Contacts of the helix formed by residues 4 - 13 (chain a) in PDB entry 4PJO
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 GLY 4 (chain a).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3a ILE* 1.3 84.8 - - - +
5a VAL* 1.3 67.1 + - - -
6a PRO* 3.2 10.2 - - - -
7a ILE* 3.3 6.6 + - - +
8a LYS* 3.2 21.1 + - - +
35b ASP* 4.2 16.4 - - - -
36b LYS* 6.4 0.2 - - - +
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Residues in contact with VAL 5 (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 ILE 3.8 1.6 + - - -
4a GLY* 1.3 71.4 - - - -
6a PRO* 1.3 69.6 - - + +
8a LYS* 3.3 15.4 + - + +
9a VAL* 3.1 20.6 + - - +
82a MET* 3.9 31.6 - - + +
83a LEU* 3.9 11.2 - - + -
33b ALA* 3.8 24.7 - - + -
34b PHE 4.4 7.8 + - - +
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Residues in contact with PRO 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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4a GLY 3.3 4.7 - - - -
5a VAL* 1.3 90.8 - - + +
7a ILE* 1.3 61.2 + - - +
9a VAL* 3.3 5.8 + - + +
10a LEU 3.1 15.8 + - - -
33b ALA 4.2 4.3 - - - -
34b PHE* 3.4 38.6 - - - +
35b ASP* 3.5 22.7 - - + +
39b ASN* 4.0 16.4 - - + +
40b LEU 4.7 1.6 - - - +
41b ILE* 3.8 24.8 - - + +
71b LEU* 3.9 13.8 - - + +
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Residues in contact with ILE 7 (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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1292 U 4.0 11.2 - - - +
3a ILE* 4.1 18.8 - - + -
4a GLY 3.3 9.7 + - - +
6a PRO* 1.3 75.6 - - + +
8a LYS* 1.3 66.9 + - - +
10a LEU* 3.0 20.4 + - + +
11a HIS* 3.0 42.1 + - + +
36a GLU 4.8 0.7 - - - +
37a ASP* 3.5 34.5 - - - +
39a MET* 3.6 28.0 - - + -
35b ASP* 4.3 13.9 - - - +
37b HIS* 6.1 1.1 - - + -
39b ASN* 4.4 3.4 - - - +
71b LEU* 5.3 2.0 - - + -
21l ARG* 5.3 0.2 - - - +
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Residues in contact with LYS 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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3a ILE* 4.0 30.6 + - + +
4a GLY 3.2 15.8 + - - +
5a VAL* 3.5 16.7 - - + +
7a ILE* 1.3 74.8 - - - +
9a VAL* 1.3 59.5 + - - +
11a HIS* 2.8 26.9 + - - +
12a GLU* 2.9 14.9 + - - +
82a MET* 3.9 22.7 - - + -
4l PHE* 4.2 19.1 - - + -
5l TYR* 3.1 40.7 + - - +
7l ASP* 3.3 18.8 + - - +
21l ARG* 5.9 1.8 - - - +
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Residues in contact with VAL 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 VAL 3.1 15.1 + - - +
6a PRO* 3.4 10.3 - - + +
7a ILE 3.1 0.2 - - - -
8a LYS* 1.3 80.7 - - - +
10a LEU* 1.3 61.1 + - - +
12a GLU* 3.3 9.7 + - - +
13a ALA* 3.3 15.2 + - - +
73a LEU* 3.8 22.1 - - + +
77a LEU* 4.2 19.9 - - + +
80a ALA* 6.0 0.9 - - + -
82a MET* 4.1 13.7 - - + -
83a LEU* 3.9 35.9 - - + -
41b ILE* 4.1 13.9 - - + -
69b LEU* 4.6 6.5 - - + -
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Residues in contact with LEU 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 PRO 3.1 6.4 + - - +
7a ILE* 3.0 17.1 + - + +
9a VAL* 1.3 76.5 - - - +
11a HIS* 1.3 62.6 + - - +
13a ALA* 3.0 15.4 + - - +
14a GLU 3.5 4.2 + - - -
32a LEU* 3.9 19.6 - - + +
35a ALA* 3.7 22.0 - - + -
36a GLU 4.6 3.6 - - - +
39a MET* 4.0 34.1 - - + -
41a CYS* 4.5 5.2 - - - -
71a LEU* 4.4 20.2 - - + -
73a LEU* 4.0 23.5 - - + +
71b LEU* 3.7 17.5 - - + -
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Residues in contact with HIS 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 ILE* 3.0 32.4 + - + +
8a LYS* 2.8 11.1 + - - +
10a LEU* 1.3 77.5 - - + +
12a GLU* 1.3 59.0 + - - +
14a GLU* 3.0 59.7 + - - +
34a GLU* 5.3 0.9 + - - -
35a ALA* 2.9 17.6 + - + -
36a GLU* 3.7 16.3 - - - -
37a ASP* 3.1 28.3 + - - -
3k GLN* 5.6 0.2 + - - -
21l ARG* 4.0 17.7 + - - -
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Residues in contact with GLU 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 LYS* 2.9 11.7 + - - +
9a VAL* 3.5 13.9 - - - +
10a LEU 3.1 0.2 - - - -
11a HIS* 1.3 78.4 - - - +
13a ALA* 1.3 59.3 + - - +
14a GLU 3.6 5.5 + - - +
16a HIS* 3.9 8.1 + - - -
77a LEU* 3.4 24.8 - - + +
80a ALA* 4.5 11.4 - - + -
82a MET* 3.4 21.3 - - + +
3k GLN* 5.6 2.8 + - - +
13k PHE* 5.2 1.5 - - + -
8l TYR* 3.0 42.5 + - - +
30l HIS* 5.6 1.4 + - - -
34l VAL* 5.5 0.9 - - - +
38l TYR* 4.6 1.3 - - - +
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Residues in contact with ALA 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 VAL 3.3 7.9 + - - +
10a LEU 3.0 12.3 + - - +
12a GLU* 1.3 76.1 - - - +
14a GLU* 1.3 64.5 + - - +
15a GLY 3.3 0.2 + - - -
16a HIS* 3.1 24.9 + - - +
18a VAL* 4.2 4.7 - - + +
32a LEU* 3.6 11.3 - - + +
73a LEU* 4.0 25.8 - - + -
74a PRO* 4.1 6.5 - - + -
77a LEU* 3.9 19.0 - - + +
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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