Contacts of the helix formed by residues 354 - 360 (chain C) in PDB entry 7A62
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 ILE 354 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226C PHE* 3.6 24.9 - - + -
227C PHE* 3.6 13.4 - - + -
231C ARG* 3.8 23.6 - - - +
350C VAL* 2.8 20.4 + - + +
352C LYS 3.5 0.4 - - - -
353C TYR* 1.3 83.3 - - - +
355C LEU* 1.3 72.3 + - + +
357C PRO* 3.2 4.2 - - - +
358C ALA* 3.0 27.0 + - + +
377C LYS* 5.4 10.5 - - + +
381C GLY* 6.3 0.2 - - - -
384C LEU* 4.5 19.7 - - + -
504C HEM 3.8 28.5 - - + -
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Residues in contact with LEU 355 (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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347C LEU* 6.4 0.9 - - + -
350C VAL* 3.1 18.4 + - + +
351C THR* 3.6 35.4 - - + +
354C ILE* 1.3 83.7 - - + +
356C ILE* 1.3 61.1 + - + +
358C ALA* 3.5 4.5 - - + +
359C SER* 2.8 27.9 + - - -
377C LYS 4.7 4.9 - - - +
378C GLY* 5.8 2.5 - - - -
381C GLY* 3.5 34.8 - - - +
382C THR* 5.3 0.4 - - - -
384C LEU* 4.6 6.5 - - + -
385C MET* 4.3 33.0 - - + +
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Residues in contact with ILE 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C PRO* 6.0 0.7 - - + -
351C THR* 2.9 31.9 + - + +
352C LYS* 3.4 26.0 - - + +
355C LEU* 1.3 75.1 - - + +
357C PRO* 1.3 76.2 - - + +
359C SER* 2.8 20.0 + - - -
360C GLN* 2.8 27.4 + - - +
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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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223C PRO* 4.0 13.9 - - + -
224C LYS* 3.3 31.1 + - + +
227C PHE* 3.8 26.3 - - + -
352C LYS 3.3 17.5 - - - +
353C TYR 3.9 11.9 - - - +
354C ILE 3.2 14.1 - - - +
356C ILE* 1.3 98.2 - - + +
358C ALA* 1.3 60.0 + - - +
360C GLN* 3.1 16.2 + - + +
361C GLN 3.6 9.7 - - - +
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Residues in contact with ALA 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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227C PHE* 3.5 26.5 - - + -
354C ILE* 3.0 22.2 + - + +
355C LEU* 3.5 6.1 - - + +
357C PRO* 1.3 71.0 - - - +
359C SER* 1.3 58.0 + - - +
360C GLN 3.0 1.6 - - - -
361C GLN* 2.7 22.7 + - - -
362C PRO* 3.2 15.5 - - + +
367C THR 4.2 6.7 - - - +
376C ALA 4.3 14.4 - - - +
377C LYS 4.7 8.5 - - - +
378C GLY* 5.3 4.9 - - - +
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Residues in contact with SER 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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355C LEU 2.8 13.6 + - - -
356C ILE* 2.8 20.2 + - - -
358C ALA* 1.3 72.7 - - - +
360C GLN* 1.3 64.1 + - - +
361C GLN 3.1 4.0 + - - -
367C THR* 3.9 23.2 - - - +
368C SER* 5.8 2.2 - - - +
378C GLY* 6.1 1.3 - - - -
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Residues in contact with GLN 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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224C LYS* 3.3 26.4 - - - +
356C ILE* 2.8 35.1 + - - +
357C PRO* 3.3 6.7 - - + +
358C ALA 3.0 0.8 - - - -
359C SER* 1.3 84.4 + - - +
361C GLN* 1.3 76.8 + - - +
367C THR* 5.1 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