Contacts of the helix formed by residues 83 - 97 (chain A) in PDB entry 6H2U
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 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A PHE* 5.3 0.2 - - - -
23A LYS* 3.2 37.4 + - - +
26A LEU* 3.9 10.8 - - + -
28A GLN* 2.8 34.5 + - - +
81A ASP* 3.0 9.1 + - - +
82A ILE* 1.3 77.0 - - - +
84A GLU* 1.3 74.3 + - - +
85A ASP* 3.2 10.0 + - - +
86A ALA* 3.2 23.9 + - + +
87A LEU* 3.3 16.2 + - - +
106A GLN* 4.2 1.6 - - - -
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Residues in contact with GLU 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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23A LYS* 5.9 0.9 - - - -
82A ILE 4.4 0.3 - - - +
83A ASP* 1.3 80.2 + - - +
85A ASP* 1.3 76.5 + - - +
87A LEU* 3.3 8.7 + - - +
88A GLU* 3.0 23.8 + - - +
106A GLN* 3.2 36.1 + - - +
111B ARG* 4.4 17.7 + - - +
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Residues in contact with ASP 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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19A PHE* 5.9 0.2 - - - -
21A LYS* 6.0 2.6 - - - +
23A LYS* 2.9 24.0 + - - +
83A ASP* 3.2 15.0 + - - +
84A GLU* 1.3 92.5 - - - +
86A ALA* 1.3 62.2 + - - +
88A GLU* 3.4 17.7 + - - +
89A ILE* 3.4 28.5 + - + +
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Residues in contact with ALA 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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19A PHE* 3.6 34.3 - - + -
28A GLN* 4.0 4.9 - - - +
61A GLY* 3.4 23.9 - - - +
62A CYS 5.0 0.2 - - - +
81A ASP* 4.1 8.1 - - - +
83A ASP* 3.2 20.9 + - - +
85A ASP* 1.3 77.2 - - - +
87A LEU* 1.3 57.1 + - - +
89A ILE* 3.1 7.8 + - - +
90A PHE 2.9 23.0 + - - -
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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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60A CYS* 3.5 31.6 - - - -
61A GLY 4.6 0.4 - - - +
81A ASP* 3.7 15.5 - - + +
83A ASP 3.3 12.8 + - - +
84A GLU* 3.3 8.9 + - - +
86A ALA* 1.3 76.7 - - - +
88A GLU* 1.3 58.8 + - - +
90A PHE* 4.0 5.4 - - + -
91A ASN* 2.8 30.8 + - - +
104A MET* 3.5 19.2 - - + +
105A VAL 3.7 6.5 - - - +
106A GLN* 3.7 41.5 - - + +
113B ILE* 3.9 25.8 - - + -
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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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84A GLU 3.0 13.4 + - - +
85A ASP* 3.6 20.9 - - - +
86A ALA 3.2 0.2 - - - -
87A LEU* 1.3 77.2 - - - +
89A ILE* 1.3 62.1 + - + +
91A ASN* 3.4 4.1 + - - +
92A ARG* 3.1 44.9 + - - +
111B ARG* 3.9 29.4 + - - +
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Residues in contact with ILE 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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17A ASP* 3.8 21.1 - - + +
18A GLY 3.5 20.0 - - - +
19A PHE* 3.8 12.8 - - + -
20A GLU* 3.5 39.7 - - + +
62A CYS* 3.9 7.2 - - + -
85A ASP* 3.4 17.7 + - + +
86A ALA 3.1 6.6 + - - +
88A GLU* 1.3 76.1 - - + +
90A PHE* 1.3 65.1 + - - +
92A ARG* 3.2 27.4 + - + +
93A ASN* 2.9 25.6 + - - +
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Residues in contact with PHE 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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60A CYS* 3.7 29.8 - - + -
61A GLY 3.5 16.4 - - - +
62A CYS 3.3 10.3 + - - +
63A GLY* 3.6 18.8 - - - -
66A SER* 3.3 31.6 - - - -
67A ILE* 4.2 15.7 - - + -
79A GLY* 4.0 13.9 - - - -
86A ALA 2.9 6.9 + - - +
87A LEU* 3.5 8.7 - - + +
89A ILE* 1.3 76.0 - - - +
91A ASN* 1.3 63.0 + - - +
93A ASN* 3.2 2.3 + - + +
94A ALA* 2.9 20.4 + - + +
102A ILE* 3.5 27.1 - - + -
103A ASP 4.3 0.7 - - - -
104A MET* 3.6 24.9 - - + -
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Residues in contact with ASN 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 2.8 20.3 + - - +
88A GLU* 3.7 7.3 + - - +
90A PHE* 1.3 72.0 - - - +
92A ARG* 1.3 64.2 + - - +
94A ALA* 3.3 5.9 + - - +
95A GLU* 3.0 50.2 + - - +
104A MET* 3.8 23.6 - - - +
31B ARG* 5.4 5.2 + - - -
111B ARG* 4.9 17.3 + - - +
113B ILE* 5.0 5.5 - - + +
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Residues in contact with ARG 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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17A ASP* 5.5 6.7 + - - +
20A GLU* 3.2 26.0 + - - -
88A GLU* 3.1 35.0 + - - +
89A ILE* 3.6 29.8 - - - +
91A ASN* 1.3 78.5 - - - +
93A ASN* 1.3 57.0 + - - +
95A GLU* 3.2 14.2 + - + +
96A GLU* 2.9 55.9 + - + +
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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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15A GLN 4.5 1.7 - - - +
16A VAL* 3.5 11.1 - - - +
17A ASP* 2.9 54.7 + - - +
62A CYS 3.0 22.3 + - - +
67A ILE* 3.9 15.3 - - + -
89A ILE* 2.9 18.7 + - - +
90A PHE 3.2 6.7 + - - +
92A ARG* 1.3 76.6 - - - +
94A ALA* 1.3 64.0 + - - +
96A GLU* 3.1 9.1 + - - +
97A PHE* 3.0 33.4 + - + -
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Residues in contact with ALA 94 (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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67A ILE* 3.7 11.8 - - + +
90A PHE* 2.9 13.8 + - + +
91A ASN* 3.3 12.5 + - - +
93A ASN* 1.3 75.1 - - - +
95A GLU* 1.3 64.2 + - + +
97A PHE 3.4 1.3 + - - +
98A GLU 3.0 17.5 + - - -
99A LEU* 3.0 21.9 + - - +
102A ILE* 4.0 32.3 - - + -
104A MET* 5.0 1.8 - - + -
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Residues in contact with GLU 95 (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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91A ASN* 3.0 37.9 + - - +
92A ARG* 3.5 13.4 - - - +
94A ALA* 1.3 77.5 - - + +
96A GLU* 1.3 63.1 + - + +
98A GLU* 3.0 20.6 + - - +
31B ARG* 4.6 18.8 + - - +
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Residues in contact with GLU 96 (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 ASP* 5.1 6.4 - - - +
92A ARG* 2.9 41.5 + - + +
93A ASN* 3.1 9.2 + - - +
95A GLU* 1.3 78.1 - - + +
97A PHE* 1.3 66.7 + - + +
98A GLU* 3.2 7.2 + - - +
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Residues in contact with PHE 97 (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 ARG* 3.2 69.1 + - - +
15A GLN* 3.8 23.6 - - + -
16A VAL* 3.6 22.7 - - + -
67A ILE* 3.8 21.1 - - + -
71A MET* 4.1 9.2 - - - -
93A ASN* 3.0 35.0 + - + +
94A ALA 3.9 0.7 - - - +
96A GLU* 1.3 81.5 - - + +
98A GLU* 1.3 70.5 + - - +
99A LEU* 3.2 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