Contacts of the helix formed by residues 57 - 68 (chain C) in PDB entry 4QGC
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 57 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C SER 3.4 0.2 - - - -
56C ARG* 1.3 79.9 - - - +
58C VAL* 1.3 59.4 + - - +
59C GLU* 3.9 7.4 + - - +
60C THR* 2.9 31.0 + - - -
61C LEU* 3.0 31.8 + - - +
90C ASN* 4.4 4.0 - - - +
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Residues in contact with VAL 58 (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 ARG 3.9 0.8 + - - -
57C SER* 1.3 72.4 - - - +
59C GLU* 1.3 64.3 + - - +
61C LEU* 3.4 9.1 + - - +
62C LYS* 3.0 51.3 + - + +
90C ASN* 4.0 34.9 - - + +
93C THR* 4.3 22.9 - - + -
94C ALA* 3.9 4.8 - - - +
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Residues in contact with GLU 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C SER* 3.3 7.5 - - - +
58C VAL* 1.3 79.5 - - - +
60C THR* 1.3 63.7 + - - +
62C LYS* 3.3 24.3 + - + +
63C GLU* 3.3 16.8 + - - +
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Residues in contact with THR 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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54C ALA 3.9 21.6 + - - +
55C SER* 3.9 15.0 - - - -
57C SER* 2.9 21.2 + - - -
59C GLU* 1.3 75.8 - - - +
61C LEU* 1.3 60.7 + - - +
63C GLU* 3.0 7.1 + - - +
64C MET* 2.9 32.2 + - - +
371C PRO* 4.6 5.8 - - + -
372C LEU* 3.7 21.3 - - + -
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Residues in contact with LEU 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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51C ILE* 3.7 26.2 - - + -
55C SER 3.3 17.7 - - - +
56C ARG* 3.6 15.3 - - - +
57C SER 3.0 22.3 + - - +
58C VAL 3.7 0.7 - - - +
60C THR* 1.3 77.0 - - - +
62C LYS* 1.3 62.2 + - - +
64C MET* 3.2 7.6 + - - +
65C ILE* 3.0 30.5 + - + +
69C MET* 4.1 13.4 - - + +
87C THR* 4.7 0.7 - - + +
90C ASN* 3.7 8.1 - - + +
91C VAL* 3.6 42.6 - - + +
94C ALA* 3.7 15.3 - - + -
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Residues in contact with LYS 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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58C VAL* 3.0 39.4 + - + +
59C GLU* 3.4 15.9 - - + +
61C LEU* 1.3 77.9 - - - +
63C GLU* 1.3 64.7 + - + +
65C ILE* 3.5 2.6 + - - +
66C LYS* 3.2 31.8 + - - +
93C THR* 5.0 1.1 - - - -
94C ALA* 3.9 13.7 - - + +
97C SER* 3.7 31.4 - - - +
98C PHE* 3.8 14.3 - - + -
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Residues in contact with GLU 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 GLU* 3.3 13.7 + - + +
60C THR* 3.0 10.1 + - - +
62C LYS* 1.3 76.3 - - - +
64C MET* 1.3 60.6 + - - +
66C LYS* 3.0 35.5 + - - +
67C SER* 2.8 33.1 + - - -
372C LEU* 3.6 22.9 - - + -
376C ARG* 4.0 14.4 + - - +
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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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49C CYS* 3.7 25.1 - - + -
51C ILE* 4.4 2.5 - - + -
55C SER* 3.4 28.5 - - - -
60C THR* 2.9 22.9 + - - +
61C LEU* 3.2 16.6 + - - +
63C GLU* 1.3 76.3 - - - +
65C ILE* 1.3 62.0 + - - +
67C SER* 3.3 7.8 + - - -
68C GLY 3.1 6.4 + - - -
69C MET* 2.9 38.8 + - + +
365C THR* 3.9 15.3 - - + -
371C PRO* 4.7 4.0 - - - +
372C LEU* 3.6 16.6 - - + -
375C VAL* 3.6 29.7 - - + +
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Residues in contact with ILE 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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61C LEU* 3.0 21.2 + - + +
62C LYS 3.7 4.9 - - - +
64C MET* 1.3 77.8 - - - +
66C LYS* 1.3 62.1 + - - +
68C GLY* 3.2 14.0 + - - -
69C MET* 3.7 27.7 + - + +
91C VAL* 4.7 1.6 - - + +
94C ALA* 3.8 14.1 - - + +
95C THR* 3.6 41.3 - - - +
98C PHE* 4.1 18.6 - - + -
106C ARG* 4.9 18.4 - - + +
108C VAL* 4.0 18.6 - - + -
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Residues in contact with LYS 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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62C LYS* 3.2 15.8 + - - +
63C GLU* 3.0 42.7 + - - +
65C ILE* 1.3 78.0 - - + +
67C SER* 1.3 60.4 + - - +
68C GLY* 3.6 0.5 + - - -
98C PHE* 3.6 29.8 - - + -
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Residues in contact with SER 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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63C GLU* 2.8 21.8 + - - -
64C MET 3.3 6.0 + - - -
65C ILE 3.1 0.4 - - - -
66C LYS* 1.3 76.9 - - - +
68C GLY* 1.3 56.4 + - - +
69C MET 3.9 0.2 - - - -
372C LEU* 3.2 7.1 - - - +
375C VAL* 3.9 14.3 - - - +
376C ARG* 3.0 45.1 + - - +
379C HIS* 3.9 25.3 + - - +
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Residues in contact with GLY 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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43C ARG* 2.9 35.6 + - - -
47C ILE* 3.7 7.2 - - - +
64C MET 3.1 1.0 + - - -
65C ILE 3.2 8.1 + - - -
66C LYS 3.3 1.3 - - - -
67C SER* 1.3 80.3 - - - +
69C MET* 1.3 66.6 + - - +
70C ASN* 3.3 10.8 + - - +
375C VAL* 4.3 4.9 - - - -
379C HIS* 4.9 1.6 - - - -
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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