Contacts of the strand formed by residues 37 - 43 (chain A) in PDB entry 4QBT
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 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ARG* 3.7 23.5 - - - +
35A GLU 4.6 0.9 + - - +
36A LEU* 1.3 73.4 - - - +
38A ILE* 1.3 61.6 + - - +
68A GLU* 3.5 42.2 + - + +
178A LYS* 3.3 21.3 - - + +
179A VAL* 4.0 7.6 - - + -
180A ASP* 2.8 51.3 + - - +
181A ALA* 3.2 6.2 + - - +
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Residues in contact with ILE 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 4.3 9.0 - - + +
37A LYS* 1.3 76.9 - - - +
39A TYR* 1.3 72.2 + - - +
62A PHE* 3.8 26.2 - - + -
67A CYS* 3.9 27.6 - - + -
68A GLU 2.8 18.0 + - - +
69A VAL* 3.2 14.0 - - + -
70A THR* 2.9 23.6 + - - -
179A VAL* 3.9 5.0 - - - +
181A ALA* 3.4 20.2 - - + +
183A PHE* 3.9 11.0 - - + +
210A LEU* 3.7 30.1 - - + -
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Residues in contact with TYR 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ILE* 1.3 80.8 - - - +
40A TRP* 1.3 78.5 + - - +
41A GLY 4.0 2.7 - - - -
62A PHE* 6.1 0.7 - - - -
69A VAL* 5.1 1.8 - - - -
70A THR* 3.1 26.9 - - + +
72A LEU* 3.9 10.5 - - + -
170A GLN 3.6 2.4 + - - -
173A ASP* 3.4 9.4 - - + +
174A GLU* 4.0 15.7 - - + +
177A LEU* 3.7 23.8 - - + -
179A VAL* 3.7 22.6 - - + +
181A ALA 3.2 9.2 + - - -
182A GLN* 3.1 42.7 + - + +
183A PHE* 3.0 27.6 + - - +
506A TYR* 2.7 38.7 + + - -
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Residues in contact with TRP 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A TYR* 1.3 81.9 - - - +
41A GLY* 1.3 70.9 + - - +
42A THR* 3.6 32.3 - - + -
52A TYR* 4.2 14.6 - + - -
55A PRO* 3.8 29.4 - - + +
56A MET* 3.4 24.2 - - + -
59A ILE* 3.8 25.6 - - + -
62A PHE* 5.8 0.7 - - + -
69A VAL* 5.4 0.6 - - + +
70A THR 3.1 6.2 + - - +
71A ILE* 3.4 18.0 - - + -
72A LEU 2.8 24.3 + - - -
101A ILE* 3.9 16.2 - - + -
182A GLN* 5.2 0.2 - - - -
183A PHE* 3.2 47.1 - + + +
184A GLY* 4.2 6.7 - - - -
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Residues in contact with GLY 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A TYR* 3.9 3.2 - - - -
40A TRP* 1.3 92.5 + - - +
42A THR* 1.3 63.1 + - - -
72A LEU* 3.4 12.3 - - - -
182A GLN* 5.0 1.2 + - - -
183A PHE 4.6 1.4 + - - -
506A TYR* 3.5 43.5 - - - +
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Residues in contact with THR 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A TRP* 3.6 29.0 - - + -
41A GLY* 1.3 74.8 - - - -
43A ALA* 1.3 61.6 + - - +
44A THR* 3.4 1.0 + - - +
52A TYR* 3.6 14.4 - - - -
71A ILE* 5.3 0.2 - - + -
72A LEU 2.9 12.5 + - - +
73A PHE* 3.5 12.1 - - + -
74A ALA* 2.8 26.0 + - - +
97A TYR* 3.7 24.4 - - + -
101A ILE* 4.4 2.7 - - + -
502A K 3.0 22.2 - - - -
506A TYR* 4.3 5.2 + - - +
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Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A THR* 1.3 73.1 + - - +
44A THR* 1.3 60.6 + - - +
45A THR* 3.0 13.9 + - - +
74A ALA* 3.4 15.3 - - - +
77A HIS* 4.5 9.2 - - + +
78A ALA* 4.0 17.3 - - + +
81A ASP* 5.9 3.1 - - + +
84A LYS* 6.2 0.9 - - + -
97A TYR* 3.2 2.8 + - - -
166A TYR* 4.7 6.3 - - + +
502A K 2.7 24.8 - - - -
506A TYR* 4.0 17.3 + - + +
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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
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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