Contacts of the helix formed by residues 66 - 81 (chain C) in PDB entry 4QUG
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 GLY 66 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C SER* 1.3 73.7 - - - +
67C THR* 1.3 62.6 + - - +
68C ASP 3.2 2.9 - - - -
69C VAL* 3.1 21.9 + - - +
70C ASP 3.3 4.5 + - - -
207C ARG* 4.6 2.7 - - - -
208C ASN 3.8 9.6 - - - -
209C SER 3.4 17.6 + - - -
212C GLY* 3.5 11.8 - - - -
302C AZI 3.1 19.3 + - - -
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Residues in contact with THR 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ASN* 2.6 30.4 + - - +
53C LYS* 3.5 30.7 - - + -
64C ARG* 2.9 51.2 + - - +
65C SER 3.4 0.6 + - - -
66C GLY* 1.3 78.1 - - - +
68C ASP* 1.3 62.8 + - - +
70C ASP* 3.2 10.7 + - - +
71C ALA 2.9 23.0 + - - -
119C LEU* 3.7 10.2 - - - +
207C ARG* 4.2 3.0 - - - +
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Residues in contact with ASP 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ASN* 3.0 25.0 + - - +
53C LYS* 2.8 34.7 + - - +
67C THR* 1.3 74.2 - - - +
69C VAL* 1.3 66.7 + - - +
71C ALA* 3.3 2.7 + - - +
72C ALA* 3.0 25.5 + - - +
89C ASN* 5.0 0.2 - - - +
302C AZI 3.2 16.9 + - - +
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Residues in contact with VAL 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C GLY* 3.1 10.5 + - - +
68C ASP* 1.3 78.8 - - - +
70C ASP* 1.3 62.8 + - - +
72C ALA* 3.4 4.8 + - - +
73C ASN* 2.9 28.1 + - + +
209C SER 5.3 0.4 - - - +
210C LYS 3.7 19.5 - - - +
211C ASP* 3.5 25.6 - - - +
212C GLY* 4.3 0.7 - - - -
302C AZI 3.4 18.4 - - - +
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Residues in contact with ASP 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ARG* 5.1 2.1 + - - -
66C GLY 3.3 3.4 + - - +
67C THR* 3.2 15.6 + - - +
69C VAL* 1.3 79.7 - - - +
71C ALA* 1.3 58.4 + - - +
73C ASN* 3.2 5.4 + - - +
74C LEU* 2.9 35.6 + - - +
119C LEU* 4.0 12.6 - - + +
161C GLN* 4.3 4.3 - - - +
207C ARG* 5.3 0.9 - - - +
211C ASP 4.6 1.2 - - - +
212C GLY* 3.3 8.1 - - - -
213C SER* 2.7 46.7 + - - +
216C ILE* 3.5 28.8 - - + +
217C GLN* 4.3 3.1 + - - +
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Residues in contact with ALA 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ILE* 4.0 3.3 - - + +
51C ASN* 3.8 28.3 - - + +
67C THR 2.9 18.4 + - - +
68C ASP* 3.3 5.3 + - - +
70C ASP* 1.3 73.4 - - - +
72C ALA* 1.3 57.0 + - - +
74C LEU* 3.6 4.5 + - - +
75C ARG* 3.0 28.9 + - - +
87C ASN* 3.6 22.5 + - - +
89C ASN* 5.3 0.7 - - - +
119C LEU* 3.9 10.0 - - + +
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Residues in contact with ALA 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ASP 3.0 17.1 + - - +
69C VAL* 3.7 5.4 - - - +
71C ALA* 1.3 76.0 - - - +
73C ASN* 1.3 63.8 + - - +
75C ARG* 3.4 9.1 + - - +
76C GLU* 3.1 24.6 + - - +
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Residues in contact with ASN 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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69C VAL* 2.9 23.6 + - + +
70C ASP* 3.6 7.3 + - - +
72C ALA* 1.3 75.8 - - - +
74C LEU* 1.3 56.0 + - - +
76C GLU* 3.4 6.3 + - - +
77C THR* 2.7 39.4 + - - -
216C ILE* 4.3 6.8 + - + +
217C GLN* 4.4 14.1 + - - +
220C CYS* 3.4 29.7 - - - +
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Residues in contact with LEU 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ILE* 3.7 17.5 - - + -
70C ASP 2.9 22.0 + - - +
71C ALA* 3.8 1.3 - - - +
73C ASN* 1.3 74.9 - - - +
75C ARG* 1.3 66.7 + - - +
77C THR* 4.3 0.9 - - - -
78C PHE* 2.8 53.1 + - + +
117C VAL* 3.6 31.9 - - + -
119C LEU* 4.0 17.0 - - + -
216C ILE* 3.6 28.7 - - + -
219C LEU* 4.5 9.6 - - + -
220C CYS* 3.8 15.9 - - - -
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Residues in contact with ARG 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ILE* 3.6 8.0 - - - +
71C ALA 3.0 19.4 + - - +
72C ALA* 3.7 8.3 - - - +
73C ASN 3.4 0.2 - - - -
74C LEU* 1.3 75.2 - - - +
76C GLU* 1.3 58.6 + - - +
79C ARG* 2.9 34.1 + - + +
85C VAL* 3.8 32.1 + - + +
87C ASN* 2.8 39.8 + - - +
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Residues in contact with GLU 76 (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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72C ALA 3.1 16.6 + - - +
73C ASN* 3.8 6.5 - - - +
75C ARG* 1.3 75.6 - - - +
77C THR* 1.3 66.7 + - - +
79C ARG* 2.8 45.6 + - - +
80C ASN* 3.1 43.4 + - - +
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Residues in contact with THR 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ASN* 2.7 27.7 + - - -
74C LEU* 3.7 3.6 - - - -
76C GLU* 1.3 77.4 - - - +
78C PHE* 1.3 65.1 + - + +
80C ASN* 3.3 10.8 + - - +
81C LEU* 3.3 23.7 + - + +
220C CYS* 3.3 31.9 + - - +
223C LEU* 3.7 39.7 - - + -
224C LYS* 4.8 6.0 - - + +
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Residues in contact with PHE 78 (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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47C CYS* 3.7 28.5 - - + -
74C LEU* 2.8 53.2 + - + +
77C THR* 1.3 74.4 - - + +
79C ARG* 1.3 64.7 + - - +
81C LEU* 3.2 23.0 + - + +
82C LYS 3.2 0.2 + - - -
83C TYR* 3.0 49.4 + + + +
85C VAL* 4.0 10.1 - - + -
115C VAL* 4.1 20.2 - - + -
117C VAL* 4.6 1.3 - - + -
157C LEU* 5.8 0.9 - - + -
159C ILE* 3.8 26.5 - - + -
219C LEU* 5.2 0.2 - - + -
223C LEU* 4.0 20.6 - - + -
232C PHE* 6.1 2.0 - + - -
275C PHE* 5.0 7.4 - + - -
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Residues in contact with ARG 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ARG* 2.9 23.9 + - + +
76C GLU* 2.8 42.8 + - - +
78C PHE* 1.3 76.8 - - - +
80C ASN* 1.3 72.1 + - - +
82C LYS* 2.9 25.5 + - - +
83C TYR 4.3 10.5 - - - +
85C VAL* 3.9 5.3 - - + +
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Residues in contact with ASN 80 (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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76C GLU* 3.1 35.3 + - - +
77C THR* 3.5 10.4 - - - +
78C PHE 3.2 0.2 - - - -
79C ARG* 1.3 100.1 + - - +
81C LEU* 1.3 62.8 - - + +
82C LYS* 3.2 20.3 + - - +
224C LYS* 5.9 5.9 - - - +
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Residues in contact with LEU 81 (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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44C MET* 3.5 19.9 - - - +
77C THR* 3.3 17.9 + - + +
78C PHE* 3.2 33.5 + - + +
79C ARG 3.1 1.2 - - - -
80C ASN* 1.3 78.5 - - + +
82C LYS* 1.3 70.7 + - - +
83C TYR* 3.4 12.0 + - + -
223C LEU* 4.3 26.5 - - + +
227C ALA* 3.5 28.5 - - + -
275C PHE* 3.9 25.8 - - + +
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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
------------------------------------------------------------
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