Contacts of the strand formed by residues 40 - 48 (chain B) in PDB entry 2RIO
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 ARG 40 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A THR* 3.5 48.1 + - + +
66A ASP* 2.9 17.6 + - - -
74A TYR* 2.9 47.5 + - + -
75A TYR 5.2 2.2 + - - -
36B SER* 3.1 2.6 - - - -
37B PHE* 2.8 51.8 + - + +
38B GLN* 3.3 4.1 + - + +
39B GLY* 1.3 70.3 - - - -
41B PRO* 1.3 76.3 - - - +
42B VAL* 3.7 4.3 - - + +
73B ARG* 3.0 5.3 - - - +
75B TYR* 3.5 37.0 + - + -
153B ARG* 3.8 11.3 - - - +
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Residues in contact with PRO 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B GLN* 5.3 3.4 - - - +
35B GLY 3.6 9.9 - - - +
36B SER* 4.3 2.2 - - - -
39B GLY 3.5 7.8 - - - +
40B ARG* 1.3 86.8 - - + +
42B VAL* 1.3 68.1 + - - +
75B TYR* 5.3 2.1 - - - -
89B GLU* 5.3 4.3 - - - +
90B LEU* 3.7 31.6 + - + +
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Residues in contact with VAL 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 4.7 0.7 - - + -
34B GLN* 3.9 0.9 - - - -
35B GLY 3.0 26.0 + - - +
36B SER* 3.6 29.4 - - - +
37B PHE* 3.9 15.0 - - + +
40B ARG* 3.7 8.5 - - + +
41B PRO* 1.3 84.5 - - - +
43B ALA* 1.3 60.6 + - - +
44B VAL* 3.9 15.9 - - + -
75B TYR* 4.1 25.4 - - + -
87B ALA* 4.1 11.4 - - + -
88B LEU 3.3 15.9 - - - +
90B LEU* 3.7 16.6 - - - +
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Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU* 3.6 13.9 - - + -
32B VAL* 3.7 6.3 - - + -
33B PHE 3.4 5.8 - - - -
42B VAL* 1.3 73.3 - - - +
44B VAL* 1.3 60.9 + - - +
45B LYS 4.0 0.2 - - - -
86B ILE 3.6 1.0 - - - +
87B ALA* 3.4 3.1 - - - -
88B LEU* 2.8 35.4 + - + +
89B GLU 3.9 2.0 - - - +
90B LEU* 4.0 3.6 - - - +
2101B ADP 3.0 46.0 - - + +
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Residues in contact with VAL 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 4.2 13.7 - - + -
17B VAL 4.6 1.8 - - - +
18B VAL* 4.1 22.4 - - + -
31B VAL 3.7 0.7 - - - +
32B VAL* 3.3 4.0 - - - +
33B PHE* 2.7 41.9 + - + +
35B GLY* 4.2 17.0 - - - -
42B VAL* 3.9 19.7 - - + -
43B ALA* 1.3 78.1 - - - +
45B LYS* 1.3 61.5 + - - +
46B ARG 3.6 1.6 + - - -
85B TYR* 3.7 41.7 - - + -
86B ILE 3.6 5.2 - - - +
87B ALA* 4.7 4.0 - - + -
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Residues in contact with LYS 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B THR* 3.7 15.7 - - + -
31B VAL 4.0 2.2 - - - -
32B VAL* 4.1 12.5 - - + +
43B ALA 4.0 1.2 - - - -
44B VAL* 1.3 70.7 - - - +
46B ARG* 1.3 59.4 + - - +
47B MET* 3.0 40.7 + - + +
58B GLU* 3.6 19.0 + - - +
84B LEU 3.2 6.4 - - - +
85B TYR* 3.3 1.5 - - - -
86B ILE* 2.8 46.6 + - + +
88B LEU* 4.3 16.8 - - + +
171B ASP* 3.2 14.6 + - - +
2101B ADP 2.5 56.8 + - - +
2103B SR 4.2 1.0 - - - -
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Residues in contact with ARG 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B PHE* 4.2 20.0 - - - +
10B GLU* 3.2 35.0 + - - -
29B GLY 4.3 5.5 + - - +
30B THR* 3.2 25.6 - - - +
31B VAL* 2.9 42.9 + - - +
33B PHE* 3.8 23.1 - - + -
44B VAL 3.6 0.4 + - - -
45B LYS* 1.3 71.8 - - - +
47B MET* 1.3 61.7 + - - +
83B PHE* 3.7 46.6 - - + -
84B LEU 3.4 2.0 - - - -
85B TYR* 3.6 18.8 - - + -
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Residues in contact with MET 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B GLY 5.6 0.4 - - - -
30B THR* 3.6 16.2 - - + +
45B LYS* 3.0 55.6 + - + +
46B ARG* 1.3 73.7 - - - +
48B LEU* 1.3 68.4 + - - +
51B PHE* 4.3 16.4 - - + -
55B ALA* 4.1 13.5 - - - -
58B GLU* 4.4 6.3 - - - +
83B PHE* 3.3 11.1 - - - +
84B LEU* 2.8 50.9 + - + +
86B ILE* 3.6 26.2 - - + -
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Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B SER 3.9 22.7 - - - +
29B GLY* 5.0 10.1 - - - +
30B THR* 5.3 1.0 + - - +
47B MET* 1.3 75.0 - - - +
49B ILE* 1.3 54.7 + - - +
50B ASP* 4.1 10.5 - - + +
51B PHE* 2.8 53.8 + - + +
52B CYS 4.0 1.2 + - - -
82B ARG 4.1 3.8 - - - +
83B PHE* 3.8 24.0 - - + -
84B LEU* 4.5 0.7 - - - +
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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