Contacts of the helix formed by residues 70 - 85 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A GLY 3.4 4.5 + - - +
69A SER* 1.3 75.3 - - - +
71A SER* 1.3 61.0 + - - +
72A GLY* 3.4 5.3 + - - -
73A THR* 2.9 31.3 + - - -
74A ILE* 2.9 28.9 + - - +
204B THR 4.4 6.9 - - - +
205B LYS* 5.5 2.8 + - - +
206B PRO* 4.2 22.8 - - - +
207B LYS* 6.1 0.5 - - - +
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Residues in contact with SER 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ASP* 1.3 77.1 - - - +
72A GLY* 1.3 59.2 + - - +
74A ILE* 3.3 10.3 + - - +
75A LEU* 2.9 38.2 + - - +
99A LEU* 4.7 6.0 - - - +
104A LEU* 3.6 32.3 - - - +
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Residues in contact with GLY 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ASN* 5.6 8.3 - - - -
70A ASP* 3.3 7.3 + - - -
71A SER* 1.3 83.6 + - - +
73A THR* 1.3 60.3 + - - +
75A LEU* 3.4 7.0 + - - +
76A THR* 3.0 29.0 + - - -
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Residues in contact with THR 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PRO* 6.3 3.6 - - + -
21A ASN* 6.5 1.1 - - + -
64A LEU 4.2 13.0 - - - +
66A PRO* 4.7 5.2 - - + -
69A SER* 3.5 24.8 - - - +
70A ASP* 2.9 28.8 + - - -
72A GLY* 1.3 71.5 - - - +
74A ILE* 1.3 66.8 + - - +
76A THR* 3.4 4.9 + - - -
77A SER* 2.9 25.4 + - - +
204B THR 5.7 0.3 + - - -
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Residues in contact with ILE 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A PHE* 3.6 24.5 - - + -
69A SER* 3.7 26.0 - - - +
70A ASP 2.9 23.7 + - - +
71A SER* 3.6 8.5 - - - +
73A THR* 1.3 75.7 - - - +
75A LEU* 1.3 57.3 + - - +
77A SER 3.2 2.3 + - - -
78A MSE 2.8 51.7 + - - +
95A ARG* 4.5 15.7 - - + +
98A ASP* 5.2 6.7 - - - +
99A LEU* 4.2 24.2 - - + -
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ASN* 4.6 25.1 - - + +
17A TYR* 5.1 0.4 - - - -
71A SER* 2.9 27.2 + - - +
72A GLY* 3.9 6.1 - - - +
74A ILE* 1.3 75.4 - - - +
76A THR* 1.3 60.4 + - - +
78A MSE 3.2 7.4 + - - +
79A ASP* 3.2 23.5 + - - -
99A LEU* 3.8 22.7 - - + -
104A LEU* 5.4 10.8 - - + -
105A THR 3.7 24.0 - - - +
106A HIS* 3.8 26.0 - - + -
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Residues in contact with THR 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LYS 5.6 1.9 + - - -
6A ARG* 6.0 0.2 - - - -
17A TYR* 3.3 54.9 + - + +
18A PHE* 4.8 2.5 - - - +
20A PRO* 4.6 15.7 - - + -
72A GLY 3.0 18.5 + - - -
73A THR* 3.7 6.1 - - - -
74A ILE 3.3 0.2 - - - -
75A LEU* 1.3 74.4 - - - +
77A SER* 1.3 65.4 + - - +
79A ASP* 3.1 20.3 + - - +
80A THR* 3.2 6.4 + - - -
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Residues in contact with SER 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PHE 5.1 1.7 + - - -
20A PRO* 5.8 4.2 - - - +
64A LEU* 2.7 41.7 + - - +
65A PHE* 3.4 22.8 - - - -
73A THR* 2.9 19.3 + - - +
76A THR* 1.3 78.5 - - - +
78A MSE 1.3 58.4 + - - +
80A THR* 3.1 11.8 + - - -
81A LEU* 2.9 29.3 + - - +
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Residues in contact with MSE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A PHE* 4.1 6.7 - - + -
74A ILE* 2.8 38.7 + - - +
75A LEU* 3.6 11.0 - - - +
76A THR 3.2 0.2 - - - -
77A SER* 1.3 75.0 - - - +
79A ASP* 1.3 64.5 + - - +
81A LEU* 3.2 10.5 + - + +
82A LEU* 3.0 26.3 + - - +
92A PHE* 3.6 33.4 - - + +
95A ARG* 3.8 18.4 - - + -
96A ASN* 3.4 40.6 - - + +
99A LEU* 3.8 14.6 - - - -
106A HIS* 3.7 14.8 - - + -
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Residues in contact with ASP 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ARG* 2.8 28.0 + - - -
17A TYR* 2.6 28.8 + - + -
18A PHE* 3.9 12.8 - - + -
75A LEU 3.2 11.1 + - - -
76A THR 3.1 10.4 + - - +
78A MSE 1.3 75.7 - - - +
80A THR* 1.3 61.6 + - - +
82A LEU* 3.2 3.3 + - - +
83A ALA* 3.0 19.8 + - - +
106A HIS* 2.6 31.0 + - - -
144A LEU* 3.3 27.9 - - + +
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Residues in contact with THR 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PHE* 2.8 35.2 + - - +
19A PHE* 3.5 37.9 - - + -
64A LEU* 3.9 18.2 - - + -
76A THR 3.2 10.2 + - - -
77A SER* 3.1 13.1 + - - -
79A ASP* 1.3 75.2 - - - +
81A LEU* 1.3 65.9 + - - +
83A ALA* 3.2 3.3 + - - +
84A LEU* 2.9 33.5 + - + +
175A PHE* 4.2 5.4 - - + -
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A VAL* 4.7 3.1 - - + -
64A LEU* 4.0 19.3 - - + -
65A PHE* 3.7 28.3 - - + -
77A SER 2.9 16.8 + - - +
78A MSE 3.2 12.7 + - + +
80A THR* 1.3 76.6 - - - +
82A LEU* 1.3 62.2 + - - +
84A LEU* 3.2 6.2 + - + +
85A GLY 3.2 17.8 + - - +
88A PHE* 3.6 46.5 - - + +
91A GLU* 3.8 14.1 - - + +
92A PHE* 3.6 36.6 - - + +
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A MSE 3.0 8.5 + - - +
79A ASP 3.2 6.7 + - - +
81A LEU* 1.3 76.1 - - - +
83A ALA* 1.3 63.5 + - - +
85A GLY* 3.1 15.5 + - - -
89A LEU* 4.5 14.4 - - + -
92A PHE* 3.5 50.9 - - + -
106A HIS* 3.6 23.3 - - + +
108A LEU* 4.1 4.5 - - + -
111A LEU* 4.0 29.8 - - + -
144A LEU* 4.2 3.8 - - + -
148A ILE* 3.8 31.9 - - + +
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Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PHE* 4.4 4.3 - - + -
79A ASP 3.0 12.9 + - - +
80A THR 3.7 3.4 - - - +
82A LEU* 1.3 78.4 - - - +
84A LEU* 1.4 61.0 + - - +
85A GLY* 3.4 1.4 + - - -
144A LEU* 3.8 16.5 - - + +
147A THR* 3.9 28.5 - - + +
148A ILE* 5.0 0.4 - - - -
156A LYS* 5.0 3.5 - - - +
160A LEU* 4.9 2.0 - - + -
175A PHE* 3.5 33.3 - - + -
179A LEU* 4.0 12.0 - - - +
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PHE* 5.0 4.9 - - + -
60A ILE* 4.1 17.9 - - + -
64A LEU* 4.3 4.5 - - + -
80A THR* 2.9 36.2 + - + +
81A LEU* 3.2 3.5 + - - +
83A ALA* 1.4 75.1 - - - +
85A GLY* 1.3 59.8 + - - +
87A ASP* 5.1 1.9 + - - +
88A PHE* 3.4 42.7 - - + -
156A LYS* 4.9 4.0 + - - -
175A PHE* 3.8 25.4 - - + -
178A ILE* 4.0 26.7 - - + -
179A LEU* 3.4 26.8 - - + +
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Residues in contact with GLY 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A LEU 3.2 4.4 + - - +
82A LEU* 3.1 16.8 + - - -
83A ALA 3.2 1.8 - - - -
84A LEU* 1.3 79.2 - - - +
86A PRO* 1.3 77.4 - - - +
87A ASP 3.1 3.4 - - - -
88A PHE* 2.9 19.9 + - - +
89A LEU* 3.7 3.2 + - - +
156A LYS* 5.6 4.7 - - - -
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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