Contacts of the helix formed by residues 65 - 75 (chain A) in PDB entry 1C06
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 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A TYR* 4.0 14.4 - - - -
63A ALA* 3.4 0.9 - - - +
64A ARG* 1.3 93.1 - - + +
66A ARG* 1.3 59.5 + - - +
67A ARG* 3.2 14.8 + - - +
68A GLN* 2.5 42.3 + - - +
69A ALA* 2.8 13.0 + - - +
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Residues in contact with ARG 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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18A HIS 3.9 5.0 + - - -
19A MET 3.2 22.6 + - - -
20A TYR* 3.2 34.6 + - - +
21A GLY* 3.5 7.5 - - - +
54A ASP* 5.8 7.4 - - + +
58A TYR* 4.6 16.7 - - + -
65A THR* 1.3 73.5 - - - +
67A ARG* 1.3 71.6 + - + +
69A ALA* 4.2 7.4 - - - +
70A ARG* 2.5 49.2 + - + +
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Residues in contact with ARG 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 THR* 3.2 8.7 - - - +
66A ARG* 1.3 92.4 - - + +
68A GLN* 1.3 78.8 + - - +
70A ARG* 4.5 5.4 - - - -
71A GLN* 3.1 31.6 + - - +
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Residues in contact with GLN 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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63A ALA* 3.3 17.3 - - + -
64A ARG* 3.6 16.2 - - + +
65A THR* 2.5 38.6 + - - +
67A ARG* 1.3 100.3 + - - +
69A ALA* 1.3 64.0 + - - +
70A ARG 3.2 1.3 - - - -
71A GLN* 3.7 12.6 + - - +
72A LEU* 3.1 27.7 + - - +
109A VAL* 3.6 24.3 - - + +
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Residues in contact with ALA 69 (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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54A ASP* 3.5 28.7 - - + +
57A VAL* 3.8 8.6 - - + +
58A TYR* 3.6 28.0 - - + +
63A ALA* 3.2 10.3 - - + +
65A THR 2.8 11.8 + - - +
66A ARG* 4.1 4.3 - - - +
68A GLN* 1.3 73.7 - - - +
70A ARG* 1.3 65.0 + - - +
72A LEU* 3.5 2.0 + - - +
73A VAL* 3.3 25.5 + - - +
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Residues in contact with ARG 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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52A ARG* 4.4 15.5 - - - +
54A ASP* 4.2 22.7 - - + -
66A ARG* 2.5 41.6 + - + +
67A ARG* 4.4 6.7 - - - +
69A ALA* 1.3 73.8 - - - +
71A GLN* 1.3 65.3 + - + +
73A VAL* 3.1 13.4 + - - +
74A THR* 3.1 28.3 + - + +
88A PRO* 3.3 36.4 - - - +
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Residues in contact with GLN 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 ARG* 3.1 23.8 + - - +
68A GLN* 4.1 12.7 - - - +
70A ARG* 1.3 81.4 - - + +
72A LEU* 1.3 64.1 + - + +
74A THR* 3.3 8.1 - - - +
75A HIS* 2.9 55.5 + - + +
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Residues in contact with LEU 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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57A VAL* 4.0 11.9 - - + -
62A LEU* 3.5 25.4 - - + +
63A ALA* 3.7 10.8 - - + -
68A GLN 3.1 23.5 + - - +
69A ALA* 3.6 5.8 - - - +
70A ARG 3.1 0.6 - - - -
71A GLN* 1.3 79.2 - - - +
73A VAL* 1.3 66.2 + - - +
75A HIS 3.6 2.4 + - - -
77A HIS* 3.3 35.7 + - + +
78A ILE* 4.2 14.1 - - + -
107A LEU* 3.7 29.6 - - + -
109A VAL* 4.6 13.0 - - + -
110A ILE* 3.9 17.3 - - + -
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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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53A LEU* 4.2 19.5 - - + -
54A ASP* 4.3 7.2 - - + +
57A VAL* 4.2 17.3 - - + -
69A ALA 3.3 12.8 + - - +
70A ARG* 3.1 7.7 + - - +
72A LEU* 1.3 76.5 - - - +
74A THR* 1.3 57.0 + - + +
76A GLY* 2.5 33.6 + - - -
77A HIS 4.0 2.2 + - - +
78A ILE* 4.9 10.3 - - + -
85A VAL 3.3 22.8 - - - +
86A ASN* 3.3 18.2 - - - +
87A ILE 3.7 15.7 - - - +
88A PRO* 3.8 11.0 - - + -
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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 ARG* 3.1 24.2 + - + +
71A GLN* 3.1 16.3 + - - +
73A VAL* 1.3 78.6 - - + +
75A HIS* 1.3 75.8 + - - -
76A GLY 2.7 6.8 + - - -
86A ASN* 3.5 25.8 + - - +
88A PRO* 4.8 17.7 - - + -
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Residues in contact with HIS 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 GLN* 2.9 48.6 + - + +
72A LEU 3.7 0.2 - - - -
73A VAL 2.9 2.4 + - - -
74A THR* 1.3 91.3 + - - +
76A GLY* 1.3 70.1 + - - +
77A HIS* 2.9 31.1 + - + +
84A ARG* 5.3 0.9 + - - -
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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