Contacts of the helix formed by residues 71 - 79 (chain A) in PDB entry 2XMS
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 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A PRO 3.2 13.1 + - - +
68A LEU 3.1 15.7 + - - +
70A GLN* 1.3 77.8 - - - +
72A GLU* 1.3 80.3 + - + +
73A ASP* 3.3 39.5 - - + -
74A MET* 3.0 15.1 + - + +
75A GLN* 3.0 11.3 + - - +
286A PRO* 3.9 24.0 - - + -
287A GLY* 3.4 33.4 - - - -
290A THR* 3.9 9.4 - - - +
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Residues in contact with GLU 72 (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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70A GLN 3.4 4.8 + - - -
71A PHE* 1.3 85.2 - - + +
73A ASP* 1.3 86.7 + - - +
75A GLN* 3.3 18.5 + - - +
76A GLU* 3.4 12.0 + - - +
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Residues in contact with ASP 73 (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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71A PHE* 3.3 23.9 - - + -
72A GLU* 1.3 91.5 - - - +
74A MET* 1.3 62.3 + - - +
76A GLU* 3.5 25.9 + - - +
77A ILE* 3.5 16.3 + - - +
287A GLY* 5.1 2.6 - - - +
290A THR* 3.7 16.9 - - + +
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Residues in contact with MET 74 (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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68A LEU* 3.2 59.7 - - + +
69A PHE* 3.9 18.6 - - + +
71A PHE* 3.0 8.3 + - + +
73A ASP* 1.3 76.9 - - - +
75A GLN* 1.3 57.6 + - - +
77A ILE* 2.9 9.7 + - - +
78A ILE* 2.9 50.4 + - + +
289A LEU 4.8 0.4 - - - +
290A THR* 3.4 26.9 - - - +
293A PHE* 3.8 33.4 - - + -
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Residues in contact with GLN 75 (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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69A PHE 3.7 13.5 - - - +
70A GLN* 3.9 26.5 + - - +
71A PHE 3.0 14.4 + - - +
72A GLU* 3.3 11.2 + - - +
74A MET* 1.3 75.9 - - - +
76A GLU* 1.3 57.1 + - - +
78A ILE* 3.7 15.7 - - - +
79A GLN* 3.1 35.5 + - - +
83A ARG* 4.8 5.9 + - - -
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Residues in contact with GLU 76 (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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72A GLU 3.4 7.7 + - - +
73A ASP* 3.7 22.9 - - - +
74A MET 3.2 0.8 - - - -
75A GLN* 1.3 75.7 - - - +
77A ILE* 1.3 66.6 + - + +
79A GLN* 3.5 26.6 - - - +
80A ASN* 4.3 7.4 + - - -
294A LYS* 5.9 2.1 + - - +
304A ALA 4.9 8.6 - - - +
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Residues in contact with ILE 77 (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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73A ASP 3.5 7.4 + - - +
74A MET* 2.9 12.5 + - - +
76A GLU* 1.3 83.1 - - + +
78A ILE* 1.3 62.5 + - + +
80A ASN* 3.1 22.9 + - - +
81A PHE* 3.7 14.3 - - + -
290A THR* 3.8 27.6 - - + +
293A PHE* 4.1 12.1 - - + -
294A LYS* 3.7 35.2 - - + +
297A LEU* 3.6 28.0 - - + -
304A ALA* 4.3 22.0 - - + +
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Residues in contact with ILE 78 (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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51A ILE* 4.1 21.8 - - + -
69A PHE* 3.2 45.1 - - + +
74A MET* 2.9 40.8 + - + +
75A GLN* 3.7 15.9 - - - +
77A ILE* 1.3 73.5 - - + +
79A GLN* 1.3 62.7 + - - +
80A ASN 2.9 6.2 + - - -
81A PHE* 2.9 28.0 + - - +
83A ARG* 2.9 40.7 + - - +
1305A CL 4.2 2.5 - - + -
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Residues in contact with GLN 79 (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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43A THR* 5.0 10.9 + - - +
45A TYR* 5.3 0.5 - - - -
75A GLN 3.1 27.3 + - - +
76A GLU* 3.5 23.5 - - - +
78A ILE* 1.3 75.7 - - - +
80A ASN* 1.3 70.2 + - - +
81A PHE 3.3 4.1 + - - +
83A ARG* 4.5 5.7 + - - +
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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