Contacts of the helix formed by residues 53 - 60 (chain A) in PDB entry 2P7I
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 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A SER* 2.9 11.0 + - - -
51A PHE 3.3 1.4 + - - -
52A LYS* 1.3 78.4 - - - +
54A ASP* 1.3 64.9 + - - +
55A PHE 3.3 2.5 - - - -
56A THR* 3.5 21.0 - - - -
57A SER* 3.0 23.6 + - - -
79A ALA* 3.8 12.8 - - - +
82A ARG* 3.9 5.0 - - - -
83A LEU* 3.7 9.2 - - - +
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Residues in contact with ASP 54 (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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25A PHE* 3.2 45.8 - - + -
29A HIS* 4.2 13.1 + - + +
50A SER 4.5 0.6 + - - -
51A PHE* 5.1 2.3 - - - -
52A LYS* 3.4 24.9 + - - +
53A GLY* 1.3 76.5 - - - +
55A PHE* 1.3 59.1 + - - +
57A SER* 2.8 21.1 + - - -
58A ARG* 4.2 8.5 + - - +
82A ARG* 3.4 26.8 + - - +
251A TRS 6.0 1.3 + - - +
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Residues in contact with PHE 55 (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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29A HIS* 3.6 56.6 - + + -
32A MSE 3.9 17.3 - - + -
33A VAL* 3.7 20.0 - - + -
36A PHE* 3.9 18.4 - + - -
47A GLU* 3.6 15.7 + - - +
53A GLY 3.3 0.2 - - - -
54A ASP* 1.3 75.2 - - - +
56A THR* 1.3 66.4 + - - +
57A SER 3.1 1.8 - - - -
58A ARG* 3.0 17.5 + - - +
59A LEU* 3.2 44.3 + - + +
107A VAL* 3.9 17.3 - - + -
109A THR* 4.3 5.2 - - - -
251A TRS 4.0 19.6 + - - +
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Residues in contact with THR 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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47A GLU* 2.4 35.2 + - - +
50A SER* 3.9 6.6 - - - -
53A GLY* 3.3 19.1 + - - -
55A PHE* 1.3 77.9 - - - +
57A SER* 1.3 56.6 - - - +
59A LEU* 3.1 6.8 + - - +
60A GLN* 2.9 27.4 + - - +
66A ILE* 4.2 8.1 - - + -
68A CYS* 3.6 19.7 - - - -
83A LEU* 3.7 14.7 - - + +
87A ILE* 3.7 22.9 - - + -
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Residues in contact with SER 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 GLY 3.0 8.2 + - - -
54A ASP 2.8 23.6 + - - -
56A THR* 1.3 77.6 - - - +
58A ARG* 1.3 64.7 + - - +
60A GLN* 3.5 18.7 + - - +
61A GLU* 3.8 13.0 - - - +
82A ARG* 4.2 13.1 + - - -
83A LEU* 3.7 22.6 - - - +
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Residues in contact with ARG 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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25A PHE 3.5 17.4 + - - -
26A ASP* 4.9 5.7 + - - +
29A HIS* 3.6 36.0 + - - +
30A PRO* 3.7 29.2 - - - +
33A VAL* 3.9 16.8 - - + +
54A ASP 4.2 9.2 + - - +
55A PHE* 3.0 11.1 + - + +
57A SER* 1.3 82.2 + - - +
59A LEU* 1.3 66.9 + - - +
61A GLU* 3.2 24.1 + - - +
62A HIS* 3.6 10.2 + - - -
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Residues in contact with LEU 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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33A VAL* 4.4 9.0 - - + -
36A PHE* 5.0 1.6 - - + -
40A PHE* 4.1 26.5 - - + -
45A LEU* 4.1 31.4 - - + -
47A GLU* 4.2 17.7 - - - +
55A PHE* 3.2 46.6 + - + +
56A THR* 3.1 7.3 + - - +
58A ARG* 1.3 72.9 - - - +
60A GLN* 1.3 57.0 + - - +
61A GLU 3.0 5.6 - - - -
62A HIS* 2.8 24.8 + - - +
63A PHE* 3.1 12.9 + - + -
66A ILE* 3.9 13.1 - - + +
107A VAL* 4.3 8.7 - - + -
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Residues in contact with GLN 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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56A THR 2.9 16.1 + - - +
57A SER* 3.5 13.5 - - - +
58A ARG 3.2 0.4 - - - -
59A LEU* 1.3 77.7 - - - +
61A GLU* 1.3 64.5 + - - +
62A HIS 3.1 0.8 + - - -
63A PHE 3.4 19.6 + - - +
64A ASN* 4.8 4.9 - - - +
66A ILE* 3.7 13.9 - - + -
83A LEU* 3.5 17.3 - - - +
84A LYS* 2.8 63.3 + - + +
85A ASP 3.4 6.5 + - - -
86A GLY 5.1 0.2 - - - -
87A ILE* 3.5 17.1 - - + +
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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