Contacts of the strand formed by residues 51 - 55 (chain F) in PDB entry 3Q3G
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 LYS 51 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F TYR* 3.2 6.5 - - - -
43F GLN* 2.9 42.9 + - + +
49F SER 4.5 3.6 - - - +
50F PRO* 1.3 75.9 - - - +
52F LEU* 1.3 90.1 + - - +
53F LEU* 3.3 4.0 + - + +
61F GLU* 3.5 21.2 - - - +
62F SER 4.5 8.3 + - - -
64F VAL* 5.3 2.8 - - + +
112H ASP 4.7 12.9 + - - -
114H TRP* 4.5 3.1 - - + -
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Residues in contact with LEU 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F ALA* 3.9 2.5 - - + -
41F TRP 3.7 5.6 - - - +
42F TYR* 3.5 24.4 - - + -
51F LYS* 1.3 97.6 + - - +
53F LEU* 1.3 57.9 - - - +
54F ILE 3.6 23.8 - - - +
55F TYR* 3.8 21.3 - - + -
61F GLU* 3.4 33.5 - - + +
64F VAL* 4.1 2.6 - - - +
109H TYR* 4.8 1.8 - - + -
110H ALA* 3.8 24.0 - - + -
111H MET 3.7 13.0 - - - +
112H ASP* 3.8 24.6 + - + +
114H TRP* 4.5 4.2 - - - -
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Residues in contact with LEU 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F TRP* 2.9 19.6 + - + +
43F GLN* 4.0 28.5 - - + +
51F LYS* 3.3 6.5 + - + +
52F LEU* 1.3 73.6 - - - +
54F ILE* 1.3 70.1 + - + +
60F ARG* 3.7 0.7 - - - -
61F GLU* 2.9 26.0 + - - -
64F VAL* 3.5 33.9 - - + +
65F PRO* 5.9 0.4 - - + -
68F PHE* 3.9 21.8 - - + -
79F LEU* 3.9 13.7 - - + -
92F TYR* 3.6 34.3 - - + -
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Residues in contact with ILE 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F ALA* 3.1 6.2 - - - +
41F TRP* 2.8 49.3 + - + +
52F LEU* 3.6 3.2 - - - +
53F LEU* 1.3 91.4 - - + +
55F TYR* 1.3 63.7 + - - +
57F ALA* 3.4 35.7 - - - +
58F SER* 3.8 4.5 - - - +
59F THR 3.2 11.9 - - - +
60F ARG* 4.1 14.6 - - + -
64F VAL* 4.7 0.2 - - + -
68F PHE* 4.1 26.9 - - + +
70F GLY* 4.4 7.9 - - - +
79F LEU* 3.5 24.9 - - + -
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Residues in contact with TYR 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F LEU 3.8 4.7 - - - -
40F ALA* 4.3 1.1 - - - +
52F LEU* 3.8 17.5 - - + -
54F ILE* 1.3 73.7 - - - +
56F TRP* 1.4 90.3 + + - +
57F ALA 3.1 6.3 + - - -
58F SER 3.5 0.2 + - - -
59F THR* 2.8 62.3 + - + +
60F ARG 3.9 6.9 + - - -
61F GLU* 3.7 39.0 + - + -
62F SER 5.4 0.3 + - - -
97F TYR* 3.8 7.9 - - - +
106H TYR* 6.1 0.4 - + - -
109H TYR* 3.2 31.0 + + + -
110H ALA* 3.9 19.1 - - + -
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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