Contacts of the helix formed by residues 359 - 367 (chain C) in PDB entry 7CAL
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 359 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355C LEU* 4.1 19.1 - - + -
356C PRO* 3.7 24.2 - - + -
357C LYS 4.5 0.4 - - - +
358C ALA* 1.3 76.4 - - - +
360C ARG* 1.3 63.2 + - - +
362C SER* 3.5 4.0 + - - -
363C ILE* 3.2 30.7 + - + +
329D ILE* 4.5 10.2 - - + +
332D GLN* 3.4 40.6 - - + +
333D MET* 3.7 33.7 - - + +
336D HIS* 5.4 4.3 - - + +
398D PHE* 5.9 2.0 - - + -
402D GLU* 5.0 8.7 - - + -
403D ASP 4.7 9.9 - - - +
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Residues in contact with ARG 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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352C LEU* 3.3 44.8 + - + +
353C ASN* 4.5 19.0 + - - +
355C LEU* 2.7 34.7 + - + +
356C PRO 3.2 14.6 + - - -
357C LYS* 4.3 8.9 - - - +
358C ALA 3.3 1.6 - - - +
359C ILE* 1.3 80.3 - - - +
361C SER* 1.3 61.5 + - - +
363C ILE* 3.3 12.7 + - + +
364C ALA* 3.2 23.0 + - - +
390C VAL 5.7 5.2 - - - -
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Residues in contact with SER 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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357C LYS 3.0 20.7 + - - -
358C ALA* 3.9 1.1 + - - -
359C ILE 3.4 0.2 - - - -
360C ARG* 1.3 77.0 - - - +
362C SER* 1.3 57.1 + - - +
364C ALA* 4.1 4.8 + - - +
365C ASN* 3.1 30.8 + - - +
390C VAL* 3.6 31.2 - - - +
406D LEU* 3.9 20.8 - - - +
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Residues in contact with SER 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C ALA 3.3 19.0 + - - -
359C ILE 4.0 0.4 - - - -
360C ARG 3.2 0.4 - - - -
361C SER* 1.3 75.4 - - - +
363C ILE* 1.3 65.4 + - - +
364C ALA 3.3 0.2 - - - -
365C ASN* 3.5 7.5 + - - +
366C TYR* 3.4 20.3 + - - +
329D ILE* 3.9 28.9 - - - +
332D GLN* 5.6 0.7 - - - -
403D ASP* 5.5 3.6 + - - -
406D LEU* 5.0 12.9 - - - +
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Residues in contact with ILE 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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352C LEU* 5.5 3.8 - - + -
355C LEU* 3.8 26.5 - - + -
359C ILE* 3.2 21.7 + - + +
360C ARG* 3.5 11.2 - - + +
362C SER* 1.3 76.1 - - - +
364C ALA* 1.3 58.5 + - + +
365C ASN 3.1 0.4 + - - -
366C TYR* 3.4 3.5 + - - +
367C LEU* 3.0 40.5 + - + +
319D PHE* 3.9 30.7 - - + -
325D LEU* 4.4 21.3 - - + -
329D ILE* 4.5 11.4 - - + -
333D MET* 4.0 17.7 - - + -
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Residues in contact with ALA 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 ARG 3.2 12.0 + - - +
361C SER* 4.1 5.4 - - - +
362C SER 3.3 0.4 - - - -
363C ILE* 1.3 80.4 - - + +
365C ASN* 1.3 65.1 + - - +
367C LEU* 2.9 19.0 - - - +
368C PHE* 4.0 17.4 - - + -
389C LEU* 3.3 34.7 - - - +
390C VAL* 4.7 7.0 - - + -
392C ASP* 6.2 0.2 - - + -
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Residues in contact with ASN 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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361C SER* 3.1 21.3 + - - +
362C SER* 3.5 7.6 + - - +
363C ILE 3.1 0.6 - - - -
364C ALA* 1.3 86.2 + - - +
366C TYR* 1.3 63.0 + - - +
367C LEU 3.4 0.2 - - - -
369C PHE* 3.2 29.0 - - + +
370C PRO* 5.4 0.2 - - - +
387C PHE* 3.3 43.5 + - + -
389C LEU* 3.4 27.1 + - - +
390C VAL* 5.3 2.4 - - - +
406D LEU* 4.9 1.4 - - - +
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Residues in contact with TYR 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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362C SER 3.4 14.7 + - - +
363C ILE 4.1 2.9 - - - +
365C ASN* 1.3 80.7 - - - +
367C LEU* 1.3 77.8 + - + +
368C PHE 3.8 1.9 + - - -
369C PHE 4.5 1.9 + - - -
370C PRO* 4.9 6.4 - - - +
323D ASN 4.6 2.2 - - - -
324D GLN 3.8 19.1 + - - -
325D LEU* 3.8 13.9 - - + -
326D PRO* 3.7 33.9 - - + +
329D ILE* 5.7 1.8 - - + -
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Residues in contact with LEU 367 (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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363C ILE* 3.0 28.2 + - + +
364C ALA 2.9 23.0 - - - +
366C TYR* 1.3 96.0 - - + +
368C PHE* 1.3 92.2 + - + +
369C PHE 3.0 3.1 + - - -
319D PHE* 4.8 2.0 - - + -
323D ASN* 3.4 44.2 - - + +
325D LEU* 3.8 17.0 - - + -
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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