 3.1 14.8 - - - +
345C LYS* 3.0 48.4 - - - +
347C LEU 3.6 21.3 + - - +
349C LYS* 4.2 16.2 - - - -
351C PHE* 1.3 76.4 - - - +
353C ASP* 1.3 81.6 + - - +
354C ILE 3.6 0.9 - - - -
355C MET* 5.3 1.6 - - - -
356C GLU* 4.4 9.6 - - - +
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Residues in contact with ASP 353 (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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349C LYS* 3.0 31.7 + - - +
350C PRO* 3.5 14.9 - - + +
351C PHE 2.9 1.4 - - - -
352C CYS* 1.3 102.2 - - - +
354C ILE* 1.3 59.5 + - - +
355C MET 3.8 0.2 - - - -
356C GLU* 5.2 2.2 - - - +
357C PRO* 3.5 19.4 - - - +
443C LEU* 3.0 25.7 - - + +
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Residues in contact with ILE 354 (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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350C PRO 4.1 9.6 - - - +
351C PHE* 3.4 16.0 + - + +
353C ASP* 1.3 78.6 - - - +
355C MET* 1.3 68.9 + - - +
357C PRO* 3.1 8.0 - - - +
358C LYS* 2.7 29.0 + - - +
440C HIS* 4.0 12.1 - - + -
443C LEU* 3.9 24.7 - - + +
444C VAL* 4.1 22.2 - - + -
447C ILE* 4.6 11.9 - - + -
777C 471 3.4 57.0 - - + +
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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
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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