Contacts of the strand formed by residues 17 - 23 (chain A) in PDB entry 2O2V
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 LEU 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A VAL* 1.3 73.3 - - - +
18A VAL* 1.3 70.7 + - - +
19A ILE* 4.1 17.9 - - + -
32A THR* 3.7 1.7 - - - -
33A VAL* 2.8 47.3 + - + +
39A LEU* 4.1 20.4 - - + -
82A LEU* 3.8 23.6 - - + -
85A TYR* 3.5 38.8 - - + -
86A TYR* 3.8 21.3 - - + +
102A LEU* 4.5 5.6 - - + -
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Residues in contact with VAL 18 (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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16A VAL* 4.2 12.9 + - + +
17A LEU* 1.3 78.9 - - - +
19A ILE* 1.3 64.2 + - - +
30A ASP* 3.9 30.1 - - + +
31A TRP 3.3 7.4 - - - +
32A THR* 3.9 17.5 - - + +
85A TYR* 4.3 3.4 + - - +
101A PRO* 3.3 22.5 - - + +
102A LEU* 3.0 27.7 + - - +
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Residues in contact with ILE 19 (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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17A LEU* 4.1 17.9 - - + -
18A VAL* 1.3 76.6 - - - +
20A ARG* 1.3 59.6 + - - +
21A ILE* 3.7 9.4 + - + +
29A VAL 3.5 3.3 - - - +
30A ASP* 3.4 0.7 - - - -
31A TRP* 2.8 58.4 + - + +
33A VAL* 4.0 18.2 - - + -
39A LEU* 4.0 20.9 - - + -
44A VAL* 4.5 9.2 - - + -
78A MET* 6.3 0.2 - - - -
81A MET* 5.7 5.2 - - + -
82A LEU* 5.5 1.8 - - + -
102A LEU* 3.5 18.6 - - + +
104A ILE* 3.6 35.4 - - + -
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Residues in contact with ARG 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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18A VAL 4.0 1.2 - - - -
19A ILE* 1.3 70.0 - - - +
21A ILE* 1.3 59.0 + - - +
22A LYS 3.6 0.2 + - - -
28A ALA* 3.4 28.0 + - + +
29A VAL 3.6 0.2 - - - -
30A ASP* 2.6 42.5 + - - +
101A PRO* 3.7 33.6 - - + +
102A LEU 2.8 13.3 + - - +
103A GLN* 3.3 26.3 - - - +
104A ILE* 2.8 31.0 + - - +
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Residues in contact with ILE 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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19A ILE* 4.0 17.0 - - + +
20A ARG* 1.3 73.2 - - - +
22A LYS* 1.3 67.2 + - - +
23A ILE* 3.4 3.2 + - + +
28A ALA* 3.2 1.9 - - - -
29A VAL* 2.7 48.2 + - + +
31A TRP* 4.4 14.1 - - + -
44A VAL* 5.9 0.7 - - + -
47A VAL* 4.0 27.6 - - + -
48A ILE* 4.2 21.8 - - + -
51A VAL* 4.6 21.1 - - + -
52A LEU* 5.0 0.2 - - + -
104A ILE* 3.8 11.4 - - + -
106A PRO* 3.6 26.5 - - + -
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Residues in contact with LYS 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 ARG* 3.6 2.2 + - - +
21A ILE* 1.3 73.2 - - - +
23A ILE* 1.3 80.2 + - - +
25A ASN 4.8 0.6 - - - +
26A SER* 3.6 14.9 - - - +
27A GLY 2.8 36.2 + - - +
28A ALA* 4.1 4.2 - - + +
52A LEU* 4.1 2.6 - - - +
103A GLN* 4.1 17.9 - - - +
104A ILE 3.0 12.1 + - - +
105A PHE* 3.4 39.7 - - + -
106A PRO* 3.3 22.8 - - + +
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Residues in contact with ILE 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 ILE 3.4 8.0 + - - +
22A LYS* 1.3 107.5 + - - +
24A PRO* 1.4 81.5 - - + +
27A GLY* 3.2 33.0 + - - +
28A ALA 3.9 1.3 - - - +
29A VAL* 4.1 17.3 - - + -
51A VAL* 3.6 30.5 - - + +
52A LEU* 3.9 11.2 - - + -
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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