Contacts of the helix formed by residues 87 - 101 (chain A) in PDB entry 1R8Y
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 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A ASP* 2.6 20.9 + - - +
86A ALA* 1.3 72.1 - - - +
88A ASP* 1.3 58.4 + - - +
89A LYS 3.4 0.5 + - - -
90A MET* 3.3 23.4 + - - +
91A LEU* 2.9 33.9 + - - +
13B ALA* 3.3 9.4 - - - +
14B ALA 3.5 19.7 - - - -
17B LEU 3.7 2.0 + - - -
19B ASP* 2.8 22.7 + - - -
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Residues in contact with ASP 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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86A ALA 3.6 4.8 + - - +
87A SER* 1.3 72.3 - - - +
89A LYS* 1.3 55.0 + - + +
91A LEU* 4.5 7.1 - - - +
92A LYS* 2.9 32.1 + - - +
114A GLU* 3.8 14.8 - - - +
19B ASP* 2.8 14.5 + - - +
89B LYS* 4.9 14.1 - - + +
92B LYS* 3.0 44.1 + - + +
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Residues in contact with LYS 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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21A TYR 5.4 0.8 - - - +
22A ALA* 3.8 32.1 - - - +
27A ALA* 4.5 3.3 - - - +
30A TRP* 4.4 20.3 - - + -
31A GLN* 5.1 6.7 - - - -
87A SER* 3.3 4.9 - - - +
88A ASP* 1.3 73.0 - - - +
90A MET* 1.3 58.6 + - - +
92A LYS* 3.6 10.0 - - - +
93A TYR* 3.3 27.9 - - - -
11B GLY* 2.7 41.1 + - - +
12B VAL 4.9 1.6 - - - +
13B ALA* 4.2 12.8 - - + -
19B ASP* 2.8 21.8 + - + +
88B ASP* 5.3 14.1 - - + +
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Residues in contact with MET 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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30A TRP* 4.2 11.7 - - + -
34A ILE* 3.7 36.6 - - + -
66A GLY* 3.3 25.7 - - - +
67A THR* 3.7 15.2 - - + +
85A ASP* 4.9 0.7 - - - +
87A SER* 3.3 19.6 + - - +
88A ASP 3.2 0.2 - - - -
89A LYS* 1.3 77.4 - - - +
91A LEU* 1.3 66.7 + - - +
92A LYS 3.1 1.3 - - - -
93A TYR* 2.9 24.5 + - - +
94A ALA 3.6 0.5 + - - -
13B ALA* 4.2 16.6 - - + +
14B ALA 4.4 5.8 - - - +
15B GLU* 3.7 38.8 - - - +
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Residues in contact with LEU 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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65A CYS* 3.6 28.7 - - - -
66A GLY 3.8 3.1 + - - +
84A VAL* 4.7 0.7 - - - -
85A ASP* 3.7 39.5 - - + +
86A ALA 5.4 0.2 - - - -
87A SER 2.9 26.6 + - - +
88A ASP* 4.0 7.9 - - - +
90A MET* 1.3 70.5 - - - +
92A LYS* 1.3 64.8 + - - +
94A ALA* 2.9 13.4 + - + +
95A LEU* 3.0 26.9 + - + +
112A ILE* 3.7 19.7 - - + -
113A GLU 4.0 12.1 - - - +
114A GLU* 4.1 17.7 - - + -
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Residues in contact with LYS 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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88A ASP 2.9 18.6 + - - +
89A LYS* 3.6 11.4 - - - +
91A LEU* 1.3 74.7 - - - +
93A TYR* 1.3 84.9 + - + +
95A LEU* 3.5 9.7 + - - +
96A LYS* 3.0 40.7 + - + +
88B ASP* 2.8 44.9 + - + +
95B LEU* 5.9 7.4 - - + -
114B GLU* 2.5 36.7 + - - -
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Residues in contact with TYR 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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30A TRP* 5.5 0.9 - + - -
31A GLN* 3.5 31.8 + - + +
34A ILE* 4.1 23.3 - - + -
38A ARG* 5.0 3.9 + - - +
67A THR* 3.7 22.9 - - + +
89A LYS 3.3 27.6 - - - -
90A MET* 2.9 12.6 + - - +
92A LYS* 1.3 100.5 + - + +
94A ALA* 1.3 64.4 + - - +
96A LYS* 3.7 23.2 - - + +
97A GLU* 3.2 22.3 + - - +
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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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65A CYS* 3.9 15.7 - - - -
66A GLY 3.9 8.5 - - - +
67A THR 3.5 25.6 + - - +
68A GLY 4.0 0.7 - - - +
90A MET 3.6 2.0 + - - -
91A LEU* 2.9 8.8 + - - +
93A TYR* 1.3 79.2 - - - +
95A LEU* 1.3 63.2 + - - +
97A GLU* 3.2 4.8 + - - +
98A ARG* 3.0 23.7 + - - +
110A TRP* 3.7 17.9 - - + -
112A ILE* 3.9 11.0 - - + -
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Residues in contact with LEU 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 LEU* 3.0 33.5 + - + +
92A LYS* 3.8 8.1 - - - +
94A ALA* 1.3 75.5 - - - +
96A LYS* 1.3 57.5 + - - +
98A ARG* 3.4 32.5 + - - +
99A TRP* 3.0 29.5 + - - +
112A ILE* 3.7 31.6 - - + +
92B LYS* 5.8 8.1 - - + -
95B LEU* 6.2 7.6 - - + -
96B LYS* 6.5 1.1 - - - -
99B TRP* 6.0 0.8 - - + -
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Residues in contact with LYS 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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92A LYS* 3.0 27.9 + - + +
93A TYR* 3.7 24.5 - - + +
95A LEU* 1.3 76.8 - - - +
97A GLU* 1.3 55.1 + - - +
99A TRP* 4.0 6.5 - - + +
100A ASN* 2.8 50.5 + - - +
95B LEU* 6.4 2.0 - - - -
113B GLU* 4.9 12.6 + - - -
114B GLU* 3.5 24.7 + - - +
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Residues in contact with GLU 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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67A THR 5.4 0.2 - - - +
72A ILE* 3.6 33.8 - - + +
93A TYR 3.2 14.6 + - - +
94A ALA 3.2 5.5 + - - +
96A LYS* 1.3 77.8 - - - +
98A ARG* 1.3 64.9 + - - +
100A ASN* 3.1 16.1 + - - +
101A ARG* 3.0 52.1 + - - +
107A PHE* 5.1 0.4 - - + -
110A TRP* 5.1 0.4 - - + -
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Residues in contact with ARG 98 (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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94A ALA 3.0 11.2 + - - +
95A LEU* 3.4 28.2 + - - +
97A GLU* 1.3 74.4 - - - +
99A TRP* 1.3 62.7 + - - +
101A ARG 3.0 12.5 + - - -
102A ARG* 3.1 12.5 + - - -
107A PHE* 3.6 24.2 - - + +
110A TRP* 2.8 58.0 + - + -
111A VAL* 3.8 2.0 - - - +
112A ILE* 3.3 39.1 + - + +
99B TRP* 3.1 64.0 - - + +
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Residues in contact with TRP 99 (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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95A LEU 3.0 18.4 + - - +
96A LYS* 4.0 6.7 - - + +
98A ARG* 1.3 76.1 - - - +
100A ASN* 1.3 72.0 + - - +
102A ARG* 3.1 83.9 + - - +
95B LEU* 5.8 1.8 - - + -
98B ARG* 2.7 75.1 - - + +
99B TRP* 4.2 23.7 - + + -
102B ARG* 4.2 17.3 - - + -
107B PHE 3.6 9.9 - - - -
108B ASP* 3.9 9.2 - - - -
110B TRP 3.9 2.2 - - - -
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Residues in contact with ASN 100 (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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96A LYS* 2.8 43.5 + - - +
97A GLU* 3.1 19.0 + - - +
99A TRP* 1.3 86.3 - - - +
101A ARG* 1.3 60.4 + - + +
102A ARG* 3.4 5.7 + - - +
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Residues in contact with ARG 101 (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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72A ILE* 3.8 7.9 - - - +
76A GLU* 2.7 34.6 + - - +
97A GLU* 3.0 38.3 + - - +
98A ARG 3.0 6.0 + - - +
100A ASN* 1.3 80.3 - - + +
102A ARG* 1.3 57.3 + - - -
103A LYS 3.0 10.2 + - - -
104A GLU* 2.9 54.9 + - - +
107A PHE* 3.4 52.6 - - + +
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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