Contacts of the helix formed by residues 55 - 61 (chain A) in PDB entry 1PTG
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 PHE 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A SER* 3.8 27.1 - - - -
35A GLY* 3.7 11.0 - - - -
37A PHE* 3.4 29.1 - + - -
54A ASP* 1.3 76.7 - - + +
56A ARG* 1.3 56.5 + - - +
58A GLN* 3.3 12.3 - - - +
59A MET* 2.9 41.9 + - + +
66A PHE* 3.9 13.5 - + - -
68A ILE* 4.2 3.4 - - + -
80A LEU* 4.0 15.7 - - + -
89A VAL* 3.7 14.4 - - + -
93A GLU* 4.9 4.5 - - + -
94A PHE* 3.7 34.8 - + + -
97A GLU* 4.2 30.3 - - + -
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Residues in contact with ARG 56 (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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54A ASP* 3.2 10.0 + - - +
55A PHE* 1.3 76.4 - - - +
57A TYR* 1.3 57.6 + - - +
59A MET* 3.2 4.4 + - - +
60A ASP* 2.8 70.1 + - - +
97A GLU* 3.7 21.9 + - + +
100A GLN* 3.7 8.1 - - - +
101A PHE* 3.2 50.0 - - - +
104A ASP* 3.4 30.1 + - - +
105A ASN* 4.4 3.8 - - - +
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Residues in contact with TYR 57 (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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53A TYR* 3.1 61.9 - + + -
54A ASP* 2.8 21.5 + - - +
56A ARG* 1.3 74.0 - - - +
58A GLN* 1.3 72.7 + - + +
60A ASP* 3.0 12.3 + - - -
61A HIS* 3.0 63.5 + + + -
276A ILE* 3.9 13.7 - - + -
277A ASN* 3.5 11.0 - - - -
278A GLU* 3.6 14.2 + - - +
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Residues in contact with GLN 58 (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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31A THR* 3.3 18.3 + - + -
34A SER* 3.2 25.8 + - - -
37A PHE* 4.0 1.6 - - - -
51A GLN* 3.8 12.2 - - - +
53A TYR* 2.9 24.8 + - + +
54A ASP 2.9 24.8 + - - +
55A PHE* 3.3 10.1 - - - +
57A TYR* 1.3 82.9 - - + +
59A MET* 1.3 60.3 + - - +
61A HIS* 3.2 12.7 + - - +
63A ALA* 3.0 29.4 + - + +
66A PHE* 3.2 26.6 - - + -
276A ILE* 4.1 19.5 - - + +
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Residues in contact with MET 59 (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 TRP 4.0 1.4 - - - +
55A PHE* 2.9 29.1 + - + +
56A ARG* 3.2 6.9 + - - +
58A GLN* 1.3 69.8 - - - +
60A ASP* 1.3 59.3 + - - +
61A HIS 2.8 10.0 + - - -
62A GLY 3.1 2.9 + - - -
63A ALA 3.7 10.3 - - - +
64A ARG* 2.6 25.0 + - - -
66A PHE* 3.4 28.0 - - + -
94A PHE* 4.0 10.1 - - + -
97A GLU 4.2 5.4 - - - +
98A ALA* 3.6 32.5 - - + +
101A PHE* 3.5 48.4 - - + -
110A ILE* 3.9 15.5 - - + -
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Residues in contact with ASP 60 (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 TRP* 3.3 21.6 - - - +
11A SER* 3.1 28.8 + - - +
56A ARG* 2.8 60.5 + - - +
57A TYR* 3.0 6.1 + - - +
59A MET* 1.3 71.7 - - - +
61A HIS* 1.3 68.2 + - + +
62A GLY 3.5 0.9 - - - -
101A PHE* 3.9 6.2 - - - -
105A ASN* 4.6 0.2 + - - -
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Residues in contact with HIS 61 (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 TRP* 4.0 16.6 - + - -
57A TYR* 3.0 67.5 + + - +
58A GLN* 3.4 7.4 - - - +
59A MET 2.8 1.6 - - - -
60A ASP* 1.3 89.6 + - + +
62A GLY* 1.3 59.7 + - - +
63A ALA 3.3 2.8 + - - -
276A ILE* 4.0 12.9 - - + +
277A ASN 4.6 1.1 - - - -
278A GLU* 3.0 24.3 + - - -
285A TYR* 3.0 55.7 - + + +
289A ILE* 4.4 1.2 - - - +
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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