Contacts of the helix formed by residues 73 - 87 (chain A) in PDB entry 5W88
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 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A PHE* 3.3 21.0 - - - -
33A ASP* 4.9 5.4 - - - +
34A GLY 4.7 2.8 - - - +
35A SER* 4.2 12.7 - - - -
71A THR* 3.9 0.6 + - - +
72A VAL* 1.3 75.4 - - - +
74A PHE* 1.3 86.1 + - - +
75A ASP* 3.6 9.8 - - - +
76A GLU* 2.7 21.9 + - - +
77A PHE* 2.9 17.8 + - - +
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Residues in contact with PHE 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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17A LYS* 3.2 28.3 - - + -
20A PHE* 3.3 12.8 - - + -
21A LYS* 3.0 54.1 - - + -
24A PHE* 3.3 30.6 - - + -
73A ASP* 1.3 87.4 + - - +
75A ASP* 1.3 54.8 + - + +
77A PHE* 2.9 7.5 + + - +
78A LEU* 2.6 66.4 + - + -
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Residues in contact with ASP 75 (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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1A MET* 3.3 23.7 - - + +
6A LYS* 4.8 8.5 - - + -
9A VAL* 5.0 9.6 - - + +
66A GLU* 5.8 2.6 - - - +
73A ASP* 4.3 10.8 + - - +
74A PHE* 1.3 80.6 - - + +
76A GLU* 1.3 69.0 + - - +
78A LEU* 3.5 11.5 - - + +
79A VAL 2.7 28.1 + - - -
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Residues in contact with GLU 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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1A MET* 4.1 5.2 - - - -
64A VAL* 3.2 48.7 - - + +
65A ASP* 3.2 7.5 - - - +
66A GLU* 2.9 31.3 + - + +
67A ASP* 3.7 12.8 + - - +
71A THR 3.5 12.9 - - - +
72A VAL* 3.6 4.5 - - + -
73A ASP* 2.7 37.5 + - - +
75A ASP* 1.3 87.7 - - - +
77A PHE* 1.3 65.3 + - - +
78A LEU 3.2 0.2 + - - -
79A VAL* 3.3 9.2 + - - +
80A MET 3.4 0.2 + - - -
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Residues in contact with PHE 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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20A PHE* 2.9 42.8 - + + -
23A ALA* 4.0 13.0 - - + -
24A PHE* 3.8 16.2 - - + -
27A PHE* 3.9 9.2 - + - -
36A ILE* 3.9 14.1 - - + -
72A VAL* 2.9 21.4 - - + +
73A ASP 2.9 7.2 + - - +
74A PHE* 2.9 13.9 + + - +
76A GLU* 1.3 71.4 - - - +
78A LEU* 1.3 59.9 + - - +
80A MET* 3.3 3.7 + - - +
81A MET* 2.8 43.9 + - + +
153A MET* 3.4 28.9 - - + -
201A 9XG 3.6 29.6 - + - -
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Residues in contact with LEU 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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9A VAL* 3.4 31.4 - - + -
12A LEU* 3.8 11.7 - - + -
17A LYS* 3.4 15.0 - - + -
20A PHE* 3.1 38.8 - - + -
74A PHE* 2.6 54.4 + - + +
75A ASP* 3.5 8.7 - - + +
77A PHE* 1.3 73.8 - - - +
79A VAL* 1.3 65.0 + - - +
81A MET* 3.9 3.4 - - + -
82A VAL* 2.9 23.6 + - - +
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Residues in contact with VAL 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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1A MET* 3.2 51.6 - - + +
2A ASP 3.7 0.2 - - - +
5A TYR* 3.3 8.5 - - + -
6A LYS* 3.1 39.7 - - - +
9A VAL* 4.4 2.8 - - + +
64A VAL* 3.2 26.5 - - + -
75A ASP 2.7 10.3 + - - -
76A GLU 3.3 1.1 + - - +
78A LEU* 1.3 71.8 - - - +
80A MET* 1.3 63.7 + - - +
82A VAL* 3.0 7.5 - - - +
83A ARG* 2.7 31.0 + - - +
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Residues in contact with MET 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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60A MET 5.2 0.2 - - - +
63A GLU* 3.6 23.3 - - - +
64A VAL* 3.5 18.8 - - + -
76A GLU 3.4 0.6 + - - +
77A PHE 3.3 4.8 + - - +
78A LEU 3.2 0.2 - - - -
79A VAL* 1.3 80.0 - - - +
81A MET* 1.3 56.9 + - - +
83A ARG* 3.2 37.9 - - - +
84A SER* 2.7 44.2 + - - -
88A ASP* 5.6 1.3 - - - +
145A ARG* 4.6 3.1 - - - +
147A ARG* 3.6 29.6 - - + +
201A 9XG 3.3 36.8 - - + +
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Residues in contact with MET 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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20A PHE* 3.2 42.8 - - + -
77A PHE* 2.8 44.6 + - + +
78A LEU* 3.3 17.0 - - + +
80A MET* 1.3 76.5 - - - +
82A VAL* 1.3 58.0 + - - +
84A SER* 2.9 7.2 + - - -
85A MET* 2.9 34.0 + - - +
150A ALA* 3.4 31.6 - - + -
153A MET* 3.7 19.7 - - - -
154A MET* 4.5 0.9 - - - -
201A 9XG 5.5 2.9 + - - +
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Residues in contact with VAL 82 (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 TYR* 3.5 28.5 - - + +
8A ALA* 3.6 30.3 - - + +
9A VAL* 4.2 4.0 - - + +
12A LEU* 4.0 11.2 - - + -
78A LEU 2.9 13.1 + - - +
79A VAL* 3.0 22.9 - - - +
81A MET* 1.3 79.4 - - - +
83A ARG* 1.3 55.5 + - - +
85A MET* 3.4 26.4 - - + +
86A LYS* 2.8 48.9 + - + +
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Residues in contact with ARG 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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1A MET 4.1 12.3 - - - +
2A ASP* 2.8 27.6 + - - +
5A TYR* 3.1 38.0 + - + -
63A GLU* 2.6 47.6 + - - +
64A VAL* 5.3 1.1 - - - +
79A VAL* 2.7 23.6 + - - +
80A MET* 3.2 32.3 - - - +
82A VAL* 1.3 73.6 - - - +
84A SER* 1.3 57.0 + - - +
87A ASP 2.9 33.2 + - - +
139A LYS* 6.3 0.2 - - - +
145A ARG* 4.2 9.5 - - - +
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Residues in contact with SER 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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80A MET* 2.7 32.6 + - - -
81A MET* 2.9 10.6 + - - -
83A ARG* 1.3 72.8 - - - +
85A MET* 1.3 64.8 + - - +
86A LYS 3.3 0.2 + - - -
87A ASP 4.6 0.2 - - - -
88A ASP* 3.1 38.2 + - - +
90A LYS* 5.1 1.6 - - - -
147A ARG* 5.3 4.0 - - - +
148A ILE 3.9 9.2 + - - -
149A SER* 4.6 1.7 - - - -
150A ALA* 3.8 22.4 + - - -
201A 9XG 5.1 7.0 - - - -
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Residues in contact with MET 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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12A LEU* 3.8 14.1 - - + -
16A GLN* 4.0 5.6 - - - +
20A PHE* 3.5 31.9 - - + -
81A MET* 2.9 28.5 + - + +
82A VAL* 3.4 35.4 - - + +
84A SER* 1.3 74.7 - - - +
86A LYS* 1.3 62.6 + - + +
90A LYS* 2.9 23.1 + - - +
150A ALA* 3.6 20.4 - - + +
151A ASP* 5.5 3.4 - - - +
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Residues in contact with LYS 86 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A TYR* 3.3 26.0 - - + +
8A ALA* 4.7 9.9 - - - -
11A GLN* 6.5 0.2 - - - -
12A LEU* 5.6 5.6 - - - -
82A VAL* 2.8 44.2 + - + +
85A MET* 1.3 79.7 - - + +
87A ASP* 1.3 61.8 + - + +
90A LYS* 2.8 22.3 + - - +
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Residues in contact with ASP 87 (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 TYR* 3.8 3.8 + - - +
83A ARG* 2.9 19.6 + - - +
84A SER 3.3 0.2 + - - -
86A LYS* 1.3 83.5 - - - +
88A ASP* 1.3 60.2 + - - +
89A SER* 3.9 0.5 + - - -
90A LYS* 2.8 38.7 + - + +
136A GLY 3.5 6.1 + - - -
137A LYS* 3.2 43.2 + - - +
139A LYS* 2.7 45.4 + - - -
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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