Contacts of the helix formed by residues 18 - 25 (chain P) in PDB entry 3JZR
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 THR 18 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A MET* 6.5 0.9 - - - -
72A GLN* 3.5 14.4 - - - +
17P LEU* 1.3 82.3 - - + +
19P PHE* 1.3 65.4 + - - +
20P GLU* 3.7 7.0 + - - +
21P HIS* 3.0 30.4 + - + +
22P TRP* 3.1 16.0 + - - -
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Residues in contact with PHE 19 (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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58A GLY* 3.4 22.0 - - - -
61A ILE* 3.6 28.3 - - + -
62A MET* 3.7 23.6 - - + -
67A TYR* 3.6 34.1 - + + -
72A GLN* 3.1 35.7 + - - +
75A VAL* 4.2 2.0 - - + -
93A VAL* 4.0 13.0 - - + -
18P THR* 1.3 72.8 - - - +
20P GLU* 1.3 71.8 + - + +
22P TRP* 3.4 2.8 + - - +
23P TRP* 2.9 68.3 + + + +
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Residues in contact with GLU 20 (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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58A GLY 6.0 0.5 - - - -
59A GLN* 3.8 21.7 + - - -
62A MET* 3.6 37.3 - - + +
18P THR* 3.2 7.2 + - - +
19P PHE* 1.3 91.2 - - + +
21P HIS* 1.3 59.9 - - - +
23P TRP* 4.2 4.5 - - + -
24P ALA* 2.8 32.9 + - - +
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Residues in contact with HIS 21 (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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17P LEU 3.6 24.1 + - - +
18P THR* 3.0 24.8 + - - +
20P GLU* 1.3 79.6 - - - +
22P TRP* 1.3 85.7 + + - +
24P ALA* 3.3 10.9 + - - +
25P GLN* 3.4 33.2 + - + +
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Residues in contact with TRP 22 (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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72A GLN 4.1 1.3 - - - +
73A HIS* 3.5 30.7 + - + +
93A VAL* 3.6 20.3 - - + +
94A LYS* 3.6 42.4 - - + -
96A HIS* 4.7 1.0 + - - -
17P LEU* 3.1 48.0 + - + +
18P THR 3.1 20.5 + - - -
19P PHE 3.8 4.0 - - - +
21P HIS* 1.3 85.3 - + - +
23P TRP* 1.3 64.0 + - - +
25P GLN* 3.1 56.3 + - - +
26P LEU* 3.6 7.6 - - - +
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Residues in contact with TRP 23 (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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54A LEU* 2.7 56.2 + - + +
55A PHE* 5.2 2.5 - - - -
57A LEU* 3.7 22.9 - - + -
58A GLY* 3.1 23.2 - - - -
61A ILE* 3.8 16.4 - - + -
91A PHE* 4.5 6.1 - + - -
93A VAL* 3.6 28.8 - - + +
99A ILE* 4.2 24.7 - - + -
19P PHE* 2.9 45.0 + + + +
20P GLU* 3.9 5.2 - - + +
22P TRP* 1.3 75.2 - - - +
24P ALA* 1.3 66.1 + - - +
25P GLN 3.2 0.7 + - - -
26P LEU* 3.2 22.9 + - + +
27P THR* 4.4 4.5 + - + +
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Residues in contact with ALA 24 (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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20P GLU 2.8 19.5 + - - +
21P HIS* 3.6 7.4 - - - +
22P TRP 3.3 0.4 - - - -
23P TRP* 1.3 78.7 - - - +
25P GLN* 1.3 57.4 + - - +
27P THR* 3.1 32.1 + - - +
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Residues in contact with GLN 25 (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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16A GLY* 4.9 11.7 - - - -
17A SER* 3.0 31.6 + - - +
94A LYS* 5.4 2.6 - - - +
96A HIS* 3.9 17.8 + - + +
21P HIS* 3.4 36.2 + - + +
22P TRP* 3.1 41.1 + - - +
24P ALA* 1.3 76.2 - - + +
26P LEU* 1.3 61.9 + - - +
27P THR 3.2 2.5 + - - +
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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