Contacts of the helix formed by residues 17 - 22 (chain M) 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 PRO 17 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16M PRO* 1.3 87.7 - - + +
18M LEU* 1.3 63.0 + - - +
19M THR 3.4 2.2 - - - -
20M GLU* 2.7 45.2 - - + +
21M ILE* 4.1 2.6 - - - +
408M ARG* 4.0 1.4 + - - -
460M ARG* 4.2 17.9 - - - +
586M ARG* 4.9 1.6 - - - +
590M ASP* 4.3 8.5 - - - +
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Residues in contact with LEU 18 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M LEU* 4.4 14.8 - - + -
16M PRO* 2.8 32.7 + - + +
17M PRO* 1.3 69.2 - - - +
19M THR* 1.3 58.4 + - - +
21M ILE* 3.0 15.9 - - - +
404M LEU* 3.9 27.8 - - + -
408M ARG* 2.3 51.1 + - - +
457M ALA* 5.5 1.3 - - - +
542M VAL* 4.0 23.3 - - + -
586M ARG* 3.6 14.8 - - + +
587M VAL* 5.1 2.5 - - + -
590M ASP* 3.5 34.1 + - + +
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Residues in contact with THR 19 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17M PRO 3.4 0.4 - - - -
18M LEU* 1.3 72.6 - - + +
20M GLU* 1.3 63.7 + - - +
21M ILE* 3.1 3.4 - - - +
22M GLN* 3.1 8.3 + - - +
23M VAL* 3.0 25.8 + - - +
124M ASP 3.5 19.7 + - - +
404M LEU* 3.5 28.9 - - + -
407M LYS* 3.5 31.2 - - + +
408M ARG* 5.2 2.2 - - + +
590M ASP* 4.5 15.7 + - - +
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Residues in contact with GLU 20 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16M PRO* 5.2 0.7 - - - +
17M PRO* 2.7 38.4 + - + +
18M LEU 3.1 0.2 - - - -
19M THR* 1.3 77.4 + - - +
21M ILE* 1.3 76.6 + - - +
22M GLN 3.1 1.4 + - - -
23M VAL* 4.4 2.9 - - - +
24M GLU* 3.1 47.0 + - + +
25M SER* 3.8 2.4 + - - -
28M ARG* 5.7 3.1 + - - -
460M ARG* 3.1 48.7 + - - +
461M VAL* 4.2 17.0 + - - +
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Residues in contact with ILE 21 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M PRO* 6.4 0.2 - - + -
17M PRO 4.1 4.0 - - - +
18M LEU 3.0 24.7 - - - +
19M THR* 4.9 0.7 - - - -
20M GLU* 1.3 95.1 - - + +
22M GLN* 1.3 59.9 + - + +
25M SER* 2.7 20.0 + - - -
138M SER* 4.2 15.5 - - - +
333M ILE* 5.7 1.3 - - + -
335M THR* 3.4 25.3 - - + +
407M LYS 5.2 3.1 - - - +
408M ARG* 3.7 25.4 - - + +
410M ILE* 6.5 1.1 - - + -
455M LEU* 4.4 22.4 - - + -
459M ALA 4.9 9.2 - - - +
460M ARG* 5.7 0.4 - - - -
461M VAL* 4.8 16.2 - - + +
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Residues in contact with GLN 22 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M THR* 3.1 9.0 + - - +
21M ILE* 1.3 87.1 - - + +
23M VAL* 1.3 63.2 + - - +
25M SER* 2.9 14.2 + - - -
26M TYR* 3.9 4.0 + - - +
121M MET* 3.1 26.9 - - + +
125M GLY* 4.3 18.8 + - - +
127M PHE* 5.8 0.8 - - - -
135M VAL* 4.0 11.7 - - - +
136M ILE* 2.9 29.9 + - - +
138M SER* 4.2 10.4 + - - -
336M VAL* 3.1 26.5 + - - +
407M LYS* 3.2 42.8 + - + +
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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
------------------------------------------------------------
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