Contacts of the helix formed by residues 81 - 98 (chain A) in PDB entry 1R6O
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 THR 81 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE* 3.7 26.2 - - + -
25A MET 3.0 13.0 + - - +
26A THR* 3.9 6.5 - - + -
80A PRO* 1.3 77.3 - - - +
82A LEU* 1.3 65.9 + - - +
83A SER 4.0 0.4 - - - -
84A PHE* 3.1 16.3 + - - +
85A GLN* 3.0 22.7 + - - +
79C GLU* 2.6 45.3 + - + +
80C VAL* 5.0 1.3 - - + -
83C THR* 3.3 18.4 - - - +
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PRO 5.2 0.4 - - - +
81A THR* 1.3 73.1 - - - +
83A SER* 1.3 57.9 + - - +
85A GLN* 3.1 23.8 + - - +
86A ARG* 2.9 47.1 + - - +
82C GLU* 3.9 30.3 - - + +
83C THR* 3.2 22.3 + - + +
86C ALA* 3.8 29.4 - - + -
87C MET* 6.5 0.2 - - + -
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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
----------------------------------------------------------
27A VAL* 3.3 10.8 - - - +
81A THR* 3.1 0.6 - - - -
82A LEU* 1.3 79.7 - - - +
84A PHE* 1.3 60.7 + - - +
86A ARG* 3.3 14.4 + - - +
87A VAL* 3.1 25.5 + - - +
115A GLU* 2.6 38.6 + - - +
118A SER* 4.5 3.5 - - - -
79C GLU* 3.8 28.4 + - - +
82C GLU* 4.3 4.4 + - - -
83C THR* 4.9 0.2 + - - -
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Residues in contact with PHE 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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10A LEU* 4.3 10.5 - - + -
13A ALA* 6.1 1.1 - - + -
25A MET* 3.6 46.7 - - + +
26A THR 3.5 19.1 - - - -
27A VAL* 3.6 10.5 - - + +
30A LEU* 3.7 33.2 - - + +
80A PRO* 3.7 14.1 - - + -
81A THR* 3.1 24.5 + - - +
83A SER* 1.3 77.2 - - - +
85A GLN* 1.3 65.5 + - - +
87A VAL* 3.3 13.2 + - - +
88A LEU* 3.3 42.2 + - + +
10C PHE* 4.1 11.2 - + - -
13C LEU* 4.4 4.5 - - + -
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Residues in contact with GLN 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PRO* 3.9 15.8 - - + +
81A THR 3.0 21.2 + - - +
82A LEU* 3.4 31.2 - - - +
84A PHE* 1.3 77.4 - - - +
86A ARG* 1.3 62.9 + - + +
88A LEU* 3.4 4.9 + - - +
89A GLN* 3.1 40.8 + - - +
13C LEU* 3.9 47.4 - - + +
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Residues in contact with ARG 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 2.9 22.9 + - - +
83A SER* 3.6 14.2 - - - +
84A PHE 3.3 0.2 - - - -
85A GLN* 1.3 77.9 - - + +
87A VAL* 1.3 56.1 + - - +
89A GLN* 3.4 13.9 + - - +
90A ARG* 2.8 43.5 + - - +
115A GLU* 2.9 39.7 + - - +
414A GOL 5.6 1.4 + - - -
82C GLU* 2.8 43.4 + - - -
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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
----------------------------------------------------------
27A VAL* 4.2 13.5 - - + -
30A LEU* 3.7 24.0 - - + -
83A SER 3.1 16.2 + - - +
84A PHE 3.3 7.6 + - - +
86A ARG* 1.3 75.7 - - - +
88A LEU* 1.3 57.2 + - - +
90A ARG* 3.3 8.8 + - - +
91A ALA* 2.9 26.5 + - - +
108A VAL* 3.7 27.6 - - + +
111A ALA* 3.4 9.7 - - + +
112A ILE* 3.8 15.9 - - + -
115A GLU* 3.5 23.1 - - + -
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 4.9 7.3 - - + +
6A LEU* 5.7 0.7 - - + -
10A LEU* 4.1 24.9 - - + -
30A LEU* 4.6 6.5 - - + -
84A PHE* 3.3 35.2 + - + +
85A GLN* 3.9 7.0 - - - +
87A VAL* 1.3 76.0 - - - +
89A GLN* 1.3 64.0 + - + +
91A ALA* 3.4 4.4 + - - +
92A VAL* 3.2 30.0 + - + +
108A VAL* 4.3 28.0 - - + -
10C PHE* 3.8 38.1 - - + +
13C LEU* 4.5 7.6 - - + -
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Residues in contact with GLN 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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85A GLN* 3.1 32.5 + - - +
86A ARG* 3.8 16.2 - - - +
88A LEU* 1.3 78.1 - - + +
90A ARG* 1.3 57.3 + - - +
92A VAL* 3.4 7.6 + - - +
93A PHE* 2.9 27.9 + - - +
11C ASP 5.7 5.4 - - - +
13C LEU* 4.9 17.9 - - + +
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Residues in contact with ARG 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 ARG* 2.8 29.9 + - - +
87A VAL* 3.6 13.6 - - - +
88A LEU 3.3 0.2 - - - -
89A GLN* 1.3 74.9 - - - +
91A ALA* 1.3 58.7 + - - +
93A PHE* 3.2 12.7 + - + +
94A HIS* 2.8 32.6 + - + +
111A ALA* 3.3 29.4 + - + +
114A SER* 3.1 35.4 + - - -
115A GLU* 2.6 40.2 + - - +
131A ARG* 6.1 2.7 - - - +
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Residues in contact with ALA 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 VAL 2.9 16.6 + - - +
88A LEU* 3.7 5.2 - - - +
90A ARG* 1.3 76.5 - - - +
92A VAL* 1.3 63.6 + - - +
94A HIS* 3.5 4.8 + - - +
95A VAL* 3.2 28.2 + - - +
103A VAL* 4.0 9.9 - - + -
107A ASN* 3.7 24.0 - - - +
108A VAL* 3.9 23.8 - - + -
111A ALA* 3.7 5.8 - - + +
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Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET 6.2 2.7 - - - +
2A LEU* 3.9 26.7 - - + -
88A LEU* 3.2 15.8 + - + +
89A GLN* 3.7 9.6 - - - +
91A ALA* 1.3 75.3 - - - +
93A PHE* 1.3 59.0 + - - +
95A VAL* 3.3 1.9 + - - +
96A GLN* 2.9 62.0 + - + +
103A VAL* 4.0 13.9 - - + -
10C PHE 6.0 1.1 - - - +
11C ASP* 5.5 7.9 - - - +
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Residues in contact with PHE 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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89A GLN 2.9 19.4 + - - +
90A ARG* 3.2 14.6 + - + +
92A VAL* 1.3 77.6 - - - +
94A HIS* 1.3 63.7 + - + +
96A GLN* 3.2 7.3 + - + +
97A SER* 2.8 48.3 + - - -
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Residues in contact with HIS 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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90A ARG* 2.8 23.5 + - + +
91A ALA* 3.9 6.1 - - - +
93A PHE* 1.3 80.1 - - + +
95A VAL* 1.3 61.6 + - + +
97A SER* 2.8 24.2 + - - -
98A SER* 3.4 10.7 + - - -
107A ASN* 5.2 14.4 - - + +
110A VAL* 4.2 23.2 - - + +
111A ALA* 6.3 1.1 - - + -
131A ARG* 3.6 26.8 + - - -
135A VAL* 4.6 14.3 - - + +
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Residues in contact with VAL 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 ALA 3.2 15.0 + - - +
92A VAL 3.8 3.4 - - - +
94A HIS* 1.3 77.1 - - + +
96A GLN* 1.3 61.6 + - + +
98A SER* 2.6 25.5 + - - -
100A ARG* 3.2 37.7 + - + +
101A ASN* 3.7 9.9 - - - +
102A GLU 3.5 20.2 - - - +
103A VAL* 4.1 8.7 - - + -
107A ASN* 3.5 39.9 - - + +
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Residues in contact with GLN 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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1A MET 5.9 3.0 - - - +
92A VAL* 2.9 41.7 + - + +
93A PHE* 3.9 6.2 - - + +
95A VAL* 1.3 78.0 - - + +
97A SER* 1.3 56.2 + - - +
98A SER 3.1 0.7 - - - -
99A GLY* 2.9 19.2 + - - -
100A ARG 3.4 15.9 - - - +
101A ASN* 4.4 15.3 + - - +
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Residues in contact with SER 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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93A PHE* 2.8 34.0 + - - -
94A HIS* 2.8 29.7 + - - -
96A GLN* 1.3 76.0 - - - +
98A SER* 1.3 56.5 + - - +
99A GLY 3.2 1.7 + - - -
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Residues in contact with SER 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 HIS 3.4 7.3 + - - -
95A VAL* 2.6 23.8 + - - -
97A SER* 1.3 79.8 + - - +
99A GLY* 1.3 57.7 + - - +
100A ARG* 3.7 22.4 + - - +
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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
------------------------------------------------------------
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