Contacts of the helix formed by residues 69 - 84 (chain A) in PDB entry 4MCA
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 CYS 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A GLU* 3.4 19.1 + - + -
68A CYS* 1.3 75.2 - - - +
70A HIS* 1.3 67.2 + - - +
71A LYS* 3.0 13.9 + - + +
72A GLU* 3.0 28.6 + - - +
73A ILE* 3.0 26.4 + - - +
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Residues in contact with HIS 70 (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 CYS* 1.3 71.3 - - - +
71A LYS* 1.3 52.9 + - - +
73A ILE* 3.6 12.1 - - + +
74A ASP* 2.8 69.7 + - - +
106A TYR* 3.8 36.8 + + - -
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Residues in contact with LYS 71 (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 CYS* 3.0 13.9 + - + +
70A HIS* 1.3 78.8 - - - +
72A GLU* 1.3 72.1 + - - +
74A ASP* 3.3 4.8 + - - +
75A ARG* 2.8 46.0 + - - +
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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
----------------------------------------------------------
64A PHE* 3.6 12.3 - - + -
65A ASN* 2.9 40.6 + - + +
67A GLU 3.7 17.5 - - - +
69A CYS* 3.0 24.3 + - - +
71A LYS* 1.3 87.0 + - - +
73A ILE* 1.3 58.1 + - + +
75A ARG* 2.9 39.6 + - - +
76A LEU* 2.9 42.3 + - + +
99A THR* 4.7 2.7 - - + -
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Residues in contact with ILE 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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68A CYS* 4.3 20.0 - - - -
69A CYS 3.0 23.6 + - - +
70A HIS* 3.6 15.9 - - + +
72A GLU* 1.3 74.3 - - - +
74A ASP* 1.3 65.5 + - - +
76A LEU 3.3 0.5 + - - -
77A GLY* 2.9 26.7 + - - -
99A THR* 4.3 11.9 - - + +
102A ALA* 3.6 20.9 - - + -
103A ILE* 3.4 30.2 - - + +
106A TYR* 3.9 31.6 - - + -
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Residues in contact with ASP 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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70A HIS* 2.8 52.1 + - - +
71A LYS* 3.8 4.8 - - - +
73A ILE* 1.3 72.2 - - - +
75A ARG* 1.3 66.6 + - - +
77A GLY* 3.3 2.6 + - - -
78A ARG* 3.1 51.4 + - - +
106A TYR* 5.7 1.6 - - - -
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Residues in contact with ARG 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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62A ALA* 5.8 0.6 - - - +
63A LEU 3.0 21.8 + - - +
65A ASN* 3.4 11.8 + - - -
71A LYS* 2.8 30.1 + - - +
72A GLU* 2.9 43.6 + - - +
74A ASP* 1.3 76.3 - - - +
76A LEU* 1.3 76.4 + - - +
78A ARG* 3.1 19.2 + - - +
79A GLU* 3.1 33.7 + - - +
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Residues in contact with LEU 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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33A LEU* 4.0 9.0 - - + +
35A ILE* 4.1 24.2 - - + -
62A ALA* 3.7 30.1 - - + -
63A LEU 4.5 3.1 - - - +
64A PHE* 4.7 0.9 - - + -
72A GLU* 2.9 34.3 + - + +
75A ARG* 1.3 97.7 - - - +
77A GLY* 1.3 63.1 + - - +
79A GLU* 3.3 7.6 + - - +
80A LEU* 3.0 24.6 + - - +
99A THR* 3.7 29.2 - - + -
103A ILE* 3.8 16.6 - - + -
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Residues in contact with GLY 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 ILE 2.9 15.4 + - - -
74A ASP* 3.6 4.7 - - - -
75A ARG 3.2 0.2 - - - -
76A LEU* 1.3 76.7 - - - +
78A ARG* 1.3 61.5 + - - +
80A LEU* 3.2 8.0 + - - +
81A LYS* 3.1 26.3 + - - +
103A ILE* 4.6 5.2 - - - +
107A GLN* 3.5 28.7 + - - -
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Residues in contact with ARG 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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74A ASP* 3.1 41.2 + - - +
75A ARG* 3.1 8.4 + - - +
77A GLY* 1.3 74.6 - - - +
79A GLU* 1.3 63.5 + - - +
81A LYS* 3.2 10.4 + - - +
82A ALA* 3.2 21.8 + - - +
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Residues in contact with GLU 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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33A LEU* 4.6 3.6 - - + -
60A HIS* 2.5 40.4 + - + +
61A ALA 4.1 1.0 - - - +
62A ALA* 3.5 21.2 - - - +
75A ARG* 3.1 33.2 + - + +
76A LEU* 3.7 11.2 - - - +
77A GLY 3.3 0.2 - - - -
78A ARG* 1.3 78.7 - - - +
80A LEU* 1.3 64.2 + - - +
82A ALA* 3.2 13.4 + - - +
83A HIS* 3.3 21.4 - - + +
85A CYS* 4.9 0.3 - - - -
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Residues in contact with LEU 80 (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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33A LEU* 4.1 17.2 - - + +
76A LEU 3.0 13.9 + - - +
77A GLY* 3.4 9.9 - - - +
79A GLU* 1.3 78.7 - - - +
81A LYS* 1.3 87.4 + - + +
82A ALA 3.1 0.2 + - - -
83A HIS 3.3 0.5 + - - -
84A GLY 3.1 18.4 + - - -
85A CYS* 3.4 43.7 + - + +
87A GLY 4.4 1.3 - - - +
88A VAL* 4.0 20.9 - - + -
103A ILE* 4.3 7.0 - - + -
107A GLN* 3.9 6.7 - - + -
109A LEU* 3.6 35.0 - - + -
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Residues in contact with LYS 81 (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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77A GLY 3.1 12.9 + - - +
78A ARG* 3.2 12.3 + - - +
80A LEU* 1.3 91.6 - - + +
82A ALA* 1.3 59.0 + - - +
84A GLY* 3.6 11.7 + - - +
107A GLN* 2.5 47.1 + - - +
109A LEU* 4.9 3.0 - - - +
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Residues in contact with ALA 82 (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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78A ARG 3.2 9.7 + - - +
79A GLU* 3.2 11.6 + - - +
80A LEU 3.1 1.0 - - - -
81A LYS* 1.3 78.9 - - - +
83A HIS* 1.3 68.7 + - + +
84A GLY 3.4 0.4 - - - -
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Residues in contact with HIS 83 (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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31A HIS* 3.1 17.1 - - + -
60A HIS* 3.3 44.8 + + - +
79A GLU* 3.3 20.2 - - + +
80A LEU 3.3 2.2 + - - -
82A ALA* 1.3 83.9 - - + +
84A GLY* 1.3 58.6 + - - +
85A CYS* 3.5 2.7 - - - -
1001A ZN 3.1 21.8 - - - -
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Residues in contact with GLY 84 (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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31A HIS* 3.1 10.5 + - - -
80A LEU* 3.1 6.4 + - - -
81A LYS* 3.6 9.7 + - - -
82A ALA 3.4 3.2 - - - -
83A HIS* 1.3 79.1 - - - +
85A CYS* 1.3 65.9 + - - +
86A ARG* 3.6 13.5 + - - +
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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