Contacts of the helix formed by residues 80 - 91 (chain A) in PDB entry 1R2B
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 PRO 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A VAL* 3.8 32.8 - - + +
39A SER* 4.1 14.8 - - - +
41A GLU* 3.6 35.7 - - + +
43A PHE* 3.9 10.2 - - + -
78A ILE 3.9 2.2 - - - +
79A ASN* 1.3 84.4 - - + +
81A GLU* 1.3 61.0 + - - +
83A PHE* 3.3 3.9 + - + +
84A ASN* 2.8 31.4 + - - +
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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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79A ASN* 3.4 11.0 + - - +
80A PRO* 1.3 76.5 - - - +
82A GLY* 1.3 66.9 + - - +
84A ASN* 2.8 19.1 + - - +
85A ILE* 2.9 23.9 + - + +
98A ARG* 3.4 19.7 + - - -
101A ASN* 2.9 40.9 + - - +
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Residues in contact with GLY 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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79A ASN* 3.0 21.0 - - - +
81A GLU* 1.3 78.4 - - - +
83A PHE* 1.3 60.6 + - - +
85A ILE* 3.5 4.9 + - - +
86A LEU* 3.3 26.9 + - - +
101A ASN* 6.0 0.7 - - - -
104A ALA* 4.7 1.6 - - - -
105A VAL* 4.1 23.5 - - - +
108A THR* 4.1 12.1 - - - -
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Residues in contact with PHE 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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36A ILE* 3.8 23.6 - - + -
38A VAL* 3.8 18.2 - - + -
43A PHE* 3.8 36.6 - + + -
50A LEU* 5.5 0.9 - - + -
57A PHE* 4.1 22.2 - + - -
74A LEU* 4.1 15.3 - - + -
78A ILE* 4.5 2.9 - - + -
79A ASN 3.5 13.1 + - - +
80A PRO* 3.3 9.4 + - + +
81A GLU 3.0 0.6 - - - -
82A GLY* 1.3 76.5 - - - +
84A ASN* 1.3 61.0 + - - +
86A LEU* 3.3 2.6 + - - +
87A LEU* 3.0 40.2 + - + +
90A MET* 5.2 3.8 - - + -
108A THR* 4.0 13.8 - - + +
112A LEU* 4.0 26.9 - - + -
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Residues in contact with ASN 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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26A ARG* 5.3 1.9 + - - -
43A PHE* 3.5 29.8 - - + -
80A PRO 2.8 20.9 + - - +
81A GLU* 2.8 8.8 + - - +
83A PHE* 1.3 70.7 - - - +
85A ILE* 1.3 69.7 + - - +
87A LEU* 3.3 8.1 + - - +
88A ASP* 3.0 38.3 + - - +
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Residues in contact with ILE 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 GLU* 2.9 32.6 + - + +
82A GLY* 3.6 6.1 - - - +
83A PHE 3.2 0.2 - - - -
84A ASN* 1.3 81.6 - - + +
86A LEU* 1.3 55.8 + - - +
88A ASP* 3.4 8.1 + - - +
89A PHE* 3.0 26.2 + - - +
94A ARG 4.5 1.4 - - - +
95A LEU* 3.9 20.0 - - + -
96A ASN* 3.2 40.3 + - + +
101A ASN* 4.0 19.1 - - - +
105A VAL* 3.7 28.7 - - + -
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Residues in contact with LEU 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 GLY 3.3 7.5 + - - +
83A PHE 3.3 6.8 + - - +
84A ASN 3.2 0.4 - - - -
85A ILE* 1.3 76.2 - - - +
87A LEU* 1.3 59.7 + - - +
89A PHE* 3.3 8.3 + - + +
90A MET* 3.0 33.3 + - + +
95A LEU* 4.1 18.4 - - + -
105A VAL* 3.7 11.0 - - + +
108A THR* 3.4 36.6 - - + -
109A ALA* 3.4 36.1 - - + +
112A LEU* 3.8 13.9 - - + -
114A MET* 4.1 17.0 - - + -
117A VAL* 4.1 8.7 - - + -
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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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26A ARG* 3.2 26.2 - - - +
43A PHE* 4.0 35.9 - - + -
44A ARG 4.5 6.5 - - - +
45A ALA* 4.4 6.1 - - + -
50A LEU* 3.9 23.3 - - + -
83A PHE* 3.0 28.0 + - + +
84A ASN* 3.3 8.0 + - - +
86A LEU* 1.3 73.7 - - - +
88A ASP* 1.3 65.7 + - - +
90A MET* 3.3 14.2 - - + +
91A TYR* 3.2 42.6 + - + -
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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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26A ARG* 2.9 27.1 + - - +
84A ASN* 3.0 33.5 + - - +
85A ILE* 3.6 7.0 - - - +
87A LEU* 1.3 72.5 - - - +
89A PHE* 1.3 57.2 + - - +
91A TYR 2.9 3.1 + - - -
92A THR* 2.8 48.4 + - + +
94A ARG 4.8 2.7 - - - +
96A ASN* 5.0 13.2 + - - +
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Residues in contact with PHE 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 ILE 3.0 13.8 + - - +
86A LEU* 3.3 13.2 - - + +
88A ASP* 1.3 76.1 - - - +
90A MET* 1.3 61.1 + - + +
92A THR* 4.0 0.4 - - - -
93A SER 2.7 33.3 + - - -
94A ARG 3.1 23.5 + - - +
95A LEU* 3.8 16.4 - - + -
114A MET* 3.8 19.3 - - + -
117A VAL* 3.7 26.7 - - + -
11B PHE* 3.4 42.4 - + + -
14B HIS* 3.4 40.2 + + - -
1424C SER* 3.9 10.1 - - - -
1425C ILE* 4.2 3.4 - - + -
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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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19A LEU* 3.6 12.0 - - - +
49A VAL* 4.4 5.5 - - + +
50A LEU* 3.7 35.4 - - + -
53A CYS* 3.5 36.2 - - + -
54A SER* 4.5 3.4 - - - -
57A PHE* 4.3 15.7 - - + -
83A PHE* 5.2 2.2 - - + -
86A LEU 3.0 22.6 + - - +
87A LEU* 3.3 16.6 - - + +
89A PHE* 1.3 77.0 - - - +
91A TYR* 1.3 64.1 + - + +
112A LEU* 4.5 5.8 - - + -
114A MET* 3.8 32.1 - - + -
14B HIS* 2.9 23.4 + - - -
18B VAL* 4.3 0.5 - - - +
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Residues in contact with TYR 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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19A LEU* 3.3 30.0 - - + +
20A LEU* 5.1 1.0 - - - -
22A LEU* 3.5 22.4 - - + -
23A ASN* 3.2 42.9 - - - +
26A ARG* 3.4 32.1 - - + +
45A ALA* 3.8 3.8 - - + -
46A HIS* 2.5 48.5 + - - +
49A VAL* 3.6 33.1 - - + +
50A LEU* 5.2 1.1 - - + -
87A LEU* 3.2 29.6 + - + -
88A ASP 2.9 7.1 + - - +
90A MET* 1.3 81.2 - - + +
92A THR* 1.3 60.9 + - - +
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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