Contacts of the strand formed by residues 19 - 23 (chain B) in PDB entry 5OC9
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 VAL 19 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 1.3 83.2 + - + +
20B VAL* 1.3 67.1 + - - +
21B ILE* 4.8 3.1 - - + -
71B LEU* 3.5 5.2 - - - +
72B VAL* 2.8 34.6 + - + +
125B GLN* 4.0 13.7 - - + +
128B ILE* 3.8 26.5 - - + -
132B LEU* 4.3 13.0 - - + -
170B VAL* 3.8 29.4 - - + -
171B PHE 3.6 6.3 - - - +
172B PRO* 4.3 1.3 - - + -
173B LEU* 5.1 0.2 - - - -
545B PHE* 3.8 27.1 - - + -
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Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B VAL* 1.3 77.7 - - - +
21B ILE* 1.3 66.8 + - - +
22B GLU 4.7 0.2 - - - +
69B LEU* 3.8 25.4 - - + -
70B TYR 3.4 9.0 - - - +
71B LEU* 3.9 14.4 - - + -
169B GLN 3.9 0.7 - - - +
170B VAL* 3.3 5.9 - - - -
171B PHE* 2.9 65.3 + - + +
173B LEU* 3.8 31.6 - - + -
482B VAL* 4.0 10.5 - - + -
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Residues in contact with ILE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B VAL* 4.8 2.0 - - + -
20B VAL* 1.3 77.5 - - - +
22B GLU* 1.3 60.6 + - - +
23B LEU* 3.6 22.8 + - + -
35B LEU* 4.5 6.5 - - + -
39B ILE* 3.8 24.0 - - + -
52B PHE* 4.3 3.4 - - + -
68B ASN 3.6 4.2 - - - +
69B LEU* 3.8 0.5 - - - -
70B TYR* 2.8 42.4 + - + +
72B VAL* 3.6 27.8 - - + -
132B LEU* 4.1 16.2 - - + -
158B LEU* 5.6 2.7 - - + -
167B VAL* 4.2 13.9 - - + -
169B GLN 3.7 3.1 - - - -
170B VAL* 3.8 26.9 - - + -
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Residues in contact with GLU 22 (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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20B VAL* 4.1 2.6 - - + -
21B ILE* 1.3 71.9 - - - +
23B LEU* 1.3 62.2 + - - +
67B GLN 4.5 6.1 - - - +
68B ASN 3.8 3.1 - - - +
69B LEU* 3.9 22.9 - - + -
167B VAL* 3.6 4.7 - - - +
168B ILE* 2.8 56.1 + - + +
169B GLN* 2.9 48.7 + - + +
171B PHE* 5.4 0.2 - - + -
486B LYS* 3.3 33.9 + - + +
487B GLU* 5.3 0.2 - - - +
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 3.6 27.6 - - + -
22B GLU* 1.3 76.6 - - - +
24B ALA* 1.4 65.8 + - - +
25B GLN* 3.8 0.5 + - - -
27B VAL* 3.7 28.7 - - + -
31B THR* 5.7 1.1 - - + -
32B LYS* 3.9 22.7 - - + -
35B LEU* 3.8 21.8 - - + -
52B PHE* 5.5 0.2 - - + -
67B GLN 4.3 2.4 - - - +
68B ASN* 3.1 29.3 + - + +
70B TYR* 3.9 22.7 - - + -
166B ILE* 3.4 14.8 - - + +
167B VAL* 4.3 7.6 - - + -
168B ILE* 3.6 10.9 - - - +
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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
------------------------------------------------------------
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