Contacts of the helix formed by residues 71 - 82 (chain C) in PDB entry 5W5T
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 ALA 71 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B GLN* 4.5 6.3 + - - +
35C ALA* 4.9 2.5 - - + -
67C THR* 3.6 36.1 - - + +
68C GLN 3.9 13.8 + - - +
69C TYR 3.8 4.5 - - - +
70C LYS* 1.3 75.1 - - - +
72C HIS* 1.3 58.4 + - - +
73C SER 3.5 0.9 - - - -
74C LEU* 3.3 10.9 + - + -
75C ILE* 2.8 40.4 + - + +
97C PRO* 6.1 0.2 - - + -
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Residues in contact with HIS 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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96B LEU* 4.7 9.3 - - + +
100B GLN* 3.5 28.3 + - + +
101B ARG* 2.8 68.1 + - + -
121B ILE* 4.7 11.9 - - + +
33C ARG 5.6 3.4 - - - +
70C LYS 3.2 3.7 - - - +
71C ALA* 1.3 78.6 - - - +
73C SER* 1.3 69.3 + - - +
75C ILE* 3.3 2.8 + - - +
76C ARG* 3.1 40.5 + - - +
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Residues in contact with SER 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ARG 4.6 4.5 + - - -
34C ARG* 3.7 29.0 + - - +
38C ALA* 4.0 6.5 - - - +
46C ARG* 4.3 18.7 + - - -
70C LYS 4.5 1.8 + - - -
71C ALA 3.5 0.2 - - - -
72C HIS* 1.3 86.1 - - - +
74C LEU* 1.3 65.6 + - - +
76C ARG* 3.6 10.2 - - - +
77C HIS* 3.1 23.7 + - - +
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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
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20C ALA* 3.6 33.7 - - + +
35C ALA* 4.7 9.0 - - + -
37C PRO* 4.1 7.0 - - + -
38C ALA* 3.9 27.1 - - + +
48C ILE* 3.7 36.8 - - + -
67C THR* 3.6 19.5 - - + -
70C LYS 5.0 0.6 + - - +
71C ALA* 3.3 14.5 + - + +
72C HIS 3.2 0.4 - - - -
73C SER* 1.3 79.3 + - - +
75C ILE* 1.3 65.0 + - - +
77C HIS* 3.3 8.6 + - + +
78C LEU* 3.0 35.7 + - + +
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Residues in contact with ILE 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLN* 5.0 0.9 - - - +
101B ARG* 3.3 42.8 - - + +
67C THR* 3.9 16.6 - - + +
71C ALA* 2.8 23.3 + - + +
72C HIS 3.7 3.4 - - - +
74C LEU* 1.3 76.2 - - - +
76C ARG* 1.3 57.4 + - - +
78C LEU* 3.2 9.1 + - - +
79C GLN* 2.9 53.5 + - - +
95C ILE* 3.9 21.4 - - + +
97C PRO* 3.8 26.0 - - + -
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Residues in contact with ARG 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ASP* 2.9 23.2 + - - -
101B ARG* 3.2 29.7 - - - +
121B ILE* 4.3 19.3 + - - +
125B TYR* 3.5 12.7 + - - -
72C HIS* 3.1 32.3 + - - +
73C SER* 3.6 9.9 - - - +
75C ILE* 1.3 77.9 - - - +
77C HIS* 1.3 60.8 + - - +
79C GLN* 3.2 13.9 + - - +
80C ARG* 3.0 68.1 + - - +
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Residues in contact with HIS 77 (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 LYS 5.9 0.4 - - - -
46C ARG* 3.3 38.0 + - + +
48C ILE* 4.1 18.5 - - + +
49C ASP* 2.8 39.5 + - - -
73C SER 3.1 14.7 + - - +
74C LEU* 3.3 9.8 + - + +
76C ARG* 1.3 75.0 - - - +
78C LEU* 1.3 66.4 + - + +
80C ARG* 4.3 2.9 - - - +
81C GLY* 2.8 30.7 + - - +
82C TRP* 4.1 4.7 + + - -
302C THR* 3.4 13.5 - - - -
303C TYR* 3.7 27.7 - - + +
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Residues in contact with LEU 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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48C ILE* 3.9 10.8 - - + -
52C LEU* 3.6 30.7 - - + -
65C VAL* 3.7 33.7 - - + -
67C THR* 4.9 1.3 - - + -
74C LEU* 3.0 31.6 + - + +
75C ILE* 3.6 7.0 - - - +
77C HIS* 1.3 85.2 - - + +
79C GLN* 1.3 57.9 + - - +
82C TRP* 3.1 40.2 + - + +
93C PHE* 4.0 10.2 - - + -
95C ILE* 3.6 30.1 - - + +
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Residues in contact with GLN 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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75B ILE* 4.7 1.0 - - - +
79B GLN* 3.0 49.6 - - + +
83B ASP* 5.6 1.9 - - - +
93B PHE 5.5 1.9 - - - +
95B ILE* 4.1 27.7 + - + +
101B ARG* 3.7 21.0 + - - +
75C ILE* 2.9 34.5 + - - +
76C ARG* 3.2 11.1 + - - +
78C LEU* 1.3 78.9 - - - +
80C ARG* 1.3 60.5 + - + +
83C ASP* 3.4 22.7 - - - +
95C ILE* 4.0 6.5 - - + -
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Residues in contact with ARG 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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86B ARG* 4.4 6.1 + - - -
87B PRO* 4.8 18.1 - - + +
92B SER* 5.4 3.0 - - - -
93B PHE 4.8 10.5 + - - +
94B ASP* 3.1 19.2 + - - -
101B ARG* 4.8 0.4 - - - +
125B TYR* 4.0 8.1 + - - -
76C ARG* 3.0 61.9 + - + +
77C HIS* 4.3 1.3 - - - +
79C GLN* 1.3 81.7 - - + +
81C GLY* 1.3 62.7 + - - +
83C ASP* 3.7 16.4 - - - +
303C TYR* 3.5 49.0 - - + -
305C GLU* 5.1 1.2 + - - -
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Residues in contact with GLY 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C HIS 2.8 16.2 + - - -
80C ARG* 1.3 81.5 - - - +
82C TRP* 1.3 63.9 + - - +
83C ASP* 3.4 7.2 + - - +
84C PHE* 3.8 3.8 - - - -
301C TRP* 2.9 26.7 + - - -
303C TYR* 3.6 27.5 - - - -
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Residues in contact with TRP 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ASP* 2.9 23.6 + - - -
52C LEU* 3.5 43.4 - - + +
53C SER* 3.5 24.0 - - - -
56C LEU* 3.9 24.0 - - + -
63C ILE* 5.3 0.7 - - + -
77C HIS* 4.1 6.2 + - - -
78C LEU* 3.1 30.8 + - + +
81C GLY* 1.3 82.2 - - - +
83C ASP* 1.3 56.5 + - - +
84C PHE* 3.5 24.4 + + - -
85C PHE* 4.1 11.0 + + - -
93C PHE* 3.6 50.5 - + + +
301C TRP* 3.5 39.3 - + + -
302C THR* 4.7 1.4 - - - +
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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