Contacts of the helix formed by residues 66 - 75 (chain F) in PDB entry 7CR3
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 66 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10F ILE* 3.8 11.2 - - + -
13F PHE 3.4 24.5 - - - -
14F LYS* 3.6 41.5 - - + -
17F PHE* 3.3 39.8 - + + -
26F GLY 4.4 1.7 + - - +
65F ASP* 1.3 73.9 - - - +
67F PRO* 1.3 68.5 - - + +
69F PHE* 3.4 6.0 + + - -
70F LEU* 2.9 71.9 + - + +
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Residues in contact with PRO 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F ASP* 3.4 17.0 - - + +
66F PHE* 1.3 95.0 - - + +
68F GLU* 1.3 59.1 + - + +
70F LEU* 3.3 12.1 + - + +
71F THR* 2.9 35.8 + - + +
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Residues in contact with GLU 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F VAL* 3.5 31.2 - - + +
57F ASP* 2.9 27.8 - - - +
58F ALA* 3.1 33.3 + - + +
59F ASP* 3.6 11.6 + - - +
64F ILE* 4.3 0.7 - - - -
65F ASP* 2.8 46.7 + - - +
67F PRO* 1.3 71.2 - - + +
69F PHE* 1.3 59.3 + - - +
71F THR* 2.6 23.5 + - - +
72F MET* 3.0 17.3 + - - +
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Residues in contact with PHE 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538A VAL* 4.9 0.4 - - + -
542A ALA* 3.5 29.6 - - + -
546A MET* 4.9 6.1 - - + -
13F PHE* 3.2 38.4 - + + -
16F ALA* 3.6 23.6 - - + -
17F PHE* 4.0 13.2 - + + -
20F PHE* 5.0 8.3 - + - -
28F ILE* 6.0 0.9 - - + -
56F VAL* 3.9 7.7 - - + +
64F ILE* 4.0 12.3 - - + -
65F ASP 3.2 19.9 + - - +
66F PHE* 3.7 17.0 - + - +
67F PRO 3.3 0.2 - - - -
68F GLU* 1.3 77.9 - - - +
70F LEU* 1.3 62.6 + - - +
72F MET* 3.3 11.7 + - + +
73F MET* 3.0 39.2 + - + +
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Residues in contact with LEU 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ILE* 3.6 32.1 - - + +
13F PHE* 3.8 23.4 - - + -
66F PHE* 2.9 64.7 + - + +
67F PRO* 3.5 9.6 - - + +
69F PHE* 1.3 78.3 - - - +
71F THR* 1.3 57.9 + - + +
73F MET* 3.2 6.7 + - - +
74F ALA* 2.8 31.1 + - - +
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Residues in contact with THR 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F VAL 5.1 1.7 + - - -
67F PRO* 2.9 15.8 + - + +
68F GLU* 2.6 27.8 + - - +
70F LEU* 1.3 76.7 - - + +
72F MET* 1.3 60.3 + - - +
74F ALA* 3.3 14.4 + - - +
75F ARG* 3.6 41.2 + - - +
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Residues in contact with MET 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542A ALA 3.7 7.6 - - - +
545A VAL* 3.6 30.9 - - + +
546A MET* 3.6 31.6 - - + -
549A LEU* 3.6 19.1 - - + -
55F GLU 5.9 0.2 - - - +
56F VAL* 3.5 32.8 - - + -
68F GLU 3.0 17.2 + - - +
69F PHE* 3.6 11.4 - - + +
71F THR* 1.3 79.2 + - - +
73F MET* 1.3 92.4 + - + +
75F ARG* 4.2 11.9 + - - +
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Residues in contact with MET 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A PHE* 6.4 0.4 - - + -
538A VAL* 4.2 11.0 - - + -
541A ARG* 4.3 19.7 - - + -
542A ALA* 3.7 16.6 - - - -
545A VAL* 4.2 11.9 - - + -
13F PHE* 3.6 48.6 - - + -
69F PHE* 3.0 41.9 + - + +
70F LEU 3.2 1.8 + - - +
72F MET* 1.3 95.7 - - + +
74F ALA* 1.3 62.6 + - - +
75F ARG 3.5 3.8 - - - +
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Residues in contact with ALA 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F PHE* 5.3 4.0 - - + -
70F LEU 2.8 16.2 + - - +
71F THR* 3.3 10.7 + - - +
73F MET* 1.3 79.1 - - - +
75F ARG* 1.3 65.2 + - + +
76F LYS* 4.0 1.4 + - - +
79F ASP* 5.4 0.5 - - - +
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Residues in contact with ARG 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A PHE* 4.5 10.9 - - - -
71F THR* 3.6 34.5 + - - +
72F MET* 4.2 10.4 + - - +
73F MET 3.5 3.9 - - - +
74F ALA* 1.3 82.2 - - + +
76F LYS* 1.3 62.8 + - - +
79F ASP* 3.8 36.9 + - + +
80F THR* 5.5 3.7 - - + +
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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