Contacts of the helix formed by residues 67 - 80 (chain C) in PDB entry 5XS0
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 GLU 67 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C TYR 4.4 2.6 + - - -
53C SER* 3.8 15.8 + - - +
65C TYR* 3.8 27.8 + - + -
66C ILE* 1.3 77.8 - - - +
68C GLY* 1.3 66.3 + - - +
69C HIS* 2.8 40.8 + - + +
70C ARG* 3.1 32.4 + - + +
71C VAL* 3.2 10.4 + - - +
152C LYS* 5.3 0.2 - - - +
167D LEU 4.4 4.9 - - - +
168D ASP* 5.1 1.0 - - - +
169D LYS* 4.4 24.1 + - - +
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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
----------------------------------------------------------
66C ILE 3.7 1.4 + - - -
67C GLU* 1.3 72.5 - - - +
69C HIS* 1.3 63.5 + - - +
71C VAL* 3.0 7.1 + - - +
72C ILE* 2.9 30.2 + - - +
148C THR* 4.4 22.7 - - - +
152C LYS* 4.6 11.0 - - - +
167D LEU* 6.0 0.9 - - - -
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Residues in contact with HIS 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C GLU* 2.8 34.3 + - + -
68C GLY* 1.3 74.9 - - - +
70C ARG* 1.3 89.6 + - + +
72C ILE* 3.3 2.6 + - - -
73C ASN* 3.0 30.5 + - - -
164D ASN* 3.1 45.1 + - - +
165D CYS* 5.8 0.6 - - - -
167D LEU* 3.9 34.3 + - + +
168D ASP* 3.6 35.8 + - + +
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Residues in contact with ARG 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ASP* 4.8 2.1 - - - +
50C GLU 3.7 15.1 + - - -
51C TYR* 3.5 46.4 + - + +
52C ILE 5.5 0.2 + - - -
53C SER* 4.1 6.1 + - - -
66C ILE* 3.9 13.2 - - + -
67C GLU* 3.1 32.8 + - + +
69C HIS* 1.3 101.4 - - + +
71C VAL* 1.3 57.1 + - - +
73C ASN* 3.4 5.3 + - - +
74C LEU* 2.9 35.1 + - - +
168D ASP* 3.6 22.4 + - - -
170D ASP* 3.9 12.9 + - - -
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Residues in contact with VAL 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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66C ILE* 3.7 26.9 - - + -
67C GLU 3.4 13.7 - - - +
68C GLY 3.0 7.0 + - - +
70C ARG* 1.3 72.8 - - - +
72C ILE* 1.3 67.3 + - + +
74C LEU* 3.3 9.1 + - + +
75C ALA* 2.9 23.4 + - - +
151C LEU* 6.0 1.1 - - + -
152C LYS* 4.1 29.6 - - + -
155C LEU* 3.7 28.0 - - + -
162C LEU* 4.4 21.8 - - + +
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Residues in contact with ILE 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 GLY 2.9 21.2 + - - +
69C HIS* 3.7 1.8 - - - +
71C VAL* 1.3 78.5 - - + +
73C ASN* 1.3 56.2 + - - +
75C ALA* 3.3 5.2 + - - +
76C ASN* 2.9 47.8 + - - +
84C TRP* 4.4 8.2 - - + -
151C LEU* 4.7 20.0 - - + -
155C LEU* 5.6 1.1 - - + -
156D ARG* 4.2 8.5 - - + +
157D SER* 3.6 36.6 - - - +
164D ASN* 3.3 34.1 - - - +
167D LEU* 5.8 2.7 - - + -
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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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195B ASP* 3.6 22.2 + - + +
69C HIS* 3.0 26.9 + - - +
70C ARG* 3.9 4.6 - - - +
72C ILE* 1.3 72.6 - - - +
74C LEU* 1.3 67.4 + - - +
76C ASN* 3.3 6.1 + - - +
77C GLU* 2.9 31.5 + - + +
159D GLY* 4.3 6.1 - - - -
160D ASN* 3.1 42.8 + - - +
164D ASN* 3.2 17.5 + - - +
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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
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192B LYS* 3.6 35.4 - - + -
195B ASP* 3.8 5.1 + - - +
47C LEU* 4.4 7.6 - - + -
51C TYR* 3.7 34.3 - - + +
66C ILE* 4.9 9.4 - - + -
70C ARG 2.9 27.0 + - - +
71C VAL* 3.5 14.6 - - + +
73C ASN* 1.3 76.5 - - - +
75C ALA* 1.3 57.0 + - - +
77C GLU* 3.3 5.4 + - - +
78C MET* 2.9 34.7 + - + +
161C ALA* 3.7 20.9 - - + +
162C LEU* 3.7 15.7 - - + -
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Residues in contact with ALA 75 (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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71C VAL 2.9 16.9 + - - +
72C ILE 3.8 3.1 - - - +
74C LEU* 1.3 74.6 - - - +
76C ASN* 1.3 64.9 + - - +
78C MET* 4.4 0.2 - - - -
79C PHE* 3.0 34.5 + - + -
84C TRP* 3.8 30.9 - - + -
155C LEU* 4.0 21.1 - - + -
162C LEU* 3.7 11.6 - - + +
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Residues in contact with ASN 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 ILE* 2.9 32.7 + - - +
73C ASN* 3.7 8.7 - - - +
75C ALA* 1.3 74.8 - - - +
77C GLU* 1.3 60.5 + - + +
80C GLY* 2.9 30.1 + - - -
81C TYR* 3.6 16.4 - - - +
84C TRP* 2.9 24.2 + - - +
40D GLN* 3.4 15.4 - - - +
121D HIS* 4.9 0.2 + - - -
157D SER 3.1 22.7 + - - +
158D PHE* 3.6 20.2 - - - +
159D GLY* 3.7 6.4 - - - +
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Residues in contact with GLU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B LYS* 5.9 0.2 - - - -
195B ASP* 3.4 38.1 - - + +
196B LEU* 3.7 16.7 - - - +
197B GLU* 4.6 11.3 + - + +
200B VAL* 4.5 3.3 - - - +
201B GLU* 5.4 2.1 + - - +
204B ARG* 2.9 21.9 + - - +
73C ASN* 2.9 23.0 + - + +
74C LEU* 3.8 4.0 - - - +
76C ASN* 1.3 80.3 - - - +
78C MET* 1.3 60.2 + - + +
40D GLN* 4.1 7.2 + - - -
44D ARG* 2.7 54.3 + - - +
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Residues in contact with MET 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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192B LYS* 5.5 5.6 - - - -
197B GLU* 4.1 16.8 - - + +
200B VAL* 3.5 12.6 - - + +
204B ARG* 2.7 16.7 + - - -
39C ILE* 3.6 54.2 - - + +
42C ALA* 4.0 22.0 - - + +
43C LEU* 3.6 29.6 - - + -
74C LEU* 2.9 22.8 + - + +
75C ALA* 3.2 3.6 + - - +
77C GLU* 1.3 77.9 - - + +
79C PHE* 1.3 70.7 + - + +
161C ALA* 4.8 7.0 - - + -
162C LEU* 4.7 7.0 - - + -
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Residues in contact with PHE 79 (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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81B TYR* 3.9 14.8 - + - -
204B ARG* 3.3 20.2 + - - +
31C TYR* 3.6 18.2 - - - +
35C GLU* 4.5 2.6 - - - +
39C ILE* 4.2 13.0 - - + -
43C LEU* 4.7 4.9 - - + -
75C ALA* 3.0 21.1 + - + +
78C MET* 1.3 86.6 - - + +
80C GLY* 1.3 59.8 + - - +
82C ASN* 4.8 0.3 - - - +
83C GLY* 3.2 34.2 - - - -
84C TRP* 3.9 10.8 - - + +
115C LEU* 3.6 37.5 - - + -
116C LYS* 4.7 2.6 + - - -
155C LEU* 4.9 1.8 - - + -
158C PHE* 4.1 15.0 - + + -
162C LEU* 3.6 32.1 - - + -
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Residues in contact with GLY 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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204B ARG* 3.5 16.7 - - - -
76C ASN 2.9 19.7 + - - -
79C PHE* 1.3 79.1 - - - +
81C TYR* 1.3 67.5 + - - -
82C ASN* 3.0 8.0 + - - -
83C GLY 3.1 9.1 + - - -
84C TRP* 3.3 15.1 - - - -
36D TYR* 4.7 1.1 - - - -
40D GLN* 3.2 9.9 - - - -
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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