Contacts of the helix formed by residues 74 - 84 (chain A) in PDB entry 5IWG
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 SER 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A THR* 4.3 0.2 - - - -
72A TYR 3.9 1.0 + - - -
73A HIS* 1.3 76.8 - - - +
75A ASP* 1.3 65.1 + - - +
76A GLU* 4.0 6.7 + - - +
77A TYR* 3.2 19.8 + - - +
78A ILE* 3.2 20.8 + - - +
99A PHE* 5.1 0.2 - - - -
149A LYS* 3.2 18.2 + - - +
150A SER* 2.7 28.0 + - - -
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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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70A THR* 3.3 30.0 + - - +
73A HIS 3.8 0.4 + - - +
74A SER* 1.3 73.3 - - - +
76A GLU* 1.3 58.9 + - - +
78A ILE* 3.5 1.4 + - - +
79A LYS* 2.9 31.7 + - - +
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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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74A SER* 3.3 6.1 + - - +
75A ASP* 1.3 79.0 - - - +
77A TYR* 1.3 55.9 + - - +
79A LYS* 3.6 9.9 + - + +
80A PHE* 3.0 28.1 + - - +
95A GLN* 3.9 11.5 + - - +
98A ARG* 2.7 43.4 + - - -
99A PHE* 3.8 12.7 - - + -
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Residues in contact with TYR 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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73A HIS* 3.7 19.3 - + + -
74A SER* 3.2 23.5 + - - +
76A GLU* 1.3 74.3 - - - +
78A ILE* 1.3 60.8 + - + +
80A PHE* 3.3 3.2 + + - +
81A LEU* 3.0 51.2 + - + +
99A PHE* 3.6 40.7 - + + -
101A VAL* 4.9 0.7 - - + -
148A LYS 4.0 2.0 - - - -
149A LYS 3.5 16.6 - - - +
150A SER* 3.8 11.4 - - - -
151A GLU 3.7 6.1 - - - -
152A ALA* 3.1 37.2 + - + +
157A TYR* 2.7 35.4 + - - +
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Residues in contact with ILE 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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66A ALA* 4.0 32.8 - - + -
69A MET* 3.7 25.8 - - + -
70A THR* 3.8 17.0 - - + -
73A HIS* 3.6 32.1 - - + -
74A SER 3.2 17.6 + - - +
75A ASP 4.1 1.1 - - - +
77A TYR* 1.3 73.1 - - + +
79A LYS* 1.3 59.4 + - - +
81A LEU* 3.3 21.0 + - + +
82A ARG* 2.9 32.9 + - - +
112A PHE* 4.3 10.1 - - + -
158A VAL* 4.3 1.8 - - + -
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Residues in contact with LYS 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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75A ASP 2.9 20.2 + - - +
76A GLU* 3.7 10.8 - - + +
77A TYR 3.4 0.2 - - - -
78A ILE* 1.3 76.7 - - - +
80A PHE* 1.3 56.3 + - - +
82A ARG* 3.4 13.6 + - + +
83A SER* 2.7 39.5 + - - +
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Residues in contact with PHE 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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76A GLU 3.0 15.1 + - - +
77A TYR* 3.3 8.5 + + - +
79A LYS* 1.3 73.0 - - - +
81A LEU* 1.3 72.1 + - + +
83A SER* 3.1 4.6 + - - -
84A ILE* 2.9 65.9 + - + +
92A TYR* 4.0 10.5 - + + -
95A GLN* 3.7 39.5 - - + +
96A MET* 3.8 29.8 - - + -
99A PHE* 3.4 28.5 - + + -
101A VAL* 3.8 27.4 - - + -
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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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77A TYR* 3.0 53.0 + - + +
78A ILE* 3.3 15.7 + - + +
80A PHE* 1.3 86.9 - - + +
82A ARG* 1.3 60.8 + - - +
83A SER 3.5 0.5 + - - -
84A ILE* 3.9 16.2 + - - +
101A VAL* 4.6 1.8 - - + -
111A LEU* 4.5 13.4 - - + +
112A PHE* 3.6 29.8 + - + +
115A CYS* 4.6 4.5 - - - -
157A TYR* 4.2 23.8 - - + -
158A VAL* 3.7 30.7 - - + -
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Residues in contact with ARG 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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66A ALA* 3.6 33.4 - - - +
78A ILE* 2.9 24.6 + - - +
79A LYS* 3.5 12.1 - - + +
80A PHE 3.3 0.2 - - - -
81A LEU* 1.3 75.7 - - - +
83A SER* 1.3 59.4 + - - +
84A ILE 5.2 0.4 - - - -
85A ARG* 5.8 1.0 + - - +
112A PHE* 3.4 39.9 - - + +
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Residues in contact with SER 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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79A LYS* 2.7 29.6 + - - +
80A PHE* 3.1 5.0 + - - -
82A ARG* 1.3 79.6 - - - +
84A ILE* 1.3 65.5 + - - +
85A ARG* 3.6 13.3 + - - -
88A ASN* 3.2 20.3 + - - -
92A TYR* 3.5 29.2 + - - -
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Residues in contact with ILE 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 PHE* 2.9 48.7 + - + +
81A LEU* 3.9 15.3 - - + +
82A ARG 5.2 0.3 - - - -
83A SER* 1.3 72.7 - - - +
85A ARG* 1.3 64.3 + - - +
88A ASN* 3.8 11.9 - - - +
89A MET* 4.2 14.4 - - - -
92A TYR* 3.5 36.3 - - + -
96A MET* 4.3 6.5 - - + -
107A VAL* 3.6 25.1 - - + +
108A PHE 5.5 0.5 - - - +
111A LEU* 4.2 25.7 - - + +
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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