Contacts of the helix formed by residues 65 - 78 (chain A) in PDB entry 2C60
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 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A PRO* 3.4 18.8 + - + +
64A VAL* 1.3 77.3 - - - +
66A TYR* 1.3 65.9 + - - +
67A GLU* 4.4 8.7 - - + +
68A ASP* 3.0 42.0 + - - +
69A VAL* 3.1 13.9 + - - +
97A GLN* 3.4 13.2 - - - +
100A LEU* 4.1 1.8 - - - -
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Residues in contact with TYR 66 (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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65A LYS* 1.3 70.4 - - - +
67A GLU* 1.3 84.7 + - + +
69A VAL* 3.1 4.2 + - - +
70A GLU* 3.0 46.7 + - - +
83A LEU* 3.9 23.5 - - + +
94A LEU* 2.8 31.1 + - + -
95A LYS* 3.2 22.7 + - - -
96A ASN* 3.5 26.9 - - - -
97A GLN* 2.8 31.2 + - - +
100A LEU* 3.7 19.0 - - + +
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Residues in contact with GLU 67 (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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65A LYS* 3.2 7.5 - - + +
66A TYR* 1.3 101.4 + - + +
68A ASP* 1.3 60.6 + - - +
70A GLU* 3.6 13.0 + - - +
71A HIS* 3.0 29.3 + - - +
96A ASN* 5.8 0.2 - - - -
97A GLN* 4.1 9.2 + - - +
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Residues in contact with ASP 68 (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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60A PHE* 4.1 9.8 - - + -
65A LYS* 3.0 33.2 + - + +
67A GLU* 1.3 79.1 - - - +
69A VAL* 1.3 59.7 + - + +
71A HIS* 3.5 8.5 + - - +
72A LYS* 2.9 29.6 + - - +
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Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ILE* 4.3 12.8 - - + -
49A PHE* 4.0 24.5 - - + -
60A PHE* 3.9 16.8 - - + -
64A VAL* 3.5 32.1 - - + -
65A LYS 3.1 7.2 + - - +
66A TYR* 3.6 6.7 - - - +
68A ASP* 1.3 73.9 - - - +
70A GLU* 1.3 65.8 + - - +
72A LYS* 3.2 2.8 + - - +
73A VAL* 2.9 22.7 + - - +
83A LEU* 4.1 25.1 - - + -
100A LEU* 4.1 11.9 - - + -
118A ILE* 6.4 0.4 - - + -
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Residues in contact with GLU 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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66A TYR* 3.0 44.8 + - + +
67A GLU* 3.8 13.3 - - - +
69A VAL* 1.3 78.9 - - - +
71A HIS* 1.3 62.7 + - - +
73A VAL* 3.3 6.3 + - - +
74A THR* 3.0 32.5 + - - +
80A PRO* 6.4 1.3 - - + -
81A LEU 5.7 5.8 - - - +
83A LEU* 5.0 10.0 - - + +
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Residues in contact with HIS 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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67A GLU 3.0 19.6 + - - +
68A ASP* 3.8 8.7 - - - +
70A GLU* 1.3 76.8 - - - +
72A LYS* 1.3 65.2 + - + +
74A THR* 3.4 6.5 + - - +
75A THR* 2.8 48.8 + - - +
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Residues in contact with LYS 72 (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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49A PHE* 5.7 0.4 - - + -
58A ILE* 4.0 24.7 - - + -
60A PHE* 3.9 26.2 - - + -
68A ASP 2.9 18.1 + - - +
69A VAL 3.2 4.5 + - - +
71A HIS* 1.3 81.5 - - + +
73A VAL* 1.3 58.0 + - - +
75A THR* 3.3 8.3 + - + +
76A VAL* 2.8 54.5 + - + +
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Residues in contact with VAL 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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49A PHE* 3.6 39.0 - - + -
58A ILE* 6.4 0.4 - - - -
69A VAL 2.9 19.7 + - - +
70A GLU* 3.6 5.8 - - - +
72A LYS* 1.3 75.7 - - - +
74A THR* 1.3 65.4 + - - +
76A VAL* 4.8 0.2 - - - -
77A PHE* 2.9 41.5 + - + +
79A GLN 4.0 0.2 - - - +
81A LEU* 3.9 38.4 - - + +
83A LEU* 4.0 11.9 - - + -
120A LEU* 4.0 8.5 - - + -
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Residues in contact with THR 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 GLU* 3.0 22.9 + - - +
71A HIS* 3.8 7.4 - - - +
73A VAL* 1.3 76.2 - - - +
75A THR* 1.3 60.0 + - - +
78A GLY* 2.9 29.2 + - - -
79A GLN* 3.4 21.0 + - - +
80A PRO* 3.6 25.9 - - + +
81A LEU 4.8 0.3 + - - -
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Residues in contact with THR 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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71A HIS* 2.8 45.2 + - - +
72A LYS* 3.6 11.0 - - + +
74A THR* 1.3 80.9 - - - +
76A VAL* 1.3 66.7 + - + +
78A GLY* 3.8 5.7 + - - -
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Residues in contact with VAL 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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56A ARG* 3.3 35.4 + - - +
58A ILE* 4.1 13.2 - - + -
72A LYS* 2.8 48.2 + - + +
75A THR* 1.3 78.9 - - + +
77A PHE* 1.3 79.5 + - + +
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Residues in contact with PHE 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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49A PHE* 4.1 20.6 - + + -
51A HIS* 3.9 33.9 - - + +
54A GLU 5.8 1.3 - - - -
56A ARG* 3.7 43.3 - - + -
58A ILE* 5.1 0.9 - - + -
73A VAL* 2.9 27.5 + - + +
76A VAL* 1.3 89.9 - - + +
78A GLY* 1.3 61.8 + - - +
79A GLN* 3.2 14.8 + - + +
81A LEU* 3.7 19.5 - - + -
120A LEU* 3.4 27.4 - - + -
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Residues in contact with GLY 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 THR* 2.9 15.2 + - - -
75A THR 3.8 4.9 + - - -
76A VAL 3.4 2.8 + - - -
77A PHE* 1.3 76.2 - - - +
79A GLN* 1.3 61.9 + - - +
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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