Contacts of the strand formed by residues 80 - 85 (chain A) in PDB entry 2R2J
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 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A VAL 3.2 2.6 - - - +
23A ASN* 3.5 2.3 - - - -
24A PHE* 2.8 38.7 + - - -
75A ILE* 4.0 21.9 - - + +
76A SER 4.5 1.6 + - - +
77A LYS* 2.6 44.4 + - - +
79A PRO* 1.3 71.5 - - - +
81A LEU* 1.3 64.0 + - - +
82A LYS* 3.8 20.4 - - + -
93A GLU* 3.5 31.4 - - - +
368A TYR* 5.6 0.2 - - - -
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Residues in contact with LEU 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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21A LEU* 4.1 13.4 - - + +
22A VAL 3.4 9.6 - - - +
23A ASN* 3.9 9.4 - - + -
35A LEU* 3.7 29.8 - - + -
39A PHE* 3.3 38.4 - - + -
79A PRO* 4.0 5.8 + - + +
80A THR* 1.3 74.8 - - - +
82A LYS* 1.3 63.5 + - - +
93A GLU* 3.6 11.1 + - - +
94A TYR* 3.4 61.7 + - + +
98A ARG* 5.9 3.8 - - + +
103A LEU* 5.0 2.9 - - + -
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Residues in contact with LYS 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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20A ALA 3.4 2.9 - - - +
21A LEU* 3.4 5.9 - - - +
22A VAL* 2.8 32.2 + - - +
24A PHE* 3.5 30.5 - - + -
73A TYR 3.7 14.1 + - - -
74A ARG* 4.8 10.4 + - - +
75A ILE* 4.3 3.1 - - + +
80A THR* 3.8 12.1 - - + -
81A LEU* 1.3 72.5 - - - +
83A LEU* 1.3 59.7 + - - +
84A PHE* 3.8 13.6 - - + -
89A MSE 3.4 42.7 - - + +
90A MSE 4.1 9.7 + - - +
91A LYS* 4.6 5.1 + - - +
93A GLU* 3.0 39.4 + - + +
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Residues in contact with LEU 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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19A VAL* 3.6 24.7 - - + -
20A ALA 3.4 16.2 - - - +
21A LEU* 4.1 14.8 - - + +
81A LEU 4.0 1.6 + - - -
82A LYS* 1.3 74.9 - - - +
84A PHE* 1.3 60.0 + - - +
85A ARG* 4.4 11.7 - - + +
89A MSE 3.6 4.0 - - - +
90A MSE 2.7 57.3 + - + +
92A ARG 4.6 8.5 + - - +
93A GLU* 5.5 0.2 - - - +
94A TYR 5.8 0.4 - - - +
106A TYR* 3.8 20.0 - - + +
107A ILE* 5.3 2.9 - - + -
110A GLN* 3.5 35.7 - - + -
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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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14A LEU* 3.8 26.0 - - + +
17A ALA 5.1 0.4 - - - -
19A VAL* 3.2 6.4 - - - +
20A ALA* 2.8 42.5 + - + +
22A VAL* 3.7 33.4 - - + -
24A PHE* 4.3 4.9 - + - -
73A TYR* 3.7 35.7 - + - -
82A LYS* 3.8 17.0 - - + -
83A LEU* 1.3 77.9 - - - +
85A ARG* 1.3 64.6 + - - +
87A GLY* 3.8 19.3 - - - +
88A MSE 3.2 6.5 - - - -
89A MSE 3.5 39.0 - - + -
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Residues in contact with ARG 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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18A ASP 3.2 11.7 + - - +
19A VAL* 4.4 18.1 - - + +
83A LEU* 4.4 7.4 - - + +
84A PHE* 1.3 76.2 - - - +
86A ASN* 1.3 70.5 + - - +
87A GLY 3.1 3.6 - - - -
88A MSE 2.8 40.4 + - + +
90A MSE 3.5 30.6 - - + +
110A GLN* 2.9 58.4 + - - +
111A LYS* 5.4 0.4 - - - +
151A ARG 5.2 0.4 - - - -
154A ASN* 3.4 48.1 + - - +
155A ILE* 4.5 4.7 - - + -
157A HIS* 4.7 0.4 + - - -
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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
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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