Contacts of the helix formed by residues 61 - 73 (chain C) in PDB entry 5GQQ
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 ASN 61 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59C PRO 3.2 0.8 + - - -
60C PHE* 1.3 69.5 - - - +
62C PRO* 1.4 72.3 - - - +
63C VAL* 2.9 24.0 + - - +
64C THR* 3.2 24.8 + - - +
65C VAL* 3.1 22.7 + - - +
138C PHE 5.2 0.8 + - - -
140C ARG* 3.5 23.3 - - - +
149C ASP* 2.7 23.2 + - + +
150C ASP* 2.9 22.1 + - - +
153C GLN* 4.4 13.5 - - - +
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Residues in contact with PRO 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ASP* 4.9 0.9 - - - +
49C GLN* 3.8 18.6 - - - +
59C PRO* 5.1 0.9 - - + +
60C PHE 3.1 7.8 - - - +
61C ASN* 1.4 89.2 - - - +
63C VAL* 1.3 59.0 + - + +
65C VAL* 3.4 7.7 + - + +
66C ARG* 3.0 27.4 + - - +
140C ARG* 4.3 11.0 - - - +
45D ASP* 5.6 2.9 - - - +
66D ARG* 3.8 36.3 - - - +
78D ALA* 6.3 2.7 - - + -
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Residues in contact with VAL 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ASN* 2.9 13.4 + - - +
62C PRO* 1.3 79.2 - - + +
64C THR* 1.3 64.0 + - - +
66C ARG* 3.3 8.2 + - + +
67C SER* 3.0 28.4 + - - +
153C GLN* 3.7 26.7 - - + +
191C VAL 6.1 1.1 - - - +
66D ARG* 4.8 20.9 - - + +
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Residues in contact with THR 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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60C PHE* 3.8 19.3 - - + -
61C ASN* 3.2 23.0 + - - +
63C VAL* 1.3 78.1 - - - +
65C VAL* 1.3 64.2 + - - +
67C SER* 3.3 2.9 + - - -
68C ILE* 3.0 35.5 + - + +
149C ASP 3.1 26.6 + - - +
152C ILE* 3.9 25.1 - - + -
153C GLN* 3.4 24.3 + - - +
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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
----------------------------------------------------------
45C ASP* 3.5 34.5 - - + +
48C LEU* 3.8 23.6 - - + -
49C GLN* 4.0 21.5 - - + -
52C LEU* 4.5 3.6 - - + -
60C PHE* 3.7 21.1 - - + -
61C ASN 3.1 17.5 + - - +
62C PRO* 3.7 8.1 - - + +
63C VAL 3.3 0.2 - - - -
64C THR* 1.3 74.0 - - - +
66C ARG* 1.3 66.1 + - - +
68C ILE* 3.2 7.4 + - - +
69C ILE* 2.9 24.4 + - + +
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Residues in contact with ARG 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ASP* 2.5 45.5 + - - +
62C PRO 3.0 13.4 + - - +
63C VAL* 3.3 13.4 + - + +
65C VAL* 1.3 75.6 - - - +
67C SER* 1.3 57.1 + - - +
69C ILE* 3.9 10.5 - - - +
70C SER* 2.9 65.4 + - - +
73C ASP* 5.4 2.0 + - - -
78C ALA* 4.1 19.4 - - - +
62D PRO* 4.1 27.2 - - + +
63D VAL* 4.4 20.6 - - + +
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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
----------------------------------------------------------
63C VAL* 3.0 17.0 + - - +
64C THR 3.6 7.4 - - - -
66C ARG* 1.3 76.8 - - - +
68C ILE* 1.3 63.6 + - - +
70C SER* 3.1 9.2 + - - -
71C MET* 3.1 31.3 + - - +
153C GLN* 3.5 21.8 + - - -
156C ILE* 4.7 16.6 - - - +
160C ARG* 4.8 14.9 + - - +
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Residues in contact with ILE 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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48C LEU* 4.5 7.2 - - + -
52C LEU* 5.3 2.2 - - + -
60C PHE* 4.9 7.0 - - + -
64C THR* 3.0 34.1 + - + +
65C VAL* 3.7 6.3 - - - +
67C SER* 1.3 79.6 - - - +
69C ILE* 1.3 65.3 + - - +
71C MET* 3.1 22.6 + - + +
72C PHE* 3.3 15.1 + - + -
88C VAL* 3.8 31.9 - - + -
91C TYR* 4.1 24.5 - - + -
92C ILE* 3.9 26.2 - - + -
152C ILE* 5.0 9.2 - - + -
156C ILE* 5.6 1.3 - - + -
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Residues in contact with ILE 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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43C ILE 4.0 20.0 - - - +
44C SER 4.3 4.3 - - - +
45C ASP* 4.0 16.4 - - - +
48C LEU* 3.7 31.4 - - + -
65C VAL* 2.9 22.5 + - + +
66C ARG* 3.8 20.4 - - - +
68C ILE* 1.3 76.0 - - - +
70C SER* 1.3 58.8 + - - +
72C PHE* 3.1 2.1 + - - -
73C ASP* 2.8 32.0 + - + +
79C GLY* 3.8 28.5 - - - +
80C VAL* 4.0 20.9 - - + +
88C VAL* 5.4 1.1 - - + -
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Residues in contact with SER 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ARG* 2.9 36.7 + - - +
67C SER* 3.1 17.2 + - - -
69C ILE* 1.3 77.4 - - - +
71C MET* 1.3 59.8 + - - +
72C PHE 3.5 0.2 + - - -
73C ASP* 3.7 16.3 - - - +
160C ARG* 5.9 0.9 + - - -
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Residues in contact with MET 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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67C SER* 3.1 23.7 + - - +
68C ILE* 3.2 11.2 - - - +
69C ILE 3.1 0.4 - - - -
70C SER* 1.3 80.1 + - - +
72C PHE* 1.3 75.2 + - + +
73C ASP 5.0 0.8 - - - +
91C TYR* 3.7 43.5 - - + +
156C ILE* 3.8 17.0 - - + -
160C ARG* 3.7 26.9 - - - +
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Residues in contact with PHE 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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68C ILE* 3.3 15.4 + - + +
69C ILE 3.1 2.2 + - - -
71C MET* 1.3 97.5 - - + +
73C ASP* 1.3 64.0 + - - +
74C ARG* 3.2 11.3 + - - +
80C VAL* 4.0 7.9 - - + -
84C GLU* 3.4 25.1 - - + +
87C GLY* 3.6 35.4 - - - -
88C VAL* 3.7 27.6 - - + -
91C TYR* 3.6 40.2 - + + -
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Residues in contact with ASP 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ARG* 5.4 2.0 + - - +
69C ILE* 2.8 26.6 + - + +
70C SER* 3.7 14.4 - - - +
71C MET 5.0 0.3 - - - +
72C PHE* 1.3 70.8 - - - +
74C ARG* 1.3 60.3 + - - +
75C GLU 2.7 23.8 + - - +
76C ASN* 3.8 1.6 + - - +
77C LYS* 2.5 48.5 + - - -
78C ALA* 3.1 13.9 + - - -
79C GLY 3.0 22.1 + - - +
80C VAL* 3.9 1.4 - - - +
84C GLU* 3.9 4.7 - - - -
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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