Contacts of the helix formed by residues 58 - 66 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A MET* 3.6 21.3 - - - +
66A ILE* 3.7 11.0 - - + +
67A GLY 5.7 0.2 - - - +
12C SER* 5.1 1.3 - - - -
13C VAL 2.9 16.9 + - - +
14C GLU* 3.7 22.6 - - - +
15C THR* 3.6 18.4 + - - +
11D LYS* 3.9 20.5 + - + +
57D SER* 1.3 73.0 - - - +
59D LYS* 1.3 84.1 + - - +
61D TRP* 3.4 9.5 + - - +
62D ALA* 3.0 21.5 + - - +
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Residues in contact with LYS 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ILE* 4.1 21.3 - - + +
15C THR* 4.0 17.4 + - - +
57D SER* 3.1 6.9 - - - +
58D ASP* 1.3 104.9 + - - +
60D GLN* 1.3 65.1 + - - +
62D ALA* 3.2 8.8 + - + +
63D GLY 3.1 16.3 + - - -
304D ILE* 3.8 17.2 - - + +
308D GLU* 4.0 7.6 - - - +
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Residues in contact with GLN 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D MET* 3.1 18.7 - - + +
57D SER* 2.9 39.8 + - - +
59D LYS* 1.3 78.6 - - - +
61D TRP* 1.3 58.7 + - - +
63D GLY* 3.0 15.9 + - - -
64D MET* 3.0 17.7 + - - +
260D LEU 3.2 19.6 + - - +
261D VAL* 3.6 8.3 - - - +
301D ALA* 3.0 29.4 + - + +
304D ILE* 3.8 24.9 - - + -
305D GLY* 3.5 15.8 - - - -
308D GLU* 3.5 2.8 - - - +
410D ARG* 2.9 16.6 + - - -
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Residues in contact with TRP 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A MET* 3.7 18.2 - - + +
61B TRP* 5.4 2.0 - + - -
64B MET* 3.7 22.2 - - + -
65B MET* 3.4 37.7 - - + -
297B ARG* 4.6 7.0 - - - -
11C LYS* 4.5 25.6 + - - +
12C SER* 4.0 25.4 - - - -
56D MET* 3.7 33.5 - - + +
57D SER 2.9 21.5 + - - +
58D ASP* 3.8 7.9 - - - +
59D LYS 3.3 0.2 - - - -
60D GLN* 1.3 77.7 - - - +
62D ALA* 1.3 61.0 + - - +
64D MET* 3.4 48.0 + - + +
65D MET* 3.5 17.1 - - + +
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Residues in contact with ALA 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ALA* 3.5 34.5 - - + +
65A MET* 3.9 9.8 - - + +
66A ILE* 3.9 14.1 - - + -
58D ASP 3.0 13.5 + - - +
59D LYS* 3.3 11.4 - - + +
60D GLN 3.1 0.4 - - - -
61D TRP* 1.3 77.1 - - - +
63D GLY* 1.3 64.6 + - - +
65D MET* 3.1 18.5 + - - +
66D ILE* 3.7 3.9 + - - +
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Residues in contact with GLY 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D LYS 3.1 9.4 + - - -
60D GLN 3.0 8.9 + - - -
62D ALA* 1.3 79.4 - - - +
64D MET* 1.3 59.6 + - - +
65D MET 3.2 0.5 + - - -
66D ILE* 3.3 22.9 + - - +
67D GLY 3.9 4.2 + - - -
297D ARG 4.3 1.4 - - - +
300D GLU* 3.6 34.1 - - - +
301D ALA 5.3 0.2 - - - -
304D ILE* 4.1 6.1 - - - -
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Residues in contact with MET 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LYS* 5.1 0.3 + - - -
61B TRP* 3.7 15.8 - - + -
64B MET* 4.7 3.1 - - + -
297B ARG* 3.3 40.8 - - - +
56D MET* 4.2 4.9 - - + -
60D GLN 3.0 20.0 + - - +
61D TRP* 3.4 45.5 - - + +
63D GLY* 1.3 77.5 - - - +
65D MET* 1.3 65.2 + - + +
66D ILE 3.6 0.5 + - - -
67D GLY 3.9 1.9 + - - -
297D ARG* 3.5 49.9 - - - +
298D ASP* 4.0 12.1 - - - +
301D ALA* 4.1 12.1 - - + -
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Residues in contact with MET 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LYS* 2.9 19.8 + - - +
58A ASP* 3.4 14.0 - - - +
61A TRP* 3.7 33.7 - - + +
62A ALA* 3.8 15.9 - - - +
65A MET* 3.9 15.9 - - + -
61B TRP* 3.3 39.5 - - + -
65B MET* 3.6 23.3 - - + -
65C MET* 5.4 3.6 - - - +
61D TRP* 3.5 24.7 - - + +
62D ALA 3.1 8.9 + - - +
63D GLY 3.1 1.0 - - - -
64D MET* 1.3 79.6 - - - +
66D ILE* 1.3 57.3 + - - +
67D GLY 3.4 0.9 - - - -
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Residues in contact with ILE 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LYS* 4.3 2.0 - - - +
58A ASP* 3.8 26.9 - - + +
59A LYS* 4.3 26.7 - - + +
62A ALA* 3.9 13.7 - - + -
62D ALA 3.9 7.2 - - - +
63D GLY* 3.3 17.2 + - - +
65D MET* 1.3 83.1 - - - +
67D GLY* 1.3 64.9 + - - +
68D ASP* 3.3 5.4 + - - +
76D ASN* 3.6 9.4 + - - +
79D HIS* 5.1 7.9 - - + -
300D GLU* 4.3 22.2 - - - +
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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