Contacts of the helix formed by residues 410 - 419 (chain C) in PDB entry 3ITX
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 GLY 410 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406C TYR 3.5 1.2 + - - -
407C ARG* 3.5 11.6 + - - -
408C ALA 3.4 3.2 - - - -
409C SER* 1.3 79.1 + - - +
411C TYR* 1.3 64.8 + - - +
412C ARG 3.4 2.5 - - - -
413C ALA* 3.4 12.5 + - - +
414C ARG* 3.1 20.9 + - - +
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Residues in contact with TYR 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ARG* 2.8 55.8 + - + -
6C ILE* 4.0 10.8 - - + -
83C ASP 3.4 5.7 + - - -
84C ASP* 2.7 29.4 + - - -
87C VAL* 3.5 12.8 - - + -
336C ILE* 3.7 15.5 - - + -
406C TYR* 3.7 29.4 + + + -
409C SER* 3.2 16.4 + - - +
410C GLY* 1.3 76.9 - - - +
412C ARG* 1.3 65.3 + - - +
414C ARG* 3.0 28.0 + - - +
415C VAL* 3.0 38.6 + - + +
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Residues in contact with ARG 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C VAL 4.9 4.0 + - - -
72C THR* 3.0 42.1 + - - +
73C GLY 3.1 19.2 + - - -
74C GLU* 4.8 3.2 + - - +
75C PRO* 5.1 2.4 - - - +
84C ASP* 5.1 2.2 + - - -
334C ASP* 2.9 40.6 + - - +
335C PRO* 4.2 11.2 - - - +
336C ILE* 3.6 20.4 - - - +
406C TYR* 3.4 23.4 + - + +
410C GLY 3.4 0.6 - - - -
411C TYR* 1.3 78.6 - - - +
413C ALA* 1.3 58.8 + - - +
415C VAL* 3.3 14.2 - - - +
416C ALA* 2.9 30.1 + - - +
419C ARG* 4.6 2.6 - - - +
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Residues in contact with ALA 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C THR* 5.5 0.4 - - - -
410C GLY* 3.4 12.8 + - - +
411C TYR 3.3 0.4 - - - -
412C ARG* 1.3 80.1 - - - +
414C ARG* 1.3 64.4 + - - +
416C ALA* 3.4 8.9 + - - +
417C ALA* 3.3 19.9 + - - +
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Residues in contact with ARG 414 (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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4C PHE 5.0 1.0 + - - -
5C ARG* 2.9 63.2 + - - +
410C GLY 3.1 13.5 + - - +
411C TYR* 3.0 26.8 + - - +
413C ALA* 1.3 77.7 - - - +
415C VAL* 1.3 63.3 + - - +
417C ALA* 3.1 13.8 + - - +
418C GLU* 3.1 43.0 + - - +
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Residues in contact with VAL 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ARG* 3.9 2.9 - - - +
73C GLY* 4.0 7.0 - - - +
411C TYR* 3.0 54.4 + - + +
412C ARG* 3.3 35.9 - - - +
414C ARG* 1.3 74.7 - - + +
416C ALA* 1.3 62.1 + - - +
417C ALA 3.1 0.2 - - - -
418C GLU* 3.6 19.3 - - - +
419C ARG* 2.8 58.5 + - - +
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Residues in contact with ALA 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C THR* 3.8 16.8 - - - +
73C GLY* 3.4 26.8 + - - +
412C ARG 2.9 19.6 + - - +
413C ALA* 3.5 10.8 - - - +
414C ARG 3.1 0.4 - - - -
415C VAL* 1.3 78.7 - - - +
417C ALA* 1.3 57.2 + - - +
419C ARG 2.9 18.9 - - - +
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Residues in contact with ALA 417 (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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413C ALA 3.3 8.0 + - - +
414C ARG* 3.1 10.6 + - - +
415C VAL 3.1 0.6 - - - -
416C ALA* 1.3 80.5 - - - +
418C GLU* 1.3 62.5 + - + +
419C ARG 3.3 3.2 - - - +
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Residues in contact with GLU 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ARG* 4.5 5.4 + - - -
414C ARG* 3.1 44.7 + - + +
415C VAL* 3.2 23.5 + - - +
417C ALA* 1.3 79.4 - - + +
419C ARG* 1.3 66.2 + - + +
420C PRO* 4.6 1.6 - - - +
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Residues in contact with ARG 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ARG* 4.4 1.2 - - - +
73C GLY* 2.9 32.1 + - - -
74C GLU 3.6 15.0 - - - +
75C PRO* 3.5 7.3 - - - +
80C ASP* 3.4 48.4 + - - +
83C ASP* 4.2 6.3 + - - +
84C ASP* 2.9 40.7 + - - -
411C TYR* 4.0 2.8 + - - -
412C ARG* 4.6 0.6 - - - +
415C VAL* 2.8 38.6 + - - +
416C ALA 2.9 18.7 - - - +
417C ALA 4.1 2.6 - - - +
418C GLU* 1.3 88.4 + - + +
420C PRO* 1.3 75.6 - - + +
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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