Contacts of the strand formed by residues 20 - 28 (chain L) in PDB entry 2O5J
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 TYR 20 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14L ARG 5.0 0.2 - - - -
15L THR* 3.2 17.5 + - - -
16L GLN* 3.3 27.7 + - + +
17L GLY 4.3 0.2 - - - +
19L GLU* 1.3 79.3 - - + +
21L GLY* 1.3 65.9 + - - +
22L GLU* 4.2 22.2 + - + -
198L ARG* 2.8 66.2 + - + -
199L ILE 3.7 4.3 - - - -
200L TRP* 3.5 45.5 - + - +
207L PRO* 3.4 5.7 - - - +
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Residues in contact with GLY 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14L ARG 3.7 6.7 - - - -
15L THR* 4.1 6.1 - - - -
20L TYR* 1.3 79.9 - - - +
22L GLU* 1.3 64.0 + - - -
23L PHE* 2.9 24.8 - - - -
198L ARG* 4.5 0.2 - - - -
199L ILE 3.0 25.8 + - - -
207L PRO* 3.6 15.3 - - - -
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Residues in contact with GLU 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L THR 4.8 0.2 - - - -
13L VAL* 3.9 0.2 - - - -
14L ARG* 2.8 86.9 + - + +
16L GLN* 5.9 2.4 - - - +
20L TYR* 4.2 27.2 + - + -
21L GLY* 1.3 71.2 - - - -
23L PHE* 1.3 74.8 + - - +
24L VAL* 4.3 2.5 - - + -
196L THR* 6.4 1.1 - - - -
197L LEU 4.0 4.0 - - - -
198L ARG* 4.2 28.6 + - + +
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Residues in contact with PHE 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225K PHE* 6.1 0.2 - - + -
11L PHE* 3.5 22.7 - + + -
12L THR 3.6 4.5 - - - -
13L VAL* 4.1 26.9 - - + -
15L THR* 5.3 2.0 - - - -
21L GLY* 2.9 19.7 - - - -
22L GLU* 1.3 87.1 - - - +
24L VAL* 1.3 62.2 + - - +
25L LEU* 5.3 0.5 - - - +
195L LEU 3.6 2.1 - - - +
196L THR* 3.0 5.8 - - - -
197L LEU* 3.0 49.1 + - + +
199L ILE* 3.8 24.2 - - + -
207L PRO* 3.3 37.9 - - + -
208L LEU* 3.9 18.2 - - + -
211L LEU* 3.8 19.3 - - + -
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Residues in contact with VAL 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10L VAL 3.4 1.5 - - - +
11L PHE* 3.1 6.9 - - - -
12L THR* 2.8 52.2 + - + +
14L ARG* 3.7 26.2 - - + +
22L GLU* 5.3 1.1 - - + -
23L PHE* 1.3 76.7 - - - +
25L LEU* 1.3 61.1 + - - +
26L GLU* 2.8 27.4 - - - +
194L LYS* 4.1 8.1 - - + +
195L LEU 3.5 2.0 - - - -
196L THR* 3.4 30.1 - - + +
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Residues in contact with LEU 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221K HIS* 5.4 0.4 - - - +
224K TYR* 3.1 25.8 - - + +
225K PHE* 3.6 39.9 - - + -
9L PRO* 3.4 21.3 - - + -
10L VAL 3.7 4.9 - - - -
11L PHE* 3.7 24.2 - - + -
23L PHE 5.3 0.4 - - - +
24L VAL* 1.3 76.2 - - - +
26L GLU* 1.3 59.9 + - - +
28L LEU* 3.3 41.0 - - + +
36L LEU* 4.8 3.6 - - + -
195L LEU* 2.8 34.7 + - + +
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Residues in contact with GLU 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L PRO* 4.1 1.3 - - - -
10L VAL* 2.9 46.8 + - + +
12L THR* 4.4 5.7 - - - +
24L VAL* 2.8 34.1 - - - +
25L LEU* 1.3 76.6 - - - +
27L PRO* 1.3 79.4 - - + +
28L LEU* 4.6 0.4 - - - -
184L THR* 4.4 8.5 - - + +
193L ASP 4.1 0.4 - - - +
194L LYS* 3.5 36.1 - - + +
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Residues in contact with PRO 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221K HIS* 6.1 0.2 - - - -
7L LYS* 3.8 37.3 + - + +
8L ALA 4.4 8.9 - - - +
9L PRO* 3.9 12.8 - - - +
10L VAL* 4.7 4.7 - - + -
26L GLU* 1.3 89.8 - - + +
28L LEU* 1.3 69.0 + - - +
184L THR* 4.6 11.9 - - + +
186L LEU* 3.9 13.2 - - + -
192L LEU* 3.5 25.6 - - + -
193L ASP 3.9 1.8 - - - +
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Residues in contact with LEU 28 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221K HIS* 5.2 10.8 - - + +
7L LYS* 6.4 0.4 - - - -
9L PRO* 4.3 6.1 - - + -
25L LEU* 3.3 44.9 - - + +
27L PRO* 1.3 84.9 - - - +
29L GLU* 1.3 70.4 + - - +
32L PHE* 4.1 9.6 - - + -
33L GLY* 3.5 30.7 - - - +
36L LEU* 4.3 14.1 - - + -
192L LEU* 3.7 10.8 - - - +
193L ASP* 3.0 32.6 + - + +
195L LEU* 3.7 16.4 - - + +
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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