Contacts of the helix formed by residues 16 - 20 (chain A) in PDB entry 1ZJA
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 TYR 16 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLN 4.1 0.4 + - - -
15A VAL* 1.3 69.9 - - - +
17A PRO* 1.3 69.2 - - + +
18A ARG* 3.2 20.4 - - + -
19A SER* 2.9 38.2 + - - -
20A PHE 3.3 8.0 + - - -
52A ASN* 3.3 24.7 - - + +
62A ASN* 3.3 40.4 + - + +
64A TYR* 5.2 2.4 - + - -
326A HIS* 3.5 34.3 - + + -
364A PHE* 4.3 12.6 - + + -
365A GLN* 2.8 23.2 + - - +
418A ARG* 3.4 36.6 + - + -
437A TRP* 4.3 0.4 - + - -
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Residues in contact with PRO 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A VAL* 3.2 22.8 - - + +
16A TYR* 1.3 81.9 - - + +
18A ARG* 1.3 63.1 + - - +
19A SER 3.0 1.6 + - - -
20A PHE* 3.3 9.2 + - + +
29A GLY* 3.2 24.7 - - - +
30A ASP 3.8 7.1 + - - +
31A PHE* 5.5 5.6 - - + -
34A LEU* 5.4 5.4 - - + -
51A ILE* 4.1 24.0 - - + -
52A ASN* 3.7 19.7 - - + +
54A HIS* 5.6 0.2 - - + -
76A TYR* 3.7 35.0 - - + +
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Residues in contact with ARG 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR* 3.1 15.7 + - + -
17A PRO* 1.3 77.9 - - - +
19A SER* 1.3 56.4 + - - +
28A ILE* 4.1 33.8 - - + +
29A GLY 2.9 20.9 + - - +
59A ASN* 4.1 28.3 + - - +
62A ASN* 3.7 32.0 + - - +
73A MET* 5.4 1.6 - - - -
75A GLU* 5.3 1.4 - - - +
76A TYR* 3.5 26.6 + - - +
383A ASP* 5.2 2.8 + - - -
431A PHE* 3.6 1.2 - - - -
437A TRP* 3.2 67.4 + - + +
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Residues in contact with SER 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A TYR* 2.9 14.8 + - - -
18A ARG* 1.3 75.4 - - - +
20A PHE* 1.3 60.0 + - - +
365A GLN* 3.4 16.3 + - - -
418A ARG 2.7 29.2 + - - -
419A THR 3.9 8.1 - - - -
420A PRO* 3.5 4.1 - - - +
421A PHE 2.9 24.8 + - - -
431A PHE* 3.6 10.5 - - - -
437A TRP* 3.0 21.9 + - - -
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Residues in contact with PHE 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A TYR* 3.8 24.7 - + - -
15A VAL* 3.8 17.9 - - + -
16A TYR 3.3 5.8 + - - +
17A PRO* 3.3 7.7 + - + +
19A SER* 1.3 80.3 - - - +
21A LYS* 1.3 64.0 + - + +
34A LEU* 3.8 30.1 - - + -
37A LYS* 3.7 24.9 - - + -
41A LEU* 4.2 20.0 - - + -
365A GLN* 3.4 26.7 - - - +
421A PHE* 3.6 14.0 - + - +
423A TRP* 2.8 50.5 + + - -
431A PHE* 3.4 9.4 - - - -
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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