Contacts of the helix formed by residues 45 - 57 (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 THR 45 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43F ASN 5.1 0.9 + - - -
44F PRO* 1.3 76.8 - - - +
46F GLU* 1.3 78.6 + - + +
47F ALA* 3.4 11.4 - - + +
48F GLU* 3.2 39.0 + - - +
49F LEU* 3.4 13.3 + - - +
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Residues in contact with GLU 46 (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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30F THR* 4.7 5.0 + - - +
31F LYS* 2.4 34.9 + - - -
45F THR* 1.3 78.6 - - + +
47F ALA* 1.3 64.5 + - - +
48F GLU 3.2 0.7 + - - -
49F LEU* 3.2 13.9 + - - +
50F GLN* 3.1 21.1 + - - +
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Residues in contact with ALA 47 (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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45F THR* 3.4 9.1 - - + +
46F GLU* 1.3 79.0 - - - +
48F GLU* 1.3 57.0 + - + +
50F GLN* 3.1 16.7 - - - +
51F ASP* 2.8 40.5 + - - +
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Residues in contact with GLU 48 (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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550A VAL* 4.5 0.7 - - - +
42F GLN* 4.7 8.7 + - - +
44F PRO* 3.5 20.2 - - + +
45F THR* 3.2 40.1 + - - +
46F GLU 3.1 0.8 - - - -
47F ALA* 1.3 78.0 - - + +
49F LEU* 1.3 62.9 + - + +
51F ASP* 3.1 10.7 + - - +
52F MET* 3.0 28.9 + - + +
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Residues in contact with LEU 49 (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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30F THR* 3.1 37.2 - - - +
31F LYS* 4.8 10.1 - - - +
33F LEU* 3.8 15.4 - - + +
34F GLY* 3.5 32.8 - - - +
37F MET* 5.1 2.5 - - + -
44F PRO* 3.8 21.3 - - + +
45F THR 3.5 15.0 - - - +
46F GLU* 3.2 10.9 + - - +
48F GLU* 1.3 75.2 - - + +
50F GLN* 1.3 62.6 + - - +
52F MET* 3.1 21.4 + - + +
53F ILE* 3.0 24.1 + - - +
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Residues in contact with GLN 50 (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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30F THR* 4.2 2.6 + - - +
46F GLU 3.1 14.0 + - - +
47F ALA* 3.1 26.8 - - - +
49F LEU* 1.3 76.7 - - - +
51F ASP* 1.3 67.3 + - - +
53F ILE* 3.0 25.9 + - + +
54F ASN* 2.6 45.9 + - - +
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Residues in contact with ASP 51 (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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550A VAL* 3.5 16.4 - - + -
554A LYS* 6.0 7.6 - - - +
557A GLU* 5.1 6.2 - - - +
47F ALA* 2.8 27.7 + - - +
48F GLU* 3.4 10.4 - - - +
50F GLN* 1.3 87.5 + - - +
52F MET* 1.3 62.7 + - - +
54F ASN* 3.1 14.9 + - - +
55F GLU* 3.0 27.3 + - - +
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Residues in contact with MET 52 (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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543A VAL* 4.0 14.4 - - + +
546A MET* 3.4 57.0 - - + +
547A ARG* 3.9 20.4 - - + -
550A VAL* 3.5 22.4 - - - +
33F LEU* 4.5 7.6 - - + -
37F MET* 5.5 4.3 - - - -
48F GLU* 3.0 19.4 + - + +
49F LEU* 3.3 22.9 - - + +
51F ASP* 1.3 74.6 - - - +
53F ILE* 1.3 63.3 + - - +
55F GLU* 3.0 7.9 + - - +
56F VAL* 3.0 26.7 + - - +
64F ILE* 5.1 1.1 - - - -
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Residues in contact with ILE 53 (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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28F ILE 5.6 0.2 - - - +
30F THR* 3.6 28.3 - - + +
33F LEU* 4.1 12.3 - - + -
49F LEU 3.0 16.0 + - - +
50F GLN* 3.0 14.8 + - + +
52F MET* 1.3 77.0 - - - +
54F ASN* 1.3 61.4 + - - +
56F VAL 3.1 0.4 + - - +
57F ASP* 2.8 37.2 + - + +
62F GLY* 3.2 37.2 - - - +
63F THR* 4.1 15.7 - - - +
64F ILE* 4.4 14.6 - - + -
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Residues in contact with ASN 54 (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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553A ARG* 2.6 41.7 + - - +
50F GLN* 2.6 48.7 + - - +
51F ASP* 3.1 14.0 + - - +
53F ILE* 1.3 79.0 - - - +
55F GLU* 1.3 54.5 + - - +
57F ASP 4.0 9.1 - - - +
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Residues in contact with GLU 55 (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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546A MET* 4.4 2.0 - - + +
549A LEU* 3.0 60.4 - - + +
550A VAL* 3.5 21.8 - - + +
553A ARG* 2.7 53.6 + - - +
51F ASP* 3.1 20.1 - - - +
52F MET* 3.0 9.5 + - - +
54F ASN* 1.3 80.5 - - - +
56F VAL* 1.3 62.9 + - + +
57F ASP 4.7 0.3 - - - +
72F MET* 5.6 0.2 - - - +
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Residues in contact with VAL 56 (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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546A MET* 3.5 31.6 - - + -
52F MET 3.0 16.8 + - - +
55F GLU* 1.3 79.9 - - + +
57F ASP* 1.3 69.2 + - - +
58F ALA* 3.7 1.9 + - - +
64F ILE* 3.5 36.8 - - + -
68F GLU* 3.5 37.8 - - + +
69F PHE* 3.9 3.6 - - + +
71F THR* 5.1 1.4 + - - -
72F MET* 3.5 20.2 - - + -
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Residues in contact with ASP 57 (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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53F ILE* 2.8 26.7 + - + +
54F ASN* 4.0 9.9 - - - +
55F GLU 4.7 0.5 - - - +
56F VAL* 1.3 78.4 - - - +
58F ALA* 1.3 73.3 + - - +
59F ASP* 2.7 26.7 + - - +
60F GLY* 2.9 9.3 + - - +
61F ASN* 2.7 32.4 + - - +
63F THR 2.7 18.4 - - - +
68F GLU* 2.9 23.5 - - - +
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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