Contacts of the strand formed by residues 66 - 74 (chain C) in PDB entry 3C5C
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 GLN 66 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C LEU* 6.2 0.7 - - + -
62C THR* 3.4 6.6 - - - +
63C VAL 3.1 30.1 + - - +
64C ASP* 3.6 16.1 + - - +
65C HIS* 1.3 81.7 - - + +
67C PRO* 1.3 72.5 - - + +
68C VAL* 3.6 1.0 - - - +
184C ARG* 3.3 30.7 + - - +
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Residues in contact with PRO 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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19C LEU* 3.9 37.0 - - + +
61C GLU 3.5 7.2 - - - +
62C THR* 4.8 2.7 - - - +
65C HIS 4.4 2.9 - - - +
66C GLN* 1.3 87.9 - - + +
68C VAL* 1.3 59.3 + - - +
69C HIS* 5.2 4.7 - - + +
184C ARG* 2.9 20.1 + - - -
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Residues in contact with VAL 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU 3.6 3.1 - - - -
21C VAL* 3.4 37.5 - - + -
60C GLU* 3.4 5.5 - - - +
61C GLU* 2.9 42.1 + - + +
63C VAL* 4.0 15.5 - - + -
66C GLN 3.6 8.3 - - - +
67C PRO* 1.3 81.1 - - - +
69C HIS* 1.3 67.9 - - - +
70C LEU* 3.4 9.1 + - + +
180C VAL* 3.9 22.4 - - + -
184C ARG* 3.4 17.3 - - - +
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Residues in contact with HIS 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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17C GLY 5.2 5.3 + - - -
19C LEU* 2.9 48.4 + - + +
20C GLU* 3.3 23.9 + - + +
21C VAL 3.0 23.0 + - - +
59C SER 3.8 3.8 - - - -
60C GLU* 4.0 28.5 + - + +
67C PRO* 5.2 4.0 - - + +
68C VAL* 1.3 77.9 - - - +
70C LEU* 1.3 61.5 + - - +
71C ARG* 3.8 6.2 + - + +
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Residues in contact with LEU 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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21C VAL* 3.6 13.9 - - + +
23C LEU* 3.5 35.4 - - + -
40C PHE* 3.5 36.8 - - + -
57C TYR 4.2 0.7 - - - -
58C SER* 3.2 5.7 - - - -
59C SER* 2.8 46.7 + - - +
61C GLU* 4.0 12.6 - - + -
68C VAL* 3.4 4.7 + - + -
69C HIS* 1.3 73.4 - - - +
71C ARG* 1.3 63.6 + - - +
72C VAL* 3.7 20.6 - - + -
176C PHE* 4.8 1.8 - - + -
177C HIS* 6.4 0.2 - - + -
180C VAL* 3.8 21.1 - - + -
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Residues in contact with ARG 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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20C GLU* 5.6 7.6 - - + +
21C VAL 3.0 6.5 + - - +
22C ASN* 3.4 24.0 - - - +
23C LEU* 2.9 28.9 + - - +
56C THR* 3.7 21.0 + - + +
57C TYR 3.3 3.6 - - - -
58C SER* 3.1 29.5 + - - -
69C HIS* 4.3 8.1 - - - +
70C LEU* 1.3 77.6 - - - +
72C VAL* 1.3 62.6 + - - +
73C MET 3.9 0.4 - - - -
90C TRP* 3.6 7.6 - - + -
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Residues in contact with VAL 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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23C LEU* 3.3 11.7 - - + +
25C ILE* 3.6 34.8 - - + -
37C THR* 4.0 21.5 - - + +
40C PHE* 5.1 4.3 - - + -
41C LEU* 5.4 4.7 - - + -
56C THR* 3.2 2.2 - - - -
57C TYR* 2.7 50.3 + - + +
59C SER* 5.9 0.2 - - - +
70C LEU* 3.7 31.0 - - + -
71C ARG* 1.3 73.0 - - - +
73C MET* 1.3 61.4 + - - +
176C PHE* 4.2 15.5 - - + -
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Residues in contact with MET 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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23C LEU 2.8 9.8 + - - +
24C ALA* 3.6 2.0 - - - -
25C ILE* 2.9 30.0 + - - +
54C GLU* 4.7 13.2 - - + +
55C ASP 3.5 7.9 - - - +
56C THR* 3.6 20.4 - - - +
71C ARG 3.9 1.4 + - - -
72C VAL* 1.3 71.1 - - - +
74C ASP* 1.3 63.0 + - - +
75C THR* 3.5 15.3 + - + +
86C ARG* 3.8 15.5 - - + +
87C TYR* 3.9 27.8 - - - -
90C TRP* 3.4 46.2 - - + +
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Residues in contact with ASP 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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25C ILE* 4.4 5.7 - - - +
33C LYS* 3.4 25.6 - - - +
34C SER* 2.4 39.3 + - - -
37C THR* 3.9 17.1 + - + +
49C TYR* 4.5 1.6 - - - -
53C LEU 4.4 6.0 - - - +
54C GLU* 3.3 25.7 - - - +
55C ASP 2.9 9.8 + - - -
57C TYR* 4.0 26.4 + - + -
72C VAL* 3.6 1.9 + - + +
73C MET* 1.3 69.0 - - - +
75C THR* 1.3 67.3 + - - +
202C MG 4.5 0.2 - - - -
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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