Contacts of the helix formed by residues 327 - 332 (chain P) in PDB entry 1HI0
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 ASP 327 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108P LYS* 3.9 10.5 + - - +
325P VAL 3.7 0.2 + - - -
326P SER* 1.3 75.1 - - - +
328P HIS* 1.3 67.1 + - - +
329P ASP 3.3 0.8 + - - -
330P THR* 2.8 47.4 + - - +
331P PHE* 3.3 24.9 + - + -
667P GTP 3.4 29.7 + - - -
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Residues in contact with HIS 328 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325P VAL* 4.3 5.2 - - + -
326P SER 3.1 4.7 + - - -
327P ASP* 1.3 74.2 - - - +
329P ASP* 1.3 88.0 + - - +
331P PHE 3.2 1.6 + - - -
332P TRP* 3.0 26.9 + + - -
391P LEU* 4.0 6.1 - - - +
402P GLY* 3.4 25.9 - - - -
405P LEU* 3.8 17.5 - - + -
406P MET* 3.7 30.6 - - + +
452P SER* 4.7 1.5 - - - -
453P ASP* 3.7 20.8 - - + +
486P MET* 3.5 20.5 - - - +
667P GTP 3.3 33.1 + - - +
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Residues in contact with ASP 329 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270P ARG* 3.4 16.3 + - - +
327P ASP 3.3 1.2 + - - -
328P HIS* 1.3 102.9 - - - +
330P THR* 1.3 65.2 + - + +
331P PHE 3.4 0.3 + - - -
332P TRP* 3.6 2.1 + - - -
389P VAL 3.8 0.5 - - - +
390P GLY* 3.5 1.2 - - - -
391P LEU* 2.9 54.7 + - + +
393P SER* 5.2 8.8 + - - -
398P THR* 6.1 0.4 - - - -
667P GTP 3.1 40.1 + - - +
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Residues in contact with THR 330 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102P LEU* 5.8 6.7 - - - -
105P ASN* 2.8 32.3 + - - +
108P LYS* 3.3 17.4 - - - +
327P ASP* 2.8 39.3 + - - +
329P ASP* 1.3 80.7 - - + +
331P PHE* 1.3 58.1 + - - +
332P TRP 3.5 0.2 - - - -
389P VAL 3.7 13.8 - - - +
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Residues in contact with PHE 331 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105P ASN* 3.7 1.3 - - - +
108P LYS* 3.3 48.0 - - + -
109P ARG* 2.7 39.4 + - + -
112P ALA* 3.9 18.8 - - + -
114P LEU* 3.8 29.2 - - + -
325P VAL* 6.1 0.2 - - + -
326P SER* 3.3 25.6 - - - -
327P ASP* 3.3 24.4 + - + +
328P HIS 3.2 0.4 + - - -
329P ASP 3.2 0.6 - - - -
330P THR* 1.3 80.6 + - - +
332P TRP* 1.3 68.6 + - - +
333P PRO 2.9 0.2 - - - -
486P MET* 3.5 22.4 - - + -
487P LYS* 4.8 13.7 - - + -
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Residues in contact with TRP 332 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105P ASN* 3.2 15.6 + - - -
328P HIS* 3.0 25.6 + + - +
329P ASP 3.7 13.7 - - - +
330P THR 3.5 0.8 - - - -
331P PHE* 1.3 73.6 - - - +
333P PRO* 1.3 87.4 - - + +
334P GLY* 3.6 2.6 + - - -
336P LEU* 4.0 17.3 - - + -
337P ARG* 3.8 36.6 - - + -
361P LEU* 4.5 9.2 - - + -
390P GLY* 3.3 18.6 - - - -
391P LEU* 3.7 27.4 - - + +
401P MET* 3.0 60.5 + - + -
405P LEU* 3.5 27.3 - - + +
486P MET* 4.4 2.2 - - - -
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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