Contacts of the helix formed by residues 79 - 93 (chain A) in PDB entry 6H1D
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 ASN 79 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ASP* 3.0 30.0 + - - +
22A VAL* 4.7 1.8 - - - +
77A ASP* 2.8 19.1 + - - +
78A ILE* 1.3 78.1 - - - +
80A PRO* 1.3 71.4 - - - +
81A GLU* 3.0 21.0 + - - +
82A ALA* 3.0 24.8 + - + +
83A ALA* 3.3 9.4 + - - +
136A HIS 3.2 13.9 - - - +
137A GLY* 3.7 19.7 + - - +
138A ILE* 3.9 1.0 - - - +
301A SAH 3.8 9.6 + - - +
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Residues in contact with PRO 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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78A ILE 3.6 9.3 - - - +
79A ASN* 1.3 90.1 - - - +
81A GLU* 1.3 70.4 + - + +
83A ALA* 3.4 5.0 + - - +
84A ALA* 3.2 20.1 + - - +
101A ILE* 3.7 34.2 - - + +
136A HIS* 4.2 10.1 - - + +
112B ARG* 5.2 1.7 + - - +
114B ILE* 4.9 1.0 - - - +
116B ASN* 5.5 4.0 - - - +
118B LEU* 6.1 1.8 - - + -
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Residues in contact with GLU 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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18A ALA* 3.6 28.9 - - - +
19A PHE* 3.6 5.0 - - - -
21A ASP* 5.5 6.7 - - + +
22A VAL* 3.6 13.0 - - + +
79A ASN* 3.0 12.0 + - - +
80A PRO* 1.3 83.1 - - + +
82A ALA* 1.3 60.2 + - - +
84A ALA* 3.7 7.3 - - - +
85A CYS* 2.8 29.6 + - - +
112B ARG* 3.7 29.1 + - - -
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Residues in contact with ALA 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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22A VAL* 3.8 11.8 - - + +
54A SER* 4.8 1.3 - - - -
55A GLY* 2.9 30.9 - - - +
77A ASP* 3.6 26.5 - - + +
79A ASN* 3.0 22.6 + - + +
81A GLU* 1.3 76.6 - - - +
83A ALA* 1.3 60.6 + - - +
85A CYS* 3.2 0.7 + - - -
86A THR* 2.8 27.9 + - - -
301A SAH 4.4 1.3 - - - +
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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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54A SER* 5.0 2.9 - - - -
77A ASP* 4.5 6.3 - - + +
79A ASN 3.3 5.1 + - - +
80A PRO 3.7 8.3 - - - +
81A GLU 3.3 0.2 - - - -
82A ALA* 1.3 79.3 - - - +
84A ALA* 1.3 61.0 + - - +
86A THR* 3.2 7.2 + - - -
87A LEU* 3.2 18.2 + - - +
99A PRO* 3.8 30.0 - - + +
100A VAL 5.0 2.5 - - - +
101A ILE* 3.8 26.9 - - + +
114B ILE* 4.0 10.5 - - + -
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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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19A PHE* 3.7 12.1 - - + -
80A PRO 3.2 13.8 + - - +
81A GLU* 3.7 9.2 - - - +
83A ALA* 1.3 73.6 - - - +
85A CYS* 1.3 66.1 + - - +
87A LEU* 3.3 8.5 + - - +
88A GLU* 3.2 20.1 + - - +
112B ARG* 3.9 32.5 - - - +
114B ILE* 3.8 14.1 - - + +
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Residues in contact with CYS 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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13A HIS* 3.6 23.6 - - - -
14A VAL* 3.8 15.3 - - - -
19A PHE* 3.4 29.1 - - + -
22A VAL* 4.1 8.5 - - + -
55A GLY 4.1 2.7 - - - +
56A SER* 3.7 17.3 - - - -
81A GLU 2.8 21.0 + - - +
82A ALA* 3.4 9.0 - - - +
84A ALA* 1.3 74.7 - - - +
86A THR* 1.3 57.7 + - - +
88A GLU* 3.1 2.8 + - - +
89A THR* 2.9 31.7 + - - -
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Residues in contact with THR 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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54A SER* 2.8 21.9 + - - +
55A GLY 3.1 8.3 + - - -
56A SER 3.6 7.4 - - - -
57A GLY* 3.4 16.9 - - - -
60A SER* 5.3 0.4 - - - -
75A CYS* 3.4 28.5 - - + -
82A ALA 2.8 18.8 + - - -
83A ALA* 3.5 7.2 - - - +
84A ALA 3.2 0.6 - - - -
85A CYS* 1.3 72.9 - - - +
87A LEU* 1.3 56.0 + - - +
89A THR* 3.4 1.7 + - - -
90A ALA* 2.9 28.2 + - - +
97A ILE* 3.8 19.8 - - + +
99A PRO* 4.7 4.0 - - + -
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Residues in contact with LEU 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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83A ALA 3.2 7.9 + - - +
84A ALA* 3.5 8.7 - - - +
86A THR* 1.3 77.3 - - - +
88A GLU* 1.3 61.3 + - - +
90A ALA* 3.4 6.3 + - + +
91A ARG* 3.1 29.9 + - - +
97A ILE 3.7 11.4 - - - +
98A GLN* 5.4 2.5 - - - +
99A PRO* 3.6 30.7 - - + -
112B ARG 4.3 9.2 - - - +
113B GLY 5.2 4.0 - - - +
114B ILE* 3.8 32.3 - - + -
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Residues in contact with GLU 88 (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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13A HIS* 3.8 29.6 - - + +
19A PHE* 4.1 16.1 - - + -
84A ALA 3.2 9.1 + - - +
85A CYS 3.1 8.7 + - - +
87A LEU* 1.3 75.1 - - - +
89A THR* 1.3 65.9 + - - +
91A ARG* 2.9 43.0 + - - +
92A CYS* 3.0 39.8 + - - -
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Residues in contact with THR 89 (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 PRO* 4.8 0.4 - - + -
10A PHE 3.9 8.3 - - - +
11A HIS* 4.9 0.2 - - + -
13A HIS* 2.8 27.9 + - + -
14A VAL* 4.6 2.3 - - - +
56A SER 2.6 29.4 + - - +
57A GLY 4.0 9.9 - - - -
58A VAL* 4.2 9.9 - - + +
61A ALA* 3.9 18.2 - - + -
85A CYS 2.9 6.0 + - - -
86A THR* 3.7 4.0 - - - -
88A GLU* 1.3 74.8 - - - +
90A ALA* 1.3 63.9 + - - +
92A CYS* 3.4 0.8 + - - +
93A ASN* 2.6 44.3 + - - +
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Residues in contact with ALA 90 (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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86A THR 2.9 18.0 + - - +
87A LEU* 3.6 9.4 - - + +
88A GLU 3.3 0.2 - - - -
89A THR* 1.3 78.2 - - - +
91A ARG* 1.3 60.9 + - - +
93A ASN 3.6 0.3 - - - -
94A LYS 3.0 3.8 + - - -
95A VAL* 3.0 51.3 + - - +
97A ILE* 3.7 34.0 - - + +
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Residues in contact with ARG 91 (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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87A LEU* 3.1 18.7 + - - +
88A GLU* 2.9 49.4 + - - +
90A ALA* 1.3 77.9 - - - +
92A CYS* 1.3 63.4 + - - +
94A LYS* 3.1 36.6 + - - +
95A VAL 4.8 1.8 - - - -
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Residues in contact with CYS 92 (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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10A PHE* 3.6 41.4 - - + +
13A HIS* 4.6 2.9 - - + -
88A GLU* 3.0 42.1 + - - +
89A THR* 4.0 4.9 - - - +
91A ARG* 1.3 78.6 - - - +
93A ASN* 1.3 63.2 + - - +
94A LYS* 3.3 7.0 + - - +
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Residues in contact with ASN 93 (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 PRO* 3.4 15.0 - - + +
10A PHE* 2.7 52.2 + - - +
61A ALA* 4.4 4.6 - - + +
65A SER* 5.9 1.0 - - - -
89A THR* 2.6 37.0 + - - +
90A ALA 3.6 1.1 - - - +
92A CYS* 1.3 78.3 - - - +
94A LYS* 1.3 69.3 + - - +
95A VAL* 3.2 20.6 + - + +
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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