Contacts of the helix formed by residues 70 - 85 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MSE 2.8 50.1 + - - +
2B ASP* 3.3 9.8 + - + +
68B GLY 3.3 4.5 + - - +
69B SER* 1.3 76.0 - - - +
71B SER* 1.3 66.3 + - - +
73B THR* 3.0 14.1 + - - -
74B ILE* 2.9 24.8 + - - +
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Residues in contact with SER 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MSE 4.2 0.2 + - - -
2B ASP* 3.6 19.2 + - - -
3B THR 4.0 9.5 + - - -
70B ASP* 1.3 77.1 - - - +
72B GLY* 1.3 60.5 + - - +
74B ILE* 3.3 8.9 + - - +
75B LEU* 2.9 39.0 + - - +
99B LEU* 5.3 2.0 - - - -
104B LEU* 3.6 32.8 - - - -
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Residues in contact with GLY 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MSE 2.9 24.3 + - - -
3B THR* 3.2 18.4 - - - -
5B LYS 6.1 0.2 - - - -
71B SER* 1.3 80.6 + - - +
73B THR* 1.3 59.4 + - - +
75B LEU* 4.0 3.9 - - - +
76B THR* 2.8 38.1 + - - -
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Residues in contact with THR 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MSE 3.4 10.8 + - - +
20B PRO* 6.1 6.6 - - + +
21B ASN* 6.3 1.8 - - + -
64B LEU 4.1 13.2 - - - +
65B PHE* 5.4 0.2 - - - -
66B PRO* 4.7 5.2 - - + -
69B SER* 3.5 25.5 - - - +
70B ASP* 3.0 27.0 + - - -
72B GLY* 1.3 74.6 - - - +
74B ILE* 1.3 59.9 + - - +
76B THR* 3.8 4.5 - - - -
77B SER* 2.9 30.3 + - - +
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Residues in contact with ILE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE* 3.7 23.9 - - + -
69B SER* 3.8 27.8 - - - +
70B ASP 2.9 23.2 + - - +
71B SER* 3.7 5.6 - - - +
73B THR* 1.3 77.0 - - - +
75B LEU* 1.3 57.5 + - - +
77B SER 3.3 0.5 + - - -
78B MSE 2.9 51.8 + - - +
95B ARG* 4.7 12.3 - - + +
99B LEU* 4.0 28.7 - - + -
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B THR 4.6 0.7 - - - +
4B ASN* 4.4 30.1 - - + +
17B TYR* 5.2 0.2 - - - -
71B SER* 2.9 30.3 + - - +
72B GLY* 4.0 3.4 - - - +
74B ILE* 1.3 76.0 - - - +
76B THR* 1.3 63.4 + - - +
78B MSE 3.3 7.2 + - - +
79B ASP* 3.1 20.3 + - - -
99B LEU* 3.7 24.9 - - + -
104B LEU* 5.5 10.5 - - + -
105B THR 3.6 24.7 - - - +
106B HIS* 3.8 26.2 + - + -
107B ASP* 5.2 3.1 - - - +
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Residues in contact with THR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LYS 5.1 6.2 + - - -
6B ARG* 5.5 0.2 - - - -
7B GLU 5.6 1.2 + - - +
17B TYR* 3.3 59.4 + - + +
18B PHE* 4.8 2.2 - - - +
20B PRO* 4.6 15.0 - - + -
72B GLY 2.8 19.3 + - - -
73B THR* 3.8 5.4 - - - -
75B LEU* 1.3 76.4 - - - +
77B SER* 1.3 62.7 + - - +
79B ASP* 3.0 21.0 + - - +
80B THR* 3.2 7.4 + - - -
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Residues in contact with SER 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B PHE 5.0 2.0 + - - -
20B PRO* 5.6 5.2 - - - +
64B LEU* 2.7 44.8 + - - +
65B PHE* 3.4 20.6 - - - -
73B THR* 2.9 17.6 + - - +
76B THR* 1.3 77.7 - - - +
78B MSE 1.3 57.1 + - - +
80B THR* 3.1 12.0 + - - -
81B LEU* 2.9 29.8 + - - +
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Residues in contact with MSE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B PHE* 4.1 7.0 - - + -
74B ILE* 2.9 24.4 + - - +
75B LEU* 3.5 8.5 - - - +
76B THR 3.2 0.2 - - - -
77B SER* 1.3 74.3 - - - +
79B ASP* 1.3 65.2 + - - +
81B LEU* 3.3 8.1 + - + -
82B LEU* 3.1 18.9 + - - +
92B PHE* 3.5 36.9 - - + +
95B ARG* 3.8 23.1 - - + -
96B ASN* 3.4 44.0 - - + +
99B LEU* 3.6 25.4 - - - -
106B HIS* 3.6 16.6 - - + -
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Residues in contact with ASP 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ARG* 2.7 28.4 + - - +
17B TYR* 2.6 29.2 + - + -
18B PHE* 4.0 12.3 - - + -
75B LEU 3.1 11.0 + - - -
76B THR 3.0 10.4 + - - +
78B MSE 1.3 76.0 - - - +
80B THR* 1.3 63.0 + - - +
82B LEU* 3.1 6.9 + - - +
83B ALA* 3.0 19.1 + - - +
106B HIS* 2.6 31.2 + - - -
144B LEU* 3.3 27.1 - - + +
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Residues in contact with THR 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B PHE* 2.8 35.3 + - - +
19B PHE* 3.5 37.9 - - + -
64B LEU* 4.0 16.4 - - + -
76B THR 3.2 10.1 + - - -
77B SER* 3.1 13.0 + - - -
79B ASP* 1.3 75.5 - - - +
81B LEU* 1.3 63.7 + - - +
83B ALA* 3.2 3.7 + - - +
84B LEU* 2.9 34.7 + - + +
175B PHE* 4.2 5.6 - - + -
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B VAL* 4.4 3.1 - - + -
64B LEU* 3.9 18.8 - - + -
65B PHE* 3.6 29.2 - - + -
77B SER 2.9 16.2 + - - +
78B MSE 3.3 12.8 + - + +
80B THR* 1.3 77.3 - - - +
82B LEU* 1.3 62.9 + - - +
84B LEU* 3.2 10.2 + - - -
85B GLY 3.3 10.6 + - - +
88B PHE* 3.6 48.3 - - + +
89B LEU* 5.7 0.9 - - - +
91B GLU* 3.8 15.9 - - + +
92B PHE* 3.6 35.4 - - + +
95B ARG* 4.4 0.2 - - + -
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B MSE 3.1 9.0 + - - +
79B ASP* 3.1 8.5 + - - +
81B LEU* 1.3 77.1 - - - +
83B ALA* 1.3 62.1 + - - +
85B GLY* 3.3 13.4 + - - -
89B LEU* 4.2 19.1 - - + -
92B PHE* 3.5 50.5 - - + -
106B HIS* 3.7 20.2 - - + +
108B LEU* 4.2 9.0 - - + -
111B LEU* 4.2 19.1 - - + -
144B LEU* 4.4 1.3 - - + -
148B ILE* 3.8 37.6 - - + +
156B LYS* 5.0 0.5 + - - -
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B PHE* 4.5 3.6 - - + -
79B ASP 3.0 12.9 + - - +
80B THR 3.2 3.6 + - - +
82B LEU* 1.3 76.7 - - - +
84B LEU* 1.3 56.8 + - - +
144B LEU* 4.0 15.1 - - + +
147B THR* 4.1 19.2 - - + +
148B ILE* 4.9 0.7 - - - -
156B LYS* 2.8 30.0 + - - -
160B LEU* 5.0 1.3 - - + -
175B PHE* 3.6 31.6 - - + -
179B LEU* 4.0 4.3 - - - +
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PHE* 5.1 4.3 - - + -
60B ILE* 4.1 15.5 - - + -
64B LEU* 4.4 2.9 - - + -
80B THR* 2.9 33.9 + - + +
81B LEU* 3.6 3.4 - - - +
82B LEU 3.1 0.6 - - - -
83B ALA* 1.3 77.7 - - - +
85B GLY* 1.3 59.3 + - - +
86B PRO* 4.2 1.9 - - - +
87B ASP* 5.0 0.9 + - - +
88B PHE* 3.4 48.5 - - + -
156B LYS* 3.9 3.0 + - - -
175B PHE* 3.8 25.8 - - + -
178B ILE* 3.9 26.7 - - + -
179B LEU* 3.5 27.3 - - + +
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Residues in contact with GLY 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B LEU 3.3 4.5 + - - +
82B LEU 3.3 14.8 + - - -
83B ALA 3.3 0.4 - - - -
84B LEU* 1.3 77.9 - - - +
86B PRO* 1.3 75.4 - - - +
87B ASP 3.4 2.2 - - - -
88B PHE* 3.0 14.9 + - - +
89B LEU* 3.5 13.6 + - - +
156B LYS* 4.0 8.5 - - - -
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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