Contacts of the helix formed by residues 3 - 15 (chain A) in PDB entry 2JZ3
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 3 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ALA* 1.3 70.5 - - + +
4A LEU* 1.3 70.9 + - - +
5A GLN* 3.4 22.5 + - + +
6A HIS* 3.9 5.7 + - + +
7A LEU* 3.6 7.1 - - - +
38C THR 4.8 0.2 - - - -
73C VAL* 4.5 4.0 - - - +
76C TYR* 2.8 31.8 - - - +
77C PHE* 4.4 11.3 - - - -
80C LYS* 4.2 3.1 - - - +
107C ALA 4.2 5.0 + - - -
110C LEU 4.3 4.0 + - - -
111C ASP 3.3 24.3 + - - +
112C CYS* 3.3 38.5 + - + -
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Residues in contact with LEU 4 (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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3A THR* 1.3 79.5 + - - +
5A GLN* 1.3 63.4 + - - +
6A HIS 3.3 0.4 - - - -
7A LEU* 3.9 7.4 - - + -
8A CYS* 2.9 22.3 + - + +
72C LYS* 3.2 10.3 - - + -
73C VAL* 2.7 53.2 - - + +
76C TYR* 3.3 8.6 - - + +
93C PHE* 4.4 12.8 - - + -
95C ILE* 4.8 4.7 - - + -
103C LEU* 3.2 50.5 - - + -
107C ALA* 3.2 4.9 - - + -
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Residues in contact with GLN 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A THR* 3.2 12.0 + - + +
4A LEU* 1.3 80.7 - - - +
6A HIS* 1.3 98.0 + - - +
8A CYS* 3.6 3.0 + - - +
9A ARG* 3.4 20.8 + - + +
103C LEU 4.8 0.4 - - - -
104C LEU* 5.3 1.1 - - - +
107C ALA* 3.1 19.3 - - - +
108C ASN* 3.1 55.5 + - + +
111C ASP* 3.9 16.0 + - - +
112C CYS* 4.6 5.1 - - - +
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Residues in contact with HIS 6 (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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2A ALA* 4.0 31.6 - - + -
3A THR* 3.9 3.2 + - + -
4A LEU 3.3 0.2 - - - -
5A GLN* 1.3 115.2 + - + +
7A LEU* 1.3 71.0 + - + +
9A ARG* 3.0 17.9 + - - +
10A LYS* 3.3 10.0 + - - +
112C CYS* 5.7 6.5 - - - -
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Residues in contact with LEU 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ALA* 4.5 3.8 - - + -
3A THR 3.6 3.8 - - - +
4A LEU* 3.4 12.3 + - + +
6A HIS* 1.3 84.6 - - + +
8A CYS* 1.3 61.3 + - - +
10A LYS* 3.2 26.4 - - + +
76C TYR* 3.4 30.3 - - + +
92C GLU* 3.5 20.9 - - + +
93C PHE* 2.9 57.0 - - + +
95C ILE* 3.2 19.7 - - + +
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Residues in contact with CYS 8 (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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4A LEU* 2.9 20.6 + - + +
5A GLN 3.7 5.4 - - - +
6A HIS 3.1 0.2 - - - -
7A LEU* 1.3 77.5 - - - +
9A ARG* 1.3 62.7 + - - +
10A LYS 3.3 0.7 + - - -
11A THR* 3.5 11.8 + - - -
12A VAL* 3.5 14.3 - - - +
95C ILE* 4.3 9.3 - - - +
100C ALA* 2.7 30.0 - - - +
103C LEU* 3.8 15.0 - - + +
104C LEU* 2.8 39.3 - - - +
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Residues in contact with ARG 9 (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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5A GLN* 3.4 11.2 + - + +
6A HIS* 3.0 14.5 + - - +
8A CYS* 1.3 79.0 - - - +
10A LYS* 1.3 58.8 + - - +
12A VAL* 3.6 32.4 - - - +
13A ASN* 2.6 52.2 + - - +
104C LEU* 4.4 21.4 - - + +
108C ASN* 6.3 0.7 - - - +
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Residues in contact with LYS 10 (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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6A HIS 3.3 5.7 + - - +
7A LEU* 3.2 23.3 + - + +
8A CYS 3.2 0.2 - - - -
9A ARG* 1.3 78.4 - - - +
11A THR* 1.3 60.9 + - - +
13A ASN* 4.0 4.6 + - - +
14A GLY* 3.0 24.9 + - - -
15A HIS 3.8 0.3 + - - -
92C GLU* 4.8 18.6 - - - +
93C PHE 3.7 17.8 + - - -
94C PRO* 4.7 2.0 - - - +
95C ILE* 4.2 25.6 + - + +
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Residues in contact with THR 11 (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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7A LEU 4.0 0.4 + - - -
8A CYS 3.5 3.4 + - - -
9A ARG 3.2 0.2 - - - -
10A LYS* 1.3 78.9 - - - +
12A VAL* 1.3 60.4 + - + +
15A HIS* 2.4 71.0 + - + +
95C ILE* 2.6 51.1 + - + +
96C ALA* 4.8 12.8 - - - +
97C PRO* 5.3 0.7 - - + -
100C ALA* 5.0 2.2 - - + -
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Residues in contact with VAL 12 (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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8A CYS* 3.5 17.3 - - - +
9A ARG* 3.2 28.4 + - - +
11A THR* 1.3 82.9 - - + +
13A ASN* 1.3 63.4 + - - +
15A HIS 3.0 12.3 - - - +
100C ALA* 6.2 0.4 - - + -
101C LEU* 5.8 5.8 - - + -
104C LEU* 4.0 28.9 - - + -
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Residues in contact with ASN 13 (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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9A ARG* 2.6 37.9 + - + +
10A LYS* 4.0 5.0 + - - +
12A VAL* 1.3 77.1 - - - +
14A GLY* 1.3 59.2 + - - +
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Residues in contact with GLY 14 (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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10A LYS 3.0 13.4 + - - -
13A ASN* 1.3 82.9 - - - +
15A HIS* 1.3 64.5 + - - +
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Residues in contact with HIS 15 (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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10A LYS 3.8 1.4 + - - -
11A THR* 2.4 61.7 + - + +
12A VAL* 3.0 18.5 - - - +
14A GLY* 1.3 73.8 - - - -
95C ILE 6.2 0.2 - - - -
96C ALA* 6.0 0.4 - - - -
97C PRO* 4.0 35.0 - - + +
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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