Contacts of the helix formed by residues 74 - 87 (chain A) in PDB entry 1I6P
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 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A HIS* 4.7 2.8 + - - -
65A ASN* 4.9 1.0 + - - -
69A LEU 5.1 0.9 - - - +
71A ILE* 3.1 31.7 + - + +
72A HIS 3.6 0.8 - - - -
73A THR* 1.3 75.0 - - - +
75A LEU* 1.3 59.4 + - - +
76A ASN* 3.2 19.6 + - - +
77A CYS* 3.2 28.7 + - + +
78A LEU* 2.9 30.2 + - - +
119A TRP* 3.9 25.7 - - + -
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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
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73A THR 3.4 7.1 + - - +
74A ASP* 1.3 71.0 + - - +
76A ASN* 1.3 58.8 + - - +
78A LEU* 3.8 18.4 - - + -
79A SER* 2.7 49.3 + - - +
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Residues in contact with ASN 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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63A HIS* 3.1 26.7 + - - -
74A ASP* 3.2 14.6 + - - +
75A LEU* 1.3 81.4 - - - +
77A CYS* 1.3 63.8 + - - +
79A SER* 3.3 4.7 + - - -
80A VAL* 3.2 21.8 + - - +
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Residues in contact with CYS 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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40A ILE* 4.3 5.6 - - - -
63A HIS* 3.8 32.3 - - - +
69A LEU 4.1 16.2 - - - +
70A VAL* 4.2 24.7 - - - -
71A ILE 5.8 0.7 - - - +
74A ASP* 3.2 22.8 + - + +
76A ASN* 1.3 78.6 + - - +
78A LEU* 1.3 67.9 + - + +
80A VAL* 3.2 4.9 + - - +
81A VAL* 3.0 37.9 + - - +
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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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70A VAL* 5.1 11.9 - - + -
71A ILE 4.6 6.3 - - - +
72A HIS* 3.5 26.0 - - - +
73A THR* 4.7 2.0 - - - -
74A ASP 2.9 30.4 + - - +
75A LEU* 4.1 17.7 - - + +
77A CYS* 1.3 78.9 - - + +
79A SER* 1.3 57.5 + - - +
81A VAL* 3.4 5.8 + - + -
82A GLN* 2.9 27.6 + - - +
158A LEU* 5.6 2.0 - - + -
161A SER* 4.4 17.7 - - - -
163A ILE* 3.4 29.2 - - + +
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Residues in contact with SER 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 LEU* 2.7 39.9 + - - +
76A ASN* 3.6 5.8 - - - -
77A CYS 3.2 0.2 - - - -
78A LEU* 1.3 74.1 - - - +
80A VAL* 1.3 65.5 + - - +
82A GLN* 4.1 6.8 - - - +
83A TYR* 3.1 26.0 + - - +
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Residues in contact with VAL 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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38A LEU* 4.0 12.3 - - + -
40A ILE* 5.9 0.2 - - + -
61A PHE* 3.8 28.6 - - + -
62A VAL 4.9 3.6 - - - +
63A HIS* 3.9 40.6 - - + +
76A ASN* 3.2 16.4 + - - +
77A CYS 3.2 8.2 + - - +
79A SER* 1.3 80.0 - - - +
81A VAL* 1.3 58.9 + - + +
83A TYR* 3.7 3.6 - - - +
84A ALA* 2.9 27.0 + - - +
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Residues in contact with VAL 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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38A LEU* 4.1 18.8 - - + -
40A ILE* 4.2 13.9 - - + -
77A CYS* 3.0 20.9 + - - +
78A LEU* 3.7 9.6 - - + +
80A VAL* 1.3 75.0 - - + +
82A GLN* 1.3 60.1 + - - +
84A ALA* 3.2 1.0 + - - +
85A VAL* 2.8 50.5 + - + +
93A ILE* 4.5 7.4 - - + -
158A LEU* 3.7 33.9 - - + -
163A ILE* 4.1 15.0 - - + -
164A MET* 4.7 1.8 - - - -
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Residues in contact with GLN 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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78A LEU 2.9 21.6 + - - +
79A SER* 4.1 7.0 - - - +
81A VAL* 1.3 71.8 - - - +
83A TYR* 1.3 62.7 + - - +
86A ASP* 2.8 72.6 + - - +
87A VAL* 4.8 7.9 - - - +
163A ILE* 3.8 26.9 - - + +
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Residues in contact with TYR 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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61A PHE* 3.5 32.1 - + - -
79A SER 3.1 18.7 + - - +
80A VAL* 3.7 3.6 - - - +
82A GLN* 1.3 83.9 + - - +
84A ALA* 1.3 57.4 + - - +
87A VAL* 2.9 53.7 + - + +
88A LEU* 3.0 38.5 + - + +
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Residues in contact with ALA 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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38A LEU* 3.8 22.2 - - + -
61A PHE* 4.0 14.4 - - + -
80A VAL 2.9 19.0 + - - +
81A VAL 3.6 3.6 - - - +
83A TYR* 1.3 78.0 - - - +
85A VAL* 1.3 52.6 + - - +
88A LEU* 3.4 13.1 - - - +
89A GLU 2.8 28.6 + - - -
90A VAL* 2.9 26.5 + - + -
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Residues in contact with VAL 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 VAL* 2.8 32.0 + - + +
82A GLN 4.2 0.7 - - - +
84A ALA* 1.3 75.0 - - + +
86A ASP* 1.3 71.5 + - - +
89A GLU* 3.2 13.9 - - - +
90A VAL* 4.4 7.6 - - + -
93A ILE* 3.9 28.7 - - + -
163A ILE* 4.4 8.1 - - + -
164A MET* 4.0 8.7 - - - -
167A ALA* 3.8 21.8 - - + -
172A GLN* 3.0 37.4 + - - +
174A VAL* 4.3 8.1 - - + -
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Residues in contact with ASP 86 (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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82A GLN* 2.8 51.7 + - - +
85A VAL* 1.3 82.3 - - - +
87A VAL* 1.3 62.3 + - + +
89A GLU* 3.9 9.8 - - - +
163A ILE* 4.7 8.0 - - - +
166A SER* 5.4 1.8 + - - -
167A ALA* 4.9 0.5 - - - +
170A ARG* 2.7 36.8 + - - +
172A GLN* 5.0 0.4 - - - -
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Residues in contact with VAL 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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34A LYS* 3.2 24.5 + - - +
82A GLN* 4.8 6.5 - - - +
83A TYR* 2.9 51.7 + - + +
86A ASP* 1.3 83.9 - - + +
88A LEU* 1.3 66.5 + - + +
89A GLU* 3.2 8.2 + - - +
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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