Contacts of the helix formed by residues 71 - 79 (chain B) in PDB entry 2XMR
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B PRO 3.3 12.7 + - - +
68B LEU 3.1 17.6 + - - +
70B GLN* 1.3 78.0 - - - +
72B GLU* 1.3 72.6 + - + +
73B ASP* 3.4 41.7 - - + -
74B MET* 3.0 6.3 + - + +
75B GLN* 3.0 19.4 + - - +
286B PRO* 4.1 22.7 - - + -
287B GLY* 3.5 31.0 - - - -
290B THR* 3.8 12.8 - - - -
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Residues in contact with GLU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B GLN 3.4 4.5 + - - +
71B PHE* 1.3 78.4 - - + +
73B ASP* 1.3 69.6 + - - +
75B GLN* 3.3 9.2 + - - +
76B GLU* 3.1 33.0 + - + +
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Residues in contact with ASP 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B PHE* 3.3 32.2 - - + -
72B GLU* 1.3 82.6 - - - +
74B MET* 1.3 60.9 + - - +
76B GLU* 3.5 21.4 - - - +
77B ILE* 3.3 25.8 + - - +
287B GLY* 4.8 6.9 - - - +
290B THR* 3.6 13.7 - - + +
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Residues in contact with MET 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B LEU* 3.3 52.3 - - + +
69B PHE* 4.0 27.6 - - + +
71B PHE* 3.0 5.7 + - + +
73B ASP* 1.3 77.5 - - - +
75B GLN* 1.3 65.7 + - - +
77B ILE* 3.0 18.5 + - - +
78B ILE* 3.1 32.1 + - + +
289B LEU* 5.0 1.3 - - + +
290B THR* 3.5 38.5 - - - +
293B PHE* 3.7 33.2 - - + -
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Residues in contact with GLN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B PHE 2.6 25.2 - - - +
70B GLN* 4.3 12.6 - - - +
71B PHE 3.0 12.8 + - - +
72B GLU* 3.3 11.0 + - - +
74B MET* 1.3 75.9 - - - +
76B GLU* 1.3 62.2 + - - +
78B ILE* 3.5 9.5 + - - +
79B GLN* 3.3 24.1 + - - +
83B ARG* 4.0 14.6 - - - +
1305B ACT 3.0 19.5 + - - +
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Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ASP* 3.1 46.1 - - - +
72B GLU* 3.1 20.5 + - + +
73B ASP* 3.5 23.8 - - - +
74B MET 3.2 0.2 - - - -
75B GLN* 1.3 77.3 - - + +
77B ILE* 1.3 62.2 + - + +
79B GLN* 2.7 39.1 + - - +
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Residues in contact with ILE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ASP 3.3 13.9 + - - +
74B MET* 3.0 25.5 + - - +
76B GLU* 1.3 81.6 - - + +
78B ILE* 1.3 59.7 + - + +
79B GLN* 3.4 1.8 + - - +
80B ASN 4.9 0.2 + - - -
81B PHE* 4.0 15.4 - - - -
290B THR* 3.7 26.9 - - + +
293B PHE* 3.7 21.3 - - + +
294B LYS* 3.7 43.5 - - + +
297B LEU* 4.6 8.6 - - + +
304B ALA* 4.8 9.0 - - - +
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Residues in contact with ILE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ILE* 3.7 23.3 - - + -
69B PHE* 3.7 25.8 - - + -
74B MET* 3.1 39.5 + - + +
75B GLN* 3.6 23.8 - - - +
77B ILE* 1.3 78.0 - - + +
79B GLN* 1.3 58.5 + - - +
80B ASN 3.2 2.9 - - - -
81B PHE* 3.0 27.8 + - + +
83B ARG* 3.2 44.1 + - - +
293B PHE* 4.2 8.5 - - + -
297B LEU* 5.5 0.2 - - + -
1305B ACT 4.1 0.2 - - + -
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Residues in contact with GLN 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LEU 4.7 2.6 - - - +
144A ASN 3.8 19.6 + - - +
145A HIS* 4.9 3.4 + - - +
146A PRO* 3.9 24.9 - - - +
147A ASP* 4.5 7.9 + - - -
42B GLY* 5.9 0.2 - - - -
43B THR* 4.3 16.8 + - - +
75B GLN* 3.3 13.8 + - - +
76B GLU* 2.7 29.3 + - - +
77B ILE 3.4 1.9 - - - -
78B ILE* 1.3 76.7 - - - +
80B ASN* 1.3 76.3 + - - +
81B PHE 3.4 3.9 + - - +
83B ARG* 4.5 7.9 + - - +
304B ALA* 5.0 2.5 - - - +
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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