Contacts of the helix formed by residues 139 - 144 (chain P) in PDB entry 1ZYR
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 ALA 139 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426N LYS* 3.9 3.2 - - - +
133P ALA* 6.1 3.6 - - - -
134P LYS* 5.0 4.1 - - - +
138P SER* 1.3 75.7 - - - +
140P ARG* 1.3 54.6 + - - +
141P VAL 2.7 11.1 + - - -
142P ARG* 2.8 22.2 + - - +
143P HIS* 3.6 5.2 + - - -
152P ASP* 3.2 45.1 - - + +
153P PRO* 4.3 5.8 - - + -
156P VAL* 6.1 0.7 - - - -
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Residues in contact with ARG 140 (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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158N TYR* 5.6 0.2 + - - -
162N ARG* 4.0 19.2 - - - +
451N ASP 6.4 0.2 - - - -
452N ILE 5.0 6.3 + - - -
453N ASP* 3.8 17.1 + - - +
454N ALA 5.9 0.4 - - - +
455N ARG* 2.8 45.5 + - - +
459N GLU* 5.3 1.6 - - - +
136P LEU 4.6 1.4 + - - -
137P GLY* 3.5 9.5 - - - -
138P SER* 3.1 38.8 + - - +
139P ALA* 1.3 76.9 - - - +
141P VAL* 1.3 92.0 + - - +
143P HIS* 3.4 20.5 + - - +
144P ILE* 3.8 11.3 + - + +
145P PRO* 3.9 3.1 - - - +
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Residues in contact with VAL 141 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558N LEU* 6.0 2.2 - - + +
567N ILE* 5.9 6.5 - - + -
133P ALA* 6.2 1.3 - - - -
136P LEU* 3.5 27.1 - - + +
137P GLY* 3.5 16.4 - - - +
138P SER 2.9 16.6 - - - +
139P ALA 2.7 2.0 + - - -
140P ARG* 1.3 104.7 - - - +
142P ARG* 1.3 59.3 + - + +
145P PRO* 2.8 39.5 - - + +
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Residues in contact with ARG 142 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126P LEU* 4.9 2.6 + - - +
129P GLU* 2.8 62.4 + - - +
130P VAL* 3.5 6.4 - - - +
133P ALA* 3.9 25.7 - - + +
139P ALA* 2.8 15.7 + - - +
141P VAL* 1.3 75.7 - - + +
143P HIS* 1.3 58.7 + - - +
145P PRO* 4.4 0.2 - - - -
146P GLY 2.6 29.6 - - - +
147P LEU 3.8 0.3 - - - -
148P LYS* 3.7 7.8 + - - -
150P THR* 3.5 32.8 + - - +
152P ASP* 4.4 15.9 - - + +
156P VAL* 4.8 12.3 - - - +
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Residues in contact with HIS 143 (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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139P ALA 3.6 4.5 + - - +
140P ARG* 3.7 15.9 - - - +
141P VAL 3.3 1.0 - - - -
142P ARG* 1.3 75.9 - - - +
144P ILE* 1.3 91.7 + - + +
147P LEU* 3.1 38.4 - - + +
148P LYS* 3.6 18.0 + - + +
152P ASP* 4.5 20.8 + - - +
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Residues in contact with ILE 144 (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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96N ALA 3.2 28.6 - - - +
97N THR* 3.9 9.4 - - + +
98N PRO* 3.9 19.7 - - + -
455N ARG* 5.2 9.6 - - - +
459N GLU* 3.0 46.2 - - + +
462N GLN* 6.4 1.3 - - + -
463N GLN* 6.1 3.1 - - + -
140P ARG 3.8 5.8 + - - +
143P HIS* 1.3 95.1 - - + +
145P PRO* 1.4 79.9 - - + +
147P LEU* 4.3 10.3 + - - +
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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