Contacts of the strand formed by residues 70 - 74 (chain S) in PDB entry 4OD2
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 GLU 70 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A TYR* 3.9 4.5 - - - -
106B TRP* 3.7 15.9 - - - -
65S ARG 5.1 0.3 - - - +
66S CYS* 4.2 2.3 - - + -
67S ASP* 2.6 51.6 + - + +
68S SER 2.5 20.5 + - - +
69S GLY* 1.3 82.6 - - - +
71S VAL* 1.3 67.1 + - - +
84S CYS* 3.9 19.5 - - + +
85S GLN 3.3 8.7 - - - +
87S GLU* 5.0 2.0 - - - -
92S ARG* 3.1 38.7 + - - +
98S GLU 6.1 0.2 - - - -
99S MET* 5.9 1.7 - - - -
100S CYS* 3.6 16.4 - - - -
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Residues in contact with VAL 71 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TYR* 3.9 13.0 - - - +
92A SER 5.0 0.2 - - - +
93A GLY* 4.0 23.8 - - - +
66S CYS* 3.9 5.4 - - - -
70S GLU* 1.3 78.2 - - - +
72S GLU* 1.3 61.1 + - - +
73S LEU* 3.3 2.9 + - - +
84S CYS* 3.0 6.1 - - - -
85S GLN* 2.7 59.3 + - + +
87S GLU* 5.0 13.5 - - + -
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Residues in contact with GLU 72 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER* 2.8 36.6 + - - +
29A TYR* 3.3 22.7 + - + +
91A SER 5.5 2.8 - - - +
92A SER 5.2 1.1 - - - +
66S CYS* 4.0 7.9 - - - -
71S VAL* 1.3 75.6 - - - +
73S LEU* 1.3 66.6 + - - +
74S SER 3.9 4.9 - - - +
75S PRO* 3.6 40.8 - - + +
76S CYS 4.6 2.6 + - - -
82S THR* 4.5 11.6 + - - +
83S VAL 3.5 3.4 - - - -
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Residues in contact with LEU 73 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71S VAL* 3.3 4.3 + - - -
72S GLU* 1.3 74.4 - - - +
74S SER* 1.3 61.1 + - - +
75S PRO* 4.2 3.5 - - - +
83S VAL* 2.7 31.6 + - + +
85S GLN* 3.2 44.6 - - + +
120S TRP* 4.7 9.6 - - + +
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Residues in contact with SER 74 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72S GLU* 3.9 5.2 - - - +
73S LEU* 1.3 82.1 - - - +
75S PRO* 1.3 68.9 - - - +
80S ARG* 3.5 30.6 + - - -
82S THR* 3.6 1.7 - - - -
83S VAL* 3.1 44.3 + - - +
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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