Contacts of the strand formed by residues 73 - 76 (chain B) in PDB entry 2O1S
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 GLN 73 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A ILE* 4.5 9.1 + - - +
383A GLY* 6.1 1.0 - - - -
70B PRO 3.2 14.7 - - - +
71B PHE 3.2 17.2 - - - +
72B ASP* 1.3 71.1 - - - +
74B LEU* 1.3 60.6 + - - +
75B ILE* 4.6 0.8 - - + +
114B GLU 5.5 0.9 - - - +
117B VAL* 3.1 40.2 - - + +
133B ILE* 3.6 28.6 - - + +
144B ARG* 3.8 24.4 + - - +
145B ARG 2.9 12.9 + - - +
146B THR* 3.5 5.8 - - + +
147B VAL* 2.9 31.8 + - - +
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 3.5 35.4 - - + -
64B HIS* 4.9 5.6 - - + +
67B TYR* 5.4 1.1 - - + -
69B THR* 4.5 16.8 - - + -
72B ASP 3.6 2.8 + - - -
73B GLN* 1.3 72.1 - - - +
75B ILE* 1.3 68.7 - - - +
76B TRP* 2.8 48.3 + - + +
85B HIS* 4.8 12.6 - - + +
115B TYR 4.4 4.2 - - - +
117B VAL* 3.2 24.8 + - + +
147B VAL* 3.2 27.4 - - + -
149B VAL* 4.5 3.1 - - + -
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Residues in contact with ILE 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLN 4.6 2.7 - - - +
74B LEU* 1.3 80.2 - - - +
76B TRP* 1.3 62.1 + - - +
77B ASP 4.0 0.2 + - - -
117B VAL* 4.2 9.9 - - + -
118B LEU* 4.1 22.4 - - + +
126B SER* 3.6 28.2 - - - -
129B ALA 4.5 0.4 - - - -
130B GLY* 3.4 26.5 - - - +
133B ILE* 3.4 33.0 - - + -
146B THR* 4.4 8.3 - - + -
147B VAL 2.8 14.9 + - - +
148B CYS* 3.3 9.7 - - - -
149B VAL* 2.7 34.1 + - - +
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Residues in contact with TRP 76 (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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56B THR* 4.3 21.8 - - + -
59B LEU* 4.5 4.0 - - + -
60B THR* 3.4 35.4 - - + -
63B LEU* 4.4 11.2 - - + -
64B HIS* 5.5 0.4 - - - -
74B LEU* 2.8 37.8 - - + +
75B ILE* 1.3 76.1 - - - +
77B ASP* 1.3 60.6 + - - +
78B VAL 3.5 0.3 + - - -
79B GLY* 4.5 15.3 - - - -
81B GLN* 4.4 19.7 - - + -
82B ALA* 4.4 10.3 - - + -
84B PRO* 5.9 0.2 - - + -
85B HIS* 3.3 45.0 + + + -
108B PRO* 4.6 9.4 - - + +
118B LEU 5.1 1.4 + - - +
120B VAL* 3.2 27.2 - - - +
126B SER* 4.4 2.5 - - - -
149B VAL* 3.6 39.3 - - + -
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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