Contacts of the helix formed by residues 58 - 65 (chain C) in PDB entry 1C7G
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 ASP 58 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B MET 3.4 23.5 - - - +
66B ILE* 4.1 8.1 - - + +
67B GLY 5.4 0.7 - - - +
11C LYS* 3.8 21.2 + - + +
57C SER* 1.3 74.6 - - - +
59C LYS* 1.3 90.0 + - - +
61C TRP* 3.2 8.1 + - - +
62C ALA* 2.9 27.7 + - - +
12D SER* 5.5 0.7 - - - -
13D VAL 3.0 15.1 + - - +
14D GLU* 3.8 22.2 - - - +
15D THR* 3.9 9.9 + - - +
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Residues in contact with LYS 59 (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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66B ILE* 3.9 23.6 + - + +
57C SER* 3.2 6.3 - - - +
58C ASP* 1.3 106.7 + - - +
60C GLN* 1.3 56.9 + - - +
62C ALA* 3.3 8.8 + - - +
63C GLY 3.0 20.4 + - - -
304C ILE* 3.7 18.1 - - + +
308C GLU* 4.0 7.6 - - - +
15D THR* 4.3 16.2 + - - +
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Residues in contact with GLN 60 (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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56C MET* 3.1 18.6 - - + +
57C SER* 2.8 38.3 + - - +
58C ASP 3.2 0.4 - - - -
59C LYS* 1.3 77.6 - - - +
61C TRP* 1.3 59.7 + - - +
63C GLY* 3.2 3.1 + - - -
64C MET* 3.0 29.8 + - - +
260C LEU* 3.2 17.6 + - - +
261C VAL* 3.9 6.1 - - - +
301C ALA* 3.0 29.6 + - + +
304C ILE* 3.5 27.1 - - + -
305C GLY* 3.2 19.8 - - - -
308C GLU* 4.1 0.9 - - - -
410C ARG* 3.0 15.8 + - - -
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Residues in contact with TRP 61 (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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61A TRP* 5.3 1.6 - + - -
64A MET* 3.6 22.2 - - + -
65A MET* 3.4 36.3 - - + -
297A ARG* 4.5 7.9 - - - -
65B MET* 3.7 18.5 - - + +
56C MET* 3.6 32.5 - - + +
57C SER 3.0 24.6 + - - +
58C ASP* 3.2 7.8 + - - +
60C GLN* 1.3 74.3 - - - +
62C ALA* 1.3 66.5 + - - +
64C MET* 3.2 48.0 + - + +
65C MET* 3.5 17.4 - - + +
11D LYS* 4.4 25.0 + - - +
12D SER* 3.9 23.8 - - - -
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Residues in contact with ALA 62 (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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62B ALA* 3.4 34.9 - - + +
65B MET* 3.7 9.4 - - + -
66B ILE* 3.9 15.3 - - + -
58C ASP 2.9 13.5 + - - +
59C LYS* 3.4 10.5 - - - +
60C GLN 3.2 0.2 - - - -
61C TRP* 1.3 76.0 - - - +
63C GLY* 1.3 59.7 + - - +
65C MET* 2.9 25.1 + - - +
66C ILE* 3.7 3.7 + - - +
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Residues in contact with GLY 63 (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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59C LYS 3.0 13.4 + - - -
60C GLN 3.2 5.6 + - - -
61C TRP 3.2 0.4 - - - -
62C ALA* 1.3 77.6 - - - +
64C MET* 1.3 60.2 + - - +
65C MET 3.1 0.9 + - - -
66C ILE* 3.4 28.4 + - - +
67C GLY 4.0 0.9 + - - -
297C ARG* 4.3 2.2 - - - +
300C GLU* 3.7 31.2 - - - +
301C ALA 5.3 0.7 - - - -
304C ILE* 4.2 5.4 - - - -
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Residues in contact with MET 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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61A TRP* 3.6 17.9 - - + -
64A MET* 4.4 4.9 - - + -
297A ARG* 3.4 44.0 - - - +
11B LYS* 5.2 0.5 + - - -
56C MET* 4.3 7.6 - - + -
60C GLN 3.0 20.2 + - - +
61C TRP* 3.4 43.3 - - + +
62C ALA 3.1 0.6 - - - -
63C GLY* 1.3 77.5 - - - +
65C MET* 1.3 62.6 + - + +
66C ILE 3.4 0.2 - - - -
67C GLY 4.2 1.6 + - - -
297C ARG* 3.7 51.8 - - - +
298C ASP* 4.3 2.7 - - - +
301C ALA* 4.1 10.8 - - + -
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Residues in contact with MET 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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61A TRP* 3.4 38.8 - - + -
65A MET* 3.6 22.2 - - + -
11B LYS* 3.1 19.3 + - - +
58B ASP* 3.3 15.7 - - - +
61B TRP* 3.6 31.8 - - + +
62B ALA* 3.7 17.7 - - - +
65B MET* 3.8 15.5 - - + -
61C TRP* 3.5 25.1 - - + +
62C ALA 2.9 9.9 + - - +
64C MET* 1.3 81.5 - - + +
66C ILE* 1.3 57.6 + - - +
67C GLY 3.5 1.1 - - - -
65D MET* 5.4 3.6 - - + +
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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