Contacts of the helix formed by residues 63 - 77 (chain C) in PDB entry 4I6U
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 SER 63 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A GLU* 2.7 28.9 + - - -
43A ARG* 3.4 18.9 + - - -
44A ASN* 3.8 8.7 - - - -
45A SER* 3.2 12.1 - - - -
57C MET* 4.8 0.2 - - - -
61C GLU 4.4 0.2 + - - -
62C VAL* 1.3 80.1 - - - +
64C ASP* 1.3 66.0 + - - +
65C VAL* 4.1 1.8 - - - -
66C VAL* 3.1 23.7 + - - +
67C PHE* 3.1 20.8 + - - +
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Residues in contact with ASP 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ARG* 2.9 32.0 + - - -
45A SER* 3.2 12.3 + - - +
4B PHE* 3.9 25.5 - - - -
5B LEU* 4.7 15.1 - - - +
75B ILE* 4.1 23.9 - - + +
54C GLU* 5.0 1.6 - - - +
57C MET* 3.5 21.8 - - - +
63C SER* 1.3 73.8 - - - +
65C VAL* 1.3 64.2 + - - +
67C PHE* 3.2 3.1 + - - +
68C PHE* 3.0 35.6 + - + -
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Residues in contact with VAL 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 6.1 0.2 - - - -
2A GLU* 3.8 30.5 - - + +
103A PEG 5.5 2.9 - - - -
72B ILE* 4.1 24.2 - - + +
75B ILE* 3.7 32.1 - - + -
76B LEU* 4.0 24.5 - - + -
63C SER* 3.3 1.2 + - - -
64C ASP* 1.3 76.9 - - - +
66C VAL* 1.3 57.9 + - - +
68C PHE* 3.3 2.6 + - - +
69C GLU* 2.8 50.1 + - - +
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Residues in contact with VAL 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 4.7 9.9 - - + -
2A GLU* 3.7 18.2 - - - +
62C VAL* 3.5 22.9 - - + -
63C SER* 3.1 23.0 + - - +
65C VAL* 1.3 75.0 - - + +
67C PHE* 1.3 63.0 + - - +
69C GLU* 3.3 9.5 + - - +
70C MET* 3.0 40.1 + - + +
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Residues in contact with PHE 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C VAL* 4.4 10.1 - - + -
12C VAL* 3.7 23.0 - - + +
13C ILE* 3.9 24.9 - - + -
16C ILE* 3.6 22.7 - - + -
53C LEU* 3.9 26.9 - - + -
56C ILE* 5.9 0.2 - - + -
57C MET* 3.7 27.4 - - + -
60C LEU* 5.1 3.4 - - + -
62C VAL* 4.0 8.3 - - + +
63C SER 3.1 13.1 + - - +
64C ASP 3.5 7.2 - - - +
66C VAL* 1.3 77.5 - - - +
68C PHE* 1.3 80.5 + + - +
70C MET* 3.3 3.7 + - - +
71C LEU* 2.9 44.3 + - + +
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Residues in contact with PHE 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LEU* 3.9 25.6 - - + -
9B VAL* 5.5 1.3 - - + -
50B ILE* 6.6 0.2 - - + -
68B PHE* 3.6 40.2 - + + -
71B LEU* 3.8 22.9 - - + -
72B ILE* 3.8 23.3 - - + -
75B ILE* 4.7 5.4 - - + -
50C ILE* 6.1 1.3 - - + -
53C LEU* 4.2 23.1 - - + -
57C MET* 4.6 5.6 - - - -
64C ASP* 3.0 34.0 + - + +
67C PHE* 1.3 90.7 - + - +
69C GLU* 1.3 64.8 + - - +
71C LEU* 3.3 13.2 + - + +
72C ILE* 3.0 28.4 + - - +
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Residues in contact with GLU 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 4.2 32.1 - - - +
72B ILE* 3.7 20.8 - - + +
76B LEU* 5.9 0.5 - - - +
65C VAL* 2.8 36.3 + - + +
66C VAL* 3.7 8.5 - - - +
68C PHE* 1.3 76.6 - - - +
70C MET* 1.3 63.1 + - + +
72C ILE* 3.5 7.2 + - + +
73C LYS* 3.2 38.2 + - - +
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Residues in contact with MET 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C VAL* 3.8 15.8 - - + +
15C LYS* 4.7 22.2 - - + -
16C ILE* 3.5 36.8 - - + +
19C GLU* 4.9 11.4 - - - +
66C VAL* 3.0 27.1 + - + +
67C PHE 3.5 6.7 - - - +
69C GLU* 1.3 75.2 - - + +
71C LEU* 1.3 63.9 + - - +
73C LYS* 3.4 13.7 + - + +
74C GLU* 3.0 24.4 + - - +
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Residues in contact with LEU 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B PHE* 3.7 31.9 - - + -
5C LEU* 4.5 0.9 - - + -
8C LYS* 3.8 40.2 - - + +
9C VAL* 3.9 23.6 - - + +
12C VAL* 3.8 10.0 - - + +
67C PHE* 2.9 29.9 + - + +
68C PHE* 3.6 20.6 - - + +
70C MET* 1.3 70.4 - - - +
72C ILE* 1.3 66.0 + - - +
74C GLU* 3.2 1.2 + - - +
75C ILE* 2.9 39.5 + - + +
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Residues in contact with ILE 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B VAL* 4.0 21.1 - - + +
68B PHE* 3.8 18.4 - - + -
69B GLU* 3.9 32.8 - - + +
72B ILE* 3.8 22.9 - - + -
68C PHE 3.0 20.7 + - - +
69C GLU* 3.7 7.2 - - - +
71C LEU* 1.3 73.9 - - - +
73C LYS* 1.3 65.6 + - + +
75C ILE* 3.2 8.4 + - - +
76C LEU* 2.9 44.8 + - + +
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Residues in contact with LYS 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C GLU* 3.2 25.9 + - - +
70C MET* 3.6 15.5 - - + +
71C LEU 3.2 0.2 - - - -
72C ILE* 1.3 80.4 - - + +
74C GLU* 1.3 58.5 + - - +
76C LEU* 3.4 8.2 + - - +
77C LYS* 3.0 28.2 + - - +
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Residues in contact with GLU 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LYS* 3.1 43.7 + - + +
11C PHE* 2.9 35.7 - - + -
12C VAL* 3.8 17.5 - - + +
15C LYS* 2.9 28.9 + - - +
70C MET 3.0 18.0 + - - +
71C LEU 3.2 4.2 + - - +
73C LYS* 1.3 76.7 - - - +
75C ILE* 1.3 65.1 + - - +
77C LYS* 3.4 28.8 + - - +
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Residues in contact with ILE 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ASP* 3.6 36.6 - - + +
65B VAL* 3.7 14.6 - - + -
68B PHE* 4.2 14.1 - - + -
4C PHE* 4.0 23.1 - - + -
5C LEU* 4.3 5.2 - - + -
8C LYS* 4.0 29.8 + - + +
71C LEU* 2.9 39.4 + - + +
72C ILE* 3.6 6.7 - - - +
74C GLU* 1.3 78.9 - - - +
76C LEU* 1.3 62.5 + - + +
77C LYS 3.4 3.5 + - - +
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Residues in contact with LEU 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B VAL* 4.1 26.0 - - + -
69B GLU* 5.9 0.2 - - - +
72C ILE* 2.9 37.2 + - + +
73C LYS* 3.7 6.3 - - - +
75C ILE* 1.3 78.3 - - + +
77C LYS* 1.3 64.3 + - - +
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Residues in contact with LYS 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LYS* 5.0 6.0 + - - +
11C PHE* 5.3 2.2 - - - -
15C LYS* 4.4 1.0 - - - +
73C LYS 3.0 13.8 + - - +
74C GLU* 3.5 34.8 + - - +
75C ILE 3.3 5.8 - - - +
76C LEU* 1.3 79.6 - - - +
19E GLU* 2.7 51.5 + - - +
20E LYS* 4.8 4.9 - - - +
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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