Contacts of the strand formed by residues 47 - 53 (chain B) 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 LEU 47 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A TYR* 5.5 1.1 - - + -
50A PRO* 3.7 35.0 - - + -
93A TYR* 3.8 29.8 - - + -
104A PHE* 3.5 55.5 - - + +
105A GLY 5.0 1.3 + - - +
39B VAL* 3.8 21.8 - - + -
40B LYS 3.6 1.3 - - - -
41B GLN* 3.5 34.1 - - + +
46B GLY* 1.3 72.1 - - - -
48B GLU* 1.3 58.8 + - - +
97B TYR* 4.5 5.4 - - + -
114B TRP* 4.3 2.9 - - + -
607B EDO 4.0 4.9 + - - -
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Residues in contact with GLU 48 (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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39B VAL* 3.7 2.8 - - - +
40B LYS* 2.7 60.8 + - + +
42B ARG* 4.1 22.0 + - - +
46B GLY 4.6 3.6 - - - +
47B LEU* 1.3 73.0 - - - +
49B TRP* 1.3 62.4 + - - +
50B ILE* 3.5 1.2 + - - +
65B LYS* 4.8 13.8 - - + +
66B PHE* 3.4 28.7 - - + -
607B EDO 3.7 16.6 - - - +
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Residues in contact with TRP 49 (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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100A TYR* 3.4 34.8 - + + -
101A PRO* 3.5 29.2 - - + -
102A LEU* 3.3 39.4 - - + +
104A PHE* 4.4 7.3 - - + -
37B GLN* 2.8 23.9 + - + -
38B TRP 3.9 12.8 - - - -
39B VAL* 4.3 8.6 - - + +
47B LEU 4.2 0.4 - - - -
48B GLU* 1.3 70.3 - - - +
50B ILE* 1.3 59.5 + - - +
51B GLY* 3.4 31.0 + - - -
52B ARG* 3.8 7.0 - - + -
61B LYS* 4.1 11.9 - - + -
62B TYR 3.9 6.3 - - - -
63B ASP* 3.7 24.5 - - + +
66B PHE* 3.5 8.7 - - - -
111B MET* 3.9 18.8 - - + -
607B EDO 2.7 28.8 + - - -
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Residues in contact with ILE 50 (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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38B TRP* 2.8 23.3 + - + +
40B LYS* 4.0 9.2 - - + +
48B GLU 4.1 5.6 - - - +
49B TRP* 1.3 74.2 - - - +
51B GLY* 1.3 57.8 + - - +
62B TYR* 3.5 5.7 - - + +
63B ASP* 2.9 27.4 + - - +
66B PHE* 3.7 35.5 - - + +
70B ALA* 3.4 31.6 - - + -
72B ILE* 4.3 5.8 - - + -
83B LEU* 3.9 20.9 - - + -
85B LEU* 4.8 2.0 - - + -
96B TYR* 3.6 38.1 - - + -
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Residues in contact with GLY 51 (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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38B TRP 3.0 24.3 + - - -
49B TRP* 3.4 20.6 + - - -
50B ILE* 1.3 81.6 - - - +
52B ARG* 1.3 63.6 + - - +
61B LYS 3.1 14.1 - - - -
62B TYR* 3.9 0.7 - - - -
72B ILE* 3.5 13.8 - - - +
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Residues in contact with ARG 52 (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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100A TYR* 3.2 21.5 + - + -
35B TYR* 3.9 32.6 - - - -
36B MET 3.1 12.6 - - - +
37B GLN* 3.2 28.7 - - - +
49B TRP* 3.8 12.8 - - + -
51B GLY* 1.3 71.2 - - - +
53B ILE* 1.3 61.0 + - - +
54B ASP* 3.7 9.3 - - - +
59B LYS 3.2 26.7 + - - -
60B THR* 3.3 5.9 - - - +
61B LYS* 2.8 50.4 + - + +
72B ILE* 3.7 8.2 - - - +
178E GLU* 2.9 20.4 + - - -
179E GLU* 2.6 32.7 + - - +
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Residues in contact with ILE 53 (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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35B TYR* 3.4 4.3 - - - -
36B MET* 2.9 50.1 + - + +
52B ARG* 1.3 79.7 - - - +
54B ASP* 1.3 70.8 + - - +
55B PRO* 3.2 13.0 - - + +
58B ASP* 4.1 18.4 - - + +
59B LYS 3.4 5.8 - - - +
60B THR* 3.7 19.7 - - + -
72B ILE* 3.6 21.8 - - + +
73B THR* 3.6 17.7 - - - +
74B ALA* 3.6 31.4 - - + +
81B ALA* 4.7 2.0 - - + -
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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