Contacts of the helix formed by residues 413 - 420 (chain C) in PDB entry 1XVP
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 413 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412C PRO* 1.3 78.4 - - - +
414C ARG* 1.3 56.9 + - - -
415C PHE 3.4 1.6 - - - -
416C ALA* 3.5 11.6 + - - +
417C LYS* 2.8 36.9 + - - +
290D LEU* 5.4 10.3 - - - -
293D GLN* 5.1 4.5 - - - -
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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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360C MET* 3.0 48.3 + - + +
361C GLN 3.1 10.1 + - - -
362C MET* 3.7 3.2 - - - +
366C GLU* 2.7 40.8 + - - +
404C CYS* 4.4 12.3 - - - +
408C TYR* 3.5 36.7 - - - -
411C GLN* 2.8 52.2 + - + +
412C PRO 2.8 9.4 + - - +
413C GLY* 1.3 70.1 - - - +
415C PHE* 1.3 59.4 + - - +
417C LYS* 3.3 9.7 + - - +
418C LEU* 2.8 35.9 + - + +
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Residues in contact with PHE 415 (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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397C TYR* 3.3 39.5 - + + -
400C LEU* 3.6 31.6 - - + -
401C GLU* 3.8 42.8 - - + +
404C CYS* 4.4 12.6 - - + +
405C LYS* 5.2 5.8 - - - +
412C PRO 4.3 1.6 + - - -
413C GLY* 3.4 0.6 - - - -
414C ARG* 1.3 77.7 - - - +
416C ALA* 1.3 65.8 + - + +
418C LEU* 3.1 19.8 - - + +
419C LEU* 3.2 35.0 + - + +
307D PHE* 4.1 21.1 - + - -
309D TYR* 6.2 2.2 - + - -
310D ALA* 5.0 2.9 - - + -
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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
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413C GLY* 3.5 10.6 + - - +
415C PHE* 1.3 82.0 - - + +
417C LYS* 1.3 51.6 - - - +
419C LEU* 3.0 8.2 + - - +
420C LEU* 2.9 34.5 + - - +
293D GLN* 3.0 43.1 - - - +
309D TYR* 3.5 20.3 - - + +
313D LEU* 4.1 3.5 - - - +
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Residues in contact with LYS 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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356C LYS* 5.3 10.5 - - - +
359C ASP 5.8 0.6 + - - -
360C MET* 4.2 37.6 - - + +
411C GLN* 6.2 0.2 - - - +
413C GLY 2.8 23.6 + - - +
414C ARG* 3.4 10.8 - - + +
416C ALA* 1.3 75.3 - - - +
418C LEU* 1.3 62.5 + - - +
420C LEU* 3.7 21.1 + - + +
421C ARG* 4.4 9.0 + - - +
286D GLU* 3.2 30.6 + - + +
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Residues in contact with LEU 418 (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 MET* 3.3 29.4 - - + -
362C MET* 4.9 7.0 - - + -
366C GLU* 3.7 27.8 - - + +
370C LEU* 3.0 28.2 - - + +
400C LEU* 3.6 25.8 - - + -
404C CYS* 3.5 26.7 - - - -
414C ARG* 2.8 25.4 + - + +
415C PHE* 3.1 13.7 - - - +
416C ALA 3.1 0.2 - - - -
417C LYS* 1.3 80.1 - - - +
419C LEU* 1.3 61.5 + - + +
420C LEU 3.5 0.2 + - - -
421C ARG* 3.6 13.3 + - - +
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Residues in contact with LEU 419 (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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370C LEU* 3.2 30.7 - - + -
373C ILE* 3.7 14.4 - - + -
397C TYR* 4.5 3.8 - - + -
400C LEU* 4.7 1.1 - - + -
415C PHE* 3.6 46.4 - - + +
416C ALA* 3.0 6.7 + - - +
418C LEU* 1.3 72.2 - - + +
420C LEU* 1.3 63.2 + - - +
421C ARG 2.8 7.6 + - - -
422C LEU* 2.9 40.7 + - + +
423C PRO* 3.9 0.3 - - - +
309D TYR* 5.5 1.8 - - + -
310D ALA* 4.1 23.3 - - + +
313D LEU* 3.4 21.7 - - + +
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Residues in contact with LEU 420 (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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356C LYS* 5.6 1.8 - - - +
416C ALA 2.9 10.9 + - - +
417C LYS* 3.7 18.8 - - + +
418C LEU 3.3 0.8 - - - -
419C LEU* 1.3 76.1 - - - +
421C ARG* 1.3 77.3 + - - +
423C PRO* 3.2 15.5 - - + +
424C ALA* 4.7 1.7 + - - +
265D MET* 3.9 18.8 - - + -
285D GLN* 2.8 40.1 - - + +
286D GLU* 4.7 16.6 - - + +
289D ALA* 4.1 4.9 - - + -
309D TYR* 3.5 24.7 - - - +
313D LEU* 3.7 9.6 - - + -
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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