Contacts of the helix formed by residues 70 - 85 (chain C) in PDB entry 5W4A
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 ASP 70 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MSE 2.6 50.7 + - - +
2C ASP* 3.3 7.7 + - + +
68C GLY 3.2 5.5 + - - +
69C SER* 1.3 75.6 - - - +
71C SER* 1.3 60.1 + - - +
73C THR* 3.0 13.1 + - - -
74C ILE* 2.9 30.1 + - - +
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Residues in contact with SER 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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1C MSE 4.2 3.6 + - - -
2C ASP* 4.5 8.5 - - - -
3C THR 4.5 5.5 + - - -
70C ASP* 1.3 77.0 - - - +
72C GLY* 1.3 60.6 + - - +
74C ILE* 3.3 10.8 + - - +
75C LEU* 2.9 39.3 + - - +
99C LEU* 5.2 4.2 - - - +
104C LEU* 3.7 30.7 - - - +
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Residues in contact with GLY 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MSE 2.9 29.2 + - - -
3C THR* 3.3 16.6 - - - -
71C SER* 1.3 79.1 + - - +
73C THR* 1.3 61.0 + - - +
75C LEU* 4.0 4.7 - - - +
76C THR* 2.9 32.7 + - - -
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Residues in contact with THR 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MSE 3.5 9.6 + - - +
20C PRO* 6.3 3.1 - - + -
64C LEU 4.1 13.2 - - - +
66C PRO* 4.7 5.8 - - + -
69C SER* 3.4 25.4 - - - +
70C ASP* 3.0 27.0 + - - -
72C GLY* 1.3 75.6 - - - +
74C ILE* 1.3 63.5 + - - +
76C THR* 3.8 4.8 - - - -
77C SER* 2.9 25.9 + - - +
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Residues in contact with ILE 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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65C PHE* 3.6 24.4 - - + -
69C SER* 3.8 27.4 - - - +
70C ASP 2.9 23.7 + - - +
71C SER* 3.7 7.9 - - - +
73C THR* 1.3 77.2 - - - +
75C LEU* 1.3 58.9 + - - +
77C SER 3.3 1.0 + - - -
78C MSE 2.8 52.5 + - - +
95C ARG* 4.5 15.0 - - + +
99C LEU* 4.1 22.2 - - + -
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Residues in contact with LEU 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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3C THR 4.9 0.4 - - - +
4C ASN* 4.6 27.6 - - + +
17C TYR* 5.1 0.2 - - - -
71C SER* 2.9 27.5 + - - +
72C GLY* 4.0 4.3 - - - +
74C ILE* 1.3 75.7 - - - +
76C THR* 1.3 63.5 + - - +
78C MSE 3.2 7.6 + - - +
79C ASP* 3.1 23.3 + - - -
99C LEU* 3.7 28.5 - - + -
104C LEU* 5.6 10.8 - - + -
105C THR 3.7 21.1 - - - +
106C HIS* 3.8 23.2 - - + -
107C ASP* 5.3 0.9 - - - +
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Residues in contact with THR 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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5C LYS 5.1 5.9 + - - -
6C ARG* 5.5 0.3 - - - -
7C GLU 5.5 1.2 + - - +
17C TYR* 3.3 57.6 + - + +
18C PHE* 4.8 2.5 - - - +
20C PRO* 4.6 14.4 - - + -
72C GLY 2.9 19.9 + - - -
73C THR* 3.8 4.7 - - - -
75C LEU* 1.3 76.1 - - - +
77C SER* 1.3 64.5 + - - +
79C ASP* 3.1 20.8 + - - +
80C THR* 3.2 8.3 + - - -
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Residues in contact with SER 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C PHE 5.1 2.6 + - - -
20C PRO* 5.8 3.5 - - - +
64C LEU* 2.7 39.6 + - - +
65C PHE* 3.4 22.9 - - - -
73C THR* 2.9 18.7 + - - +
76C THR* 1.3 78.9 - - - +
78C MSE 1.3 57.1 + - - +
80C THR* 3.1 12.1 + - - -
81C LEU* 2.9 28.9 + - - +
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Residues in contact with MSE 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C PHE* 4.1 6.5 - - + -
74C ILE* 2.8 29.7 + - - +
75C LEU* 3.5 11.9 - - - +
76C THR 3.2 0.2 - - - -
77C SER* 1.3 73.6 - - - +
79C ASP* 1.3 65.4 + - - +
81C LEU* 3.2 10.4 + - + +
82C LEU* 3.0 26.9 + - - +
92C PHE* 3.5 29.6 - - + +
95C ARG* 3.8 17.5 - - + -
96C ASN* 3.4 44.6 - - + +
99C LEU* 3.7 24.5 - - - -
106C HIS* 3.7 14.1 - - + -
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Residues in contact with ASP 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ARG* 2.7 28.7 + - - +
17C TYR* 2.6 28.7 + - + -
18C PHE* 3.9 13.0 - - + -
75C LEU 3.1 10.9 + - - -
76C THR 3.1 11.0 + - - +
78C MSE 1.3 74.1 - - - +
80C THR* 1.3 62.4 - - - +
82C LEU* 3.2 4.2 + - - +
83C ALA* 3.0 18.7 + - - +
106C HIS* 2.7 30.2 + - - -
140C ILE* 5.0 0.2 - - - +
144C LEU* 3.3 31.8 - - + +
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Residues in contact with THR 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C PHE* 2.8 34.3 + - - +
19C PHE* 3.5 38.1 - - + -
64C LEU* 3.7 17.9 - - + -
76C THR 3.2 9.9 + - - -
77C SER* 3.1 11.3 + - - -
79C ASP* 1.3 78.0 - - - +
81C LEU* 1.3 62.6 + - - +
83C ALA* 3.2 4.3 + - - +
84C LEU* 3.0 33.6 + - + +
175C PHE* 4.2 5.4 - - + -
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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
----------------------------------------------------------
61C VAL* 4.6 4.5 - - + -
64C LEU* 4.0 11.7 - - + -
65C PHE* 3.6 33.9 - - + -
77C SER 2.9 16.4 + - - +
78C MSE 3.2 13.0 + - + +
80C THR* 1.3 76.0 - - - +
82C LEU* 1.3 62.3 + - - +
84C LEU* 3.2 13.4 + - + +
85C GLY 3.3 10.4 + - - +
88C PHE* 3.6 46.3 - - + +
89C LEU* 5.6 0.6 - - - -
91C GLU* 3.8 15.3 - - + +
92C PHE* 3.6 35.0 - - + +
95C ARG* 4.6 0.2 - - + -
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Residues in contact with LEU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C MSE 3.0 9.6 + - - +
79C ASP* 3.2 8.7 + - - +
81C LEU* 1.3 75.9 - - - +
83C ALA* 1.3 62.7 + - - +
85C GLY* 3.3 13.1 + - - -
89C LEU* 4.1 19.7 - - + -
92C PHE* 3.5 49.1 - - + -
106C HIS* 3.7 20.9 - - + +
108C LEU* 4.3 7.6 - - + -
111C LEU* 4.3 17.9 - - + -
144C LEU* 4.4 1.1 - - + -
148C ILE* 3.9 37.6 - - + +
156C LYS* 5.0 0.7 + - - -
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Residues in contact with ALA 83 (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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18C PHE* 4.6 2.2 - - + -
79C ASP 3.0 12.7 + - - +
80C THR 3.2 3.6 + - - +
82C LEU* 1.3 77.7 - - - +
84C LEU* 1.3 53.6 + - - +
144C LEU* 4.0 15.8 - - + +
147C THR* 4.2 18.1 - - + +
148C ILE* 4.9 2.0 - - - +
156C LYS* 2.7 34.2 + - - +
160C LEU* 5.1 1.3 - - + -
175C PHE* 3.6 32.3 - - + -
179C LEU* 3.9 4.9 - - - +
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Residues in contact with LEU 84 (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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19C PHE* 5.1 5.2 - - + -
60C ILE* 4.1 15.0 - - + -
64C LEU* 4.4 3.6 - - + -
80C THR* 3.0 34.9 + - + +
81C LEU* 3.2 4.2 + - - +
83C ALA* 1.3 77.2 - - - +
85C GLY* 1.3 60.0 + - - +
86C PRO* 4.2 1.6 - - - +
87C ASP* 4.9 1.0 + - - +
88C PHE* 3.4 47.1 - - + -
156C LYS* 3.9 3.0 + - - -
175C PHE* 3.9 25.6 - - + -
178C ILE* 4.0 26.9 - - + -
179C LEU* 3.6 25.5 - - + +
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Residues in contact with GLY 85 (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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81C LEU 3.3 3.7 + - - +
82C LEU* 3.3 12.4 + - - -
83C ALA 3.3 3.0 - - - -
84C LEU* 1.3 78.3 - - - +
86C PRO* 1.3 74.5 - - - +
87C ASP 3.3 2.5 - - - -
88C PHE* 3.0 15.8 + - - +
89C LEU* 3.6 8.9 + - - +
156C LYS* 4.1 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
------------------------------------------------------------
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