Contacts of the strand formed by residues 19 - 25 (chain A) in PDB entry 2RD0
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 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A PRO* 2.7 19.4 + - - +
18A PRO* 1.3 87.6 - - + +
20A ILE* 1.3 59.8 + - - +
35A GLU* 2.8 45.3 + - + +
36A CYS 3.3 13.0 - - - +
37A LEU* 4.4 14.6 - - + -
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Residues in contact with ILE 20 (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* 5.0 7.9 - - + -
16A MET* 3.6 29.6 - - + -
17A PRO* 3.7 34.5 - - + +
19A ARG* 1.3 75.0 - - - +
21A LEU* 1.3 69.1 + - - +
22A VAL* 3.8 14.3 + - + -
35A GLU* 3.4 4.3 - - - -
36A CYS 2.9 33.6 + - - +
38A ARG* 5.2 1.6 - - + -
89A LEU* 3.6 29.8 - - + -
94A LEU* 6.4 0.2 - - + -
97A PRO* 4.3 11.9 - - + -
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Residues in contact with LEU 21 (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 ILE* 1.3 74.8 - - - +
22A VAL* 1.3 62.5 + - - +
23A GLU* 4.1 1.9 + - - +
33A THR* 3.9 23.2 - - + +
34A LEU 3.4 4.3 - - - +
35A GLU* 4.1 26.2 - - + +
97A PRO* 3.7 21.5 - - - +
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Residues in contact with VAL 22 (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 ILE* 3.8 27.3 + - + -
21A LEU* 1.3 74.4 - - - +
23A GLU* 1.3 64.6 + - - +
24A CYS* 3.2 10.0 + - - -
33A THR* 4.3 1.6 - - - -
34A LEU* 2.8 43.9 + - + +
36A CYS* 3.3 31.4 - - + -
45A ILE* 5.1 2.9 - - + -
89A LEU* 4.0 19.5 - - + -
97A PRO* 3.0 19.5 - - + +
98A PHE* 4.8 2.5 - - - -
99A LEU* 5.3 9.2 - - + +
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Residues in contact with GLU 23 (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 2.4 + - - +
22A VAL* 1.3 69.8 - - - +
24A CYS* 1.3 59.7 + - - +
25A LEU* 3.3 5.4 - - + +
31A ILE* 3.8 30.6 - - + +
32A VAL 3.5 4.7 - - - -
33A THR* 4.3 14.4 - - + +
96A GLN* 5.5 0.9 - - - +
97A PRO* 3.0 12.5 + - - +
98A PHE* 3.3 16.5 - - + +
99A LEU 3.0 27.6 + - - +
494B PHE* 3.9 14.8 - - + -
534B ARG* 3.1 50.1 + - - +
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Residues in contact with CYS 24 (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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22A VAL* 3.2 17.2 + - - -
23A GLU* 1.3 75.2 - - - +
25A LEU* 1.3 61.1 + - - +
26A LEU 4.2 0.2 - - - -
31A ILE* 3.2 8.3 - - - +
32A VAL* 2.7 53.4 + - + +
34A LEU* 4.5 14.6 - - - -
45A ILE* 4.8 4.9 - - - -
49A LEU* 3.6 34.5 - - + -
70A PHE* 4.7 4.5 - - + -
99A LEU* 3.4 17.3 - - - +
101A VAL* 5.5 0.2 - - + -
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Residues in contact with LEU 25 (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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23A GLU* 3.3 25.1 - - + +
24A CYS* 1.3 76.7 - - - +
26A LEU* 1.3 61.7 + - - +
30A MET 4.3 0.9 - - - -
31A ILE* 4.5 6.7 - - + +
98A PHE* 4.0 9.2 - - + -
99A LEU 3.1 14.6 + - - +
100A LYS* 4.1 11.7 - - + +
101A VAL* 2.8 35.5 + - - +
493B ILE* 4.2 20.4 - - + -
494B PHE* 3.6 38.8 - - + -
497B GLN* 3.5 35.2 - - + +
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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