Contacts of the helix formed by residues 301 - 308 (chain C) in PDB entry 1NTZ
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 LEU 301 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98C VAL* 3.9 30.1 - - + -
102C LEU* 5.2 3.8 - - + -
113C TRP* 2.6 36.5 + - + -
117C VAL* 3.8 24.2 - - + -
120C LEU* 3.9 27.1 - - + -
297C SER 5.6 0.4 - - - +
298C ILE* 3.4 21.5 - - + +
299C LEU 3.1 0.4 - - - -
300C ILE* 1.3 82.2 - - + +
302C ALA* 1.3 56.5 + - - +
303C LEU 3.2 0.6 + - - -
304C ILE* 3.7 28.3 + - + +
305C PRO* 3.7 1.2 - - - +
358C TYR* 5.7 2.5 - - - +
362C ILE* 6.4 0.7 - - + -
382C HEM 4.7 5.4 - - + -
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Residues in contact with ALA 302 (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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113C TRP* 4.7 2.2 - - - +
114C ASN* 4.6 21.3 + - - +
117C VAL* 4.5 11.8 - - + +
299C LEU* 3.1 17.8 + - + +
300C ILE 3.0 1.0 - - - -
301C LEU* 1.3 80.7 - - - +
303C LEU* 1.3 67.0 + - + +
305C PRO* 4.1 7.7 - - - +
306C LEU* 4.7 7.6 - - - +
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Residues in contact with LEU 303 (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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296C PHE* 4.0 28.3 - - + -
299C LEU 4.8 2.2 - - - +
300C ILE* 2.6 27.4 + - + +
302C ALA* 1.3 80.9 - - + +
304C ILE* 1.3 64.1 + - - +
305C PRO* 3.5 1.1 - - - -
306C LEU* 2.9 35.1 + - + +
307C LEU* 3.4 23.1 + - + +
363C LEU* 4.5 12.6 - - + -
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Residues in contact with ILE 304 (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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102C LEU* 3.8 35.4 - - + -
107C TYR* 4.1 33.0 - - + +
113C TRP* 4.7 4.3 - - + -
300C ILE 3.1 10.2 + - - +
301C LEU* 3.9 26.2 - - + +
302C ALA 3.5 0.2 - - - -
303C LEU* 1.3 75.9 - - - +
305C PRO* 1.3 66.3 - - + +
307C LEU* 2.8 29.2 + - + +
308C HIS* 3.4 8.1 + - - +
362C ILE* 4.2 30.3 - - + -
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Residues in contact with PRO 305 (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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107C TYR* 3.7 40.2 - - + +
108C THR* 5.4 1.3 - - + -
110C LEU* 3.8 25.6 - - + -
113C TRP* 4.0 11.0 - - + +
114C ASN* 5.1 3.6 - - - +
301C LEU 3.7 11.2 - - - +
302C ALA 4.1 7.0 - - - +
303C LEU 3.7 2.7 - - - -
304C ILE* 1.3 94.1 - - + +
306C LEU* 1.3 66.6 + - + +
307C LEU 3.2 0.7 + - - -
308C HIS* 3.6 14.1 + - - +
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Residues in contact with LEU 306 (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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110C LEU* 6.1 5.4 - - + -
302C ALA 4.7 7.0 - - - +
303C LEU* 2.9 33.2 + - + +
305C PRO* 1.3 85.3 - - + +
307C LEU* 1.3 66.8 + - + +
308C HIS 3.4 4.7 + - - +
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Residues in contact with LEU 307 (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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303C LEU* 3.5 30.7 - - + +
304C ILE* 2.8 12.2 + - + +
306C LEU* 1.3 84.4 - - + +
308C HIS* 1.3 64.0 + - - +
309C THR* 3.4 3.7 + - - -
362C ILE* 3.9 22.7 - - + +
363C LEU* 4.0 35.9 - - + +
367C PRO* 3.8 32.7 - - + +
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Residues in contact with HIS 308 (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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107C TYR* 2.5 46.4 + + + -
108C THR* 5.1 10.2 - - + +
304C ILE 3.4 3.4 + - - -
305C PRO 3.8 13.5 - - - +
306C LEU 3.4 5.9 - - - +
307C LEU* 1.3 77.5 - - - +
309C THR* 1.3 61.1 + - - +
310C SER* 3.1 32.1 + - - -
312C GLN 3.1 19.4 + - - -
313C ARG* 3.7 11.5 - - - -
318C ARG* 3.6 17.0 + - - -
38F HIS* 5.5 7.3 + + - -
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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