Contacts of the strand formed by residues 41 - 44 (chain V) in PDB entry 4ADV
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 MET 41 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33V ILE* 3.8 24.0 - - + -
35V PRO* 3.6 33.0 - - - -
39V GLN* 3.6 20.9 + - + +
40V ALA* 1.3 77.1 - - - +
42V VAL* 1.3 61.8 + - - +
55V VAL* 4.2 2.9 - - - -
59V LEU* 3.9 18.6 - - + -
61V GLN 5.4 2.8 + - - -
62V LEU* 3.6 21.1 - - + +
63V THR* 3.1 25.3 + - - -
109V ARG* 3.3 38.8 - - + +
111V PHE* 4.0 14.8 - - + -
137V HIS* 6.2 0.4 - - - +
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Residues in contact with VAL 42 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41V MET* 1.3 76.8 - - - +
43V GLU* 1.3 63.8 + - - +
44V ILE* 5.2 0.7 - - + -
63V THR* 3.1 26.7 - - + +
65V ILE* 3.9 30.3 - - + -
97V PHE* 4.5 4.9 - - + -
100V LEU* 4.1 9.2 - - + -
108V LEU* 4.1 22.4 - - + -
109V ARG 3.0 6.4 + - - +
110V VAL* 3.4 30.2 - - + +
111V PHE* 3.0 27.9 + - - +
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Residues in contact with GLU 43 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42V VAL* 1.3 74.4 - - - +
44V ILE* 1.3 70.7 + - - +
45V GLY 3.8 3.5 + - - +
46V PRO* 3.5 19.6 - - + +
51V LEU* 3.6 23.9 + - - +
52V THR* 2.4 42.0 + - - +
62V LEU* 5.1 0.4 - - + -
63V THR 2.9 7.9 + - - +
64V VAL* 3.3 13.7 - - + +
65V ILE* 2.8 28.8 + - - +
111V PHE* 3.3 38.7 - - + +
112V GLY* 4.3 2.9 - - - -
113V ASN 5.1 0.9 + - - -
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Residues in contact with ILE 44 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42V VAL* 4.9 0.9 - - + +
43V GLU* 1.3 72.9 - - - +
45V GLY* 1.3 68.5 + - - +
65V ILE* 3.8 22.4 - - + +
92V ALA* 3.8 20.4 - - + -
97V PHE* 4.2 13.5 - - + -
110V VAL* 3.5 30.7 - - + -
111V PHE 2.8 9.9 + - - +
112V GLY* 3.5 17.7 - - - -
113V ASN 4.0 3.8 + - - +
114V LEU* 3.8 20.4 - - + +
115V PRO* 6.0 1.3 - - + -
118V ILE* 5.6 2.0 - - + -
122V LEU* 3.7 22.9 - - + -
126V LEU* 4.5 1.6 - - + -
138V PHE* 3.8 11.9 - - + -
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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
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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