Contacts of the helix formed by residues 59 - 74 (chain F) in PDB entry 4CQM
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 LYS 59 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34F ARG* 5.9 0.4 - - - +
56F ASP* 2.9 51.1 + - + +
57F VAL 4.4 0.2 - - - -
58F ALA* 1.3 78.3 - - + +
60F GLU* 1.3 65.6 + - - +
61F HIS 4.8 0.9 - - - +
62F ASP* 3.5 32.2 + - - +
63F VAL* 3.2 16.6 + - - +
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Residues in contact with GLU 60 (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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58F ALA 3.5 4.4 + - - -
59F LYS* 1.3 71.6 - - - +
61F HIS* 1.3 78.8 + - + +
63F VAL* 3.0 15.2 + - + +
64F GLN* 3.1 17.9 + - + +
113F LEU* 3.8 32.8 - - + -
116F LYS* 4.4 14.2 + - - -
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Residues in contact with HIS 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F LYS* 3.5 0.6 - - + +
60F GLU* 1.3 93.3 + - + +
62F ASP* 1.3 66.8 + - - +
64F GLN* 4.5 5.7 - - + +
65F ASN* 3.2 28.6 + - - +
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Residues in contact with ASP 62 (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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55F CYS* 3.6 10.8 - - - -
56F ASP 3.8 16.3 + - - +
59F LYS* 3.4 45.7 + - - +
60F GLU 3.1 0.6 - - - -
61F HIS* 1.3 83.5 - - - +
63F VAL* 1.3 54.0 + - - +
65F ASN* 3.9 1.2 - - - +
66F THR* 2.2 39.5 + - - -
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Residues in contact with VAL 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F PHE* 5.1 2.7 - - + -
55F CYS* 3.9 9.6 - - - -
56F ASP 3.8 1.3 - - - +
57F VAL* 3.6 33.2 - - + +
59F LYS 3.2 15.5 - - - +
60F GLU* 3.0 8.8 + - - +
62F ASP* 1.3 74.9 - - - +
64F GLN* 1.3 61.3 + - - +
66F THR* 3.1 3.5 + - - -
67F PHE* 3.0 35.7 + - + -
113F LEU* 3.8 33.7 - - + +
114F THR* 4.1 11.4 - - - +
117F ALA* 4.0 12.3 - - + -
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Residues in contact with GLN 64 (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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60F GLU* 3.1 17.4 + - + +
61F HIS* 4.5 6.7 - - + +
63F VAL* 1.3 81.9 - - + +
65F ASN* 1.3 57.7 + - - +
67F PHE* 3.9 4.1 + - - +
68F GLU* 3.4 21.0 + - - +
117F ALA* 4.9 0.7 - - + -
120F ARG* 4.0 29.6 + - - +
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Residues in contact with ASN 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F HIS* 3.2 20.2 + - - +
62F ASP* 4.4 2.0 - - - +
63F VAL 3.2 0.6 - - - -
64F GLN* 1.3 76.8 + - - +
66F THR* 1.3 65.1 + - - +
67F PHE 3.4 0.2 - - - -
68F GLU* 3.0 31.5 + - - +
69F GLU* 3.2 36.4 + - - +
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Residues in contact with THR 66 (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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8F PHE* 4.9 2.9 - - + -
32F ILE* 4.4 11.2 - - + -
53F PHE* 4.1 14.6 - - + -
54F SER 4.0 5.3 + - - +
55F CYS* 3.2 30.5 - - + +
62F ASP* 2.2 28.2 + - - -
63F VAL 3.5 4.7 - - - -
65F ASN* 1.3 77.3 - - - +
67F PHE* 1.3 58.6 + - - +
69F GLU* 2.9 13.7 + - - +
70F LEU* 2.8 51.2 + - + +
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Residues in contact with PHE 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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6F ALA* 5.1 3.6 - - + -
8F PHE* 3.4 38.1 - + - -
63F VAL* 3.0 22.9 + - + +
64F GLN* 3.9 6.1 - - - +
66F THR* 1.3 77.2 - - - +
68F GLU* 1.3 56.8 + - - +
70F LEU* 3.5 12.0 + - + +
71F GLU* 3.0 28.2 + - - +
77F VAL* 4.9 23.1 - - + +
80F LEU* 4.2 8.1 - - + -
114F THR* 3.7 20.0 - - + -
117F ALA* 3.5 33.7 - - + -
118F ALA* 3.7 25.6 - - + -
120F ARG* 4.7 7.9 - - - +
121F THR* 4.9 9.2 - - + -
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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
----------------------------------------------------------
64F GLN 3.4 14.7 + - - +
65F ASN* 3.0 36.4 + - - +
66F THR 3.1 0.8 - - - -
67F PHE* 1.3 78.9 - - - +
69F GLU* 1.3 68.3 + - + +
71F GLU* 3.4 16.9 - - - +
72F LYS* 3.4 46.0 + - - +
120F ARG* 5.3 5.4 - - - +
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Residues in contact with GLU 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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53F PHE* 4.5 14.9 - - + +
65F ASN* 3.2 22.4 + - - +
66F THR* 2.9 13.3 + - - +
68F GLU* 1.3 82.0 - - + +
70F LEU* 1.3 65.2 + - - +
71F GLU 3.2 1.6 - - - -
72F LYS* 3.5 11.8 + - + +
73F HIS* 3.4 33.9 + - + +
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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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6F ALA* 3.9 19.1 - - + -
8F PHE* 5.4 1.1 - - + -
30F ALA* 4.0 6.3 - - + -
32F ILE* 3.7 23.1 - - + -
53F PHE* 3.4 44.4 - - + -
66F THR* 2.8 39.8 + - + +
67F PHE* 3.7 17.0 - - + +
69F GLU* 1.3 75.6 - - - +
71F GLU* 1.3 57.8 + - - +
74F LEU* 2.7 45.9 + - + +
75F GLY 3.4 5.2 + - - -
77F VAL* 4.8 12.8 - - + -
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Residues in contact with GLU 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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67F PHE 3.0 16.6 + - - +
68F GLU* 3.4 18.2 - - - +
69F GLU 3.2 0.2 - - - -
70F LEU* 1.3 78.2 - - - +
72F LYS* 1.3 64.3 + - + +
75F GLY* 3.2 34.7 + - - +
77F VAL* 5.6 0.9 - - - +
120F ARG* 5.2 5.9 + - - -
121F THR* 5.4 8.0 - - + +
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Residues in contact with LYS 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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68F GLU* 3.4 39.6 + - - +
69F GLU* 3.5 12.9 + - + +
70F LEU 3.3 0.2 - - - -
71F GLU* 1.3 80.4 - - + +
73F HIS* 1.3 74.0 + - + +
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Residues in contact with HIS 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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28F ARG* 3.9 13.5 + - - -
51F LEU* 4.2 27.7 - - + +
53F PHE* 3.5 33.8 - + + -
69F GLU* 3.4 18.1 + - + +
70F LEU 3.3 2.1 + - - +
72F LYS* 1.3 93.4 + - + +
74F LEU* 1.3 67.9 + - + +
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Residues in contact with LEU 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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1F MET 5.4 1.2 - - - +
4F VAL* 3.7 39.4 - - + +
28F ARG* 3.6 43.4 + - + +
29F LEU 5.1 4.3 - - - +
30F ALA* 3.8 29.6 - - + -
49F ASP 4.5 0.9 - - - +
51F LEU* 3.6 24.0 - - + -
53F PHE* 4.0 17.7 - - + -
70F LEU* 2.7 26.2 + - + +
73F HIS* 1.3 76.4 - - - +
75F GLY* 1.3 58.1 + - - +
76F ARG 4.3 0.2 + - - -
77F VAL* 5.2 1.1 - - + -
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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