Contacts of the helix formed by residues 482 - 491 (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 HIS 482 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377C LEU 5.8 0.6 + - - -
378C PHE* 6.4 0.2 - - - -
379C GLN 3.3 27.1 + - - -
380C GLY* 4.7 11.3 + - - -
381C VAL* 4.9 12.0 - - + +
480C HIS* 3.1 7.1 - - + -
481C ALA* 1.3 77.1 - - - +
483C ALA* 1.3 65.8 + - - +
484C ASP 3.2 2.2 - - - -
485C ASP* 3.0 26.9 + - + +
486C GLY* 3.1 18.1 + - - -
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Residues in contact with ALA 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C LEU* 3.8 35.1 - - + +
378C PHE* 4.5 17.3 - - + -
381C VAL* 5.9 2.0 - - + +
385C PHE* 5.2 2.7 - - + -
480C HIS* 4.0 19.1 + - + +
481C ALA 3.4 0.6 - - - -
482C HIS* 1.3 81.1 + - - +
484C ASP* 1.3 59.9 + - - +
486C GLY* 3.3 10.4 + - - +
487C ARG* 3.5 8.8 + - - +
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Residues in contact with ASP 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C GLY 3.7 22.1 - - - +
446C GLU* 4.9 11.3 - - - +
481C ALA* 4.0 11.7 + - - +
482C HIS 3.2 0.8 - - - -
483C ALA* 1.3 78.3 - - - +
485C ASP* 1.3 58.4 + - - +
487C ARG* 4.1 9.0 + - - +
488C VAL* 4.2 10.7 + - - +
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Residues in contact with ASP 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481C ALA 4.2 3.7 + - - +
482C HIS* 3.0 28.2 + - + +
484C ASP* 1.3 76.6 - - - +
486C GLY* 1.3 63.1 + - - +
487C ARG 3.2 2.7 + - - -
488C VAL* 3.4 25.4 + - - +
489C ILE* 3.6 15.6 - - - +
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Residues in contact with GLY 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C TYR* 3.9 23.5 - - - +
377C LEU* 4.7 6.3 - - - -
482C HIS* 3.1 19.9 + - - -
483C ALA* 3.3 5.5 + - - -
485C ASP* 1.3 75.6 - - - +
487C ARG* 1.3 61.4 + - - +
488C VAL 3.5 0.2 - - - -
489C ILE* 3.9 13.1 + - - +
490C MET 3.9 6.6 + - - -
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Residues in contact with ARG 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C TYR* 4.5 7.2 + - + +
377C LEU* 3.8 23.6 - - + -
442C GLU* 5.5 7.0 - - + +
446C GLU* 3.3 22.0 - - - +
483C ALA 3.5 7.9 + - - +
484C ASP* 4.3 10.1 - - - +
485C ASP 3.2 1.0 - - - -
486C GLY* 1.3 76.9 - - - +
488C VAL* 1.3 63.6 + - - +
489C ILE 3.2 0.4 - - - -
490C MET* 3.3 13.3 + - - +
491C ASN* 3.3 16.8 + - - +
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Residues in contact with VAL 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C GLU* 4.3 13.7 + - - +
484C ASP 4.2 6.0 + - - +
485C ASP* 3.4 26.8 + - - +
487C ARG* 1.3 76.8 - - - +
489C ILE* 1.3 70.6 + - + +
490C MET 3.4 0.2 - - - -
491C ASN* 3.5 11.2 + - + -
492C ASN 3.3 24.2 + - - +
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Residues in contact with ILE 489 (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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485C ASP* 3.6 23.1 - - - +
486C GLY* 4.1 10.8 - - - +
487C ARG 3.2 0.8 - - - -
488C VAL* 1.3 82.9 - - + +
490C MET* 1.3 59.3 + - - +
492C ASN* 3.0 27.3 + - - +
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Residues in contact with MET 490 (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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376C TYR* 3.5 55.9 - - + +
442C GLU* 4.6 8.1 - - - +
486C GLY 3.9 2.2 + - - +
487C ARG 3.3 6.3 + - - +
489C ILE* 1.3 80.4 - - - +
491C ASN* 1.3 73.7 + - - +
492C ASN* 3.2 11.4 + - - +
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Residues in contact with ASN 491 (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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446C GLU* 3.0 29.2 - - - +
487C ARG* 3.3 13.6 + - - +
488C VAL* 3.8 11.2 - - + +
489C ILE 3.2 1.0 - - - -
490C MET* 1.3 95.0 + - - +
492C ASN* 1.3 70.6 + - - +
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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