Contacts of the helix formed by residues 60 - 74 (chain C) in PDB entry 6XWQ
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 VAL 60 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ASN* 5.4 2.7 - - - +
56C LEU 4.2 0.9 - - - +
57C LYS* 3.2 17.7 - - + +
58C MET 3.3 1.0 - - - -
59C LEU* 1.3 78.7 - - - +
61C MET* 1.3 79.2 + - + +
63C ILE 4.3 0.4 - - - -
64C VAL* 3.3 26.2 + - - +
153C VAL* 5.1 4.7 - - + +
281C SER* 3.6 19.9 + - - +
311C THR* 5.7 5.2 - - + -
356C ALA* 4.1 12.1 - - + -
357C GLY 3.7 26.0 - - - +
358C VAL* 3.7 22.2 - - + -
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Residues in contact with MET 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ASN* 3.3 25.4 - - - +
145B PHE* 3.8 22.4 - - + -
58C MET 4.4 0.4 + - - -
60C VAL* 1.3 85.3 - - + +
62C PRO* 1.3 69.8 - - + +
64C VAL* 3.1 17.8 - - - +
65C LEU* 3.0 24.9 + - - +
148C LEU* 3.9 11.2 - - + +
151C GLY* 3.4 24.5 - - - +
152C GLU 3.3 19.1 - - - +
153C VAL* 3.8 15.5 - - + -
156C VAL* 3.7 27.1 - - - -
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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
----------------------------------------------------------
144B PRO* 3.7 26.9 - - + -
145B PHE* 4.3 20.9 - - + -
159B PHE* 4.6 2.0 - - + -
58C MET 3.4 18.2 - - - +
59C LEU 4.7 0.7 - - - -
60C VAL 4.0 0.9 - - - +
61C MET* 1.3 94.1 - - + +
63C ILE* 1.3 62.7 + - - +
65C LEU* 3.9 2.4 - - + +
66C ALA* 2.9 29.6 + - - +
192C LEU* 5.0 8.7 - - + +
196C MET* 3.6 34.3 - - + -
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Residues in contact with ILE 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C LEU* 3.1 31.9 - - + +
60C VAL 4.2 1.5 + - - +
61C MET 3.3 0.6 - - - -
62C PRO* 1.3 77.4 - - - +
64C VAL* 1.3 65.6 + - - +
66C ALA* 5.1 1.1 - - - -
67C SER* 2.8 34.0 + - - +
193C ALA* 5.8 0.9 - - - +
196C MET* 3.5 30.3 - - + +
197C TYR* 4.1 17.7 - - + -
200C VAL* 3.4 31.6 - - + -
281C SER* 4.1 9.9 - - - +
284C LEU* 3.7 31.2 - - + -
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Residues in contact with VAL 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C VAL* 3.3 17.2 + - + +
61C MET* 3.1 33.0 + - + +
63C ILE* 1.3 79.9 - - - +
65C LEU* 1.3 68.7 + - - +
67C SER* 5.0 0.2 - - - -
68C LEU* 2.9 42.9 + - + +
153C VAL* 4.9 6.3 - - + -
156C VAL* 4.3 7.4 - - + -
157C ILE* 3.6 30.3 - - + -
160C ALA* 5.4 0.2 - - - -
281C SER* 5.8 1.3 - - - +
307C PRO 4.8 0.7 - - - +
311C THR* 3.8 26.5 - - + +
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Residues in contact with LEU 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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145B PHE* 4.2 16.4 - - + -
61C MET 3.0 16.8 + - - +
62C PRO 3.9 2.2 - - - +
64C VAL* 1.3 80.8 - - - +
66C ALA* 1.3 67.5 + - - +
69C VAL* 3.0 35.1 + - + +
148C LEU* 4.0 24.0 - - + -
156C VAL* 3.9 20.9 - - + -
159C PHE* 4.7 15.9 - - + -
160C ALA* 3.6 22.8 - - + +
163C LEU* 6.0 0.2 - - + -
189C PHE* 4.7 21.3 - - + -
192C LEU* 5.5 4.9 - - + -
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Residues in contact with ALA 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 PRO 2.9 20.0 + - - +
65C LEU* 1.3 76.5 - - - +
67C SER* 1.3 58.7 + - - +
69C VAL* 3.2 6.7 + - - +
70C VAL* 2.9 32.9 + - - +
189C PHE* 3.7 26.2 - - + +
192C LEU* 3.9 19.3 - - + -
193C ALA* 3.8 18.2 - - + +
196C MET* 5.8 0.2 - - + -
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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 ILE* 2.8 28.7 + - - -
64C VAL* 4.5 0.4 - - - -
66C ALA* 1.3 70.5 - - - +
68C LEU* 1.3 60.8 + - - +
70C VAL* 3.9 3.2 - - - +
71C GLY* 2.9 27.5 + - - -
193C ALA* 4.0 12.1 - - - +
197C TYR* 3.1 25.1 + - - -
284C LEU* 5.6 0.2 - - - -
303C SER 4.1 3.6 + - - +
307C PRO* 3.0 29.5 - - - +
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Residues in contact with LEU 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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64C VAL* 2.9 46.1 + - + +
67C SER* 1.3 75.5 - - - +
69C VAL* 1.3 64.0 + - - +
71C GLY* 5.2 0.7 - - - -
72C ALA* 2.9 28.4 + - - +
157C ILE* 4.5 15.0 - - + -
160C ALA* 3.8 18.8 - - + -
161C ILE* 5.0 6.7 - - + -
304C PHE* 3.9 31.8 - - + +
307C PRO* 3.5 32.1 - - + +
308C LEU* 4.1 21.8 - - + +
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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
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65C LEU* 3.0 22.5 + - + +
66C ALA 3.2 6.7 + - - +
68C LEU* 1.3 77.7 - - - +
70C VAL* 1.3 59.3 + - + +
72C ALA 3.7 0.7 - - - -
73C ALA* 2.9 28.8 + - - +
160C ALA* 3.3 33.0 - - + +
163C LEU* 4.3 9.0 - - + -
164C GLY* 3.8 4.6 - - - -
167C ILE* 4.3 17.7 - - + -
186C LEU* 4.8 4.0 - - + -
189C PHE* 3.3 44.6 - - + -
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Residues in contact with VAL 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ARG* 6.0 0.9 - - - +
66C ALA 2.9 19.7 + - - +
67C SER* 3.9 5.6 - - - +
69C VAL* 1.3 76.3 - - - +
71C GLY* 1.3 60.4 + - - +
73C ALA* 3.3 0.9 + - - +
74C SER* 2.9 39.6 + - - +
186C LEU* 4.2 14.5 - - + +
189C PHE* 3.5 10.3 - - + +
190C ASP* 3.5 54.5 - - + +
193C ALA* 4.7 3.8 - - + -
303C SER* 4.9 8.1 - - - +
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Residues in contact with GLY 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 2.9 12.5 + - - -
68C LEU 3.9 0.7 - - - -
70C VAL* 1.3 80.1 - - - +
72C ALA* 1.3 57.6 + - - +
73C ALA 3.4 0.7 + - - -
74C SER* 3.5 3.0 + - - -
75C ILE* 3.2 30.1 - - - +
303C SER* 3.2 35.3 + - - -
304C PHE* 4.2 8.7 - - - -
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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
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68C LEU 2.9 19.0 + - - +
69C VAL 3.7 2.2 - - - +
71C GLY* 1.3 75.7 - - - +
73C ALA* 1.3 58.3 + - - +
74C SER 3.6 0.2 - - - -
75C ILE 4.1 6.5 - - - +
80C LEU* 3.2 35.4 - - + +
161C ILE* 3.7 38.6 - - + +
164C GLY* 3.5 12.7 - - - +
165C ILE 4.0 0.2 + - - -
168C THR* 4.2 1.7 - - - +
304C PHE* 4.5 4.8 - - + -
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Residues in contact with ALA 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 18.1 + - + +
70C VAL 3.7 0.2 - - - -
72C ALA* 1.3 78.5 - - - +
74C SER* 1.3 55.6 + - - +
75C ILE 3.2 5.6 - - - -
164C GLY* 3.3 21.3 - - - +
167C ILE* 3.9 13.7 - - + -
168C THR* 3.3 20.2 + - - +
171C MET* 4.1 13.7 - - - +
186C LEU* 3.6 25.2 - - + +
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Residues in contact with SER 74 (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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70C VAL* 2.9 28.6 + - - +
71C GLY* 3.5 5.9 + - - -
73C ALA* 1.3 74.6 - - - +
75C ILE* 1.3 63.2 + - - +
79C ARG* 5.2 4.7 + - - -
171C MET* 6.0 0.7 - - - -
186C LEU* 4.9 9.3 - - - +
299C LYS* 6.6 0.4 - - - -
300C GLY* 5.6 1.7 - - - -
303C SER* 5.5 5.6 - - - -
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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