Contacts of the strand formed by residues 54 - 60 (chain A) in PDB entry 2QCB
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 TYR 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A THR* 3.1 7.8 - - - -
43A TYR* 2.9 40.8 + - - +
44A GLU* 5.1 0.2 - - - -
45A SER 5.4 0.7 - - - -
49A ASN 4.2 1.4 + - - -
50A ALA* 3.2 17.8 - - + -
51A GLU 3.0 40.2 + - - -
52A SER 3.5 5.8 - - - -
53A ARG* 1.3 75.1 - - - +
55A VAL* 1.3 64.9 + - - +
77A VAL* 3.6 20.2 - - + -
78A ALA 3.8 2.0 - - - +
79A TRP* 3.5 43.9 + + - -
80A LYS 3.7 24.2 - - - +
81A ASN* 3.2 27.4 + - + -
84A ARG* 4.0 10.6 - - - +
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Residues in contact with VAL 55 (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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41A GLY 3.8 7.6 - - - +
42A THR* 4.7 4.5 - - + +
54A TYR* 1.3 75.6 - - - +
56A LEU* 1.3 73.0 + - - +
57A THR* 5.7 3.1 - - + -
76A THR 4.0 0.3 - - - +
77A VAL* 3.9 18.4 - - - +
78A ALA 4.5 4.4 + - - +
80A LYS 5.5 2.2 + - - -
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Residues in contact with LEU 56 (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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29A PHE* 3.5 35.7 - - + -
30A ILE 4.0 1.3 - - - +
31A VAL* 4.4 5.8 - - + -
39A LEU* 4.6 1.3 - - + +
40A THR* 3.7 10.4 - - - +
41A GLY* 3.0 44.3 + - - +
42A THR 3.3 34.3 - - - +
43A TYR* 3.9 7.0 - - + +
54A TYR 3.5 0.2 + - - -
55A VAL* 1.3 81.9 - - - +
57A THR* 1.3 70.6 + - - +
75A TRP* 4.1 17.3 - - + -
76A THR 3.2 14.1 - - - +
77A VAL* 3.7 9.6 - - + -
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Residues in contact with THR 57 (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 LEU 3.3 12.1 + - - -
40A THR* 4.6 6.7 - - - +
55A VAL* 5.7 3.8 - - + -
56A LEU* 1.3 77.6 - - - +
58A GLY* 1.3 61.8 + - - +
75A TRP* 4.0 4.7 - - - -
76A THR* 2.9 34.6 + - - +
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Residues in contact with GLY 58 (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 ALA* 3.7 1.6 - - - +
39A LEU* 2.8 36.1 + - - +
57A THR* 1.3 80.5 + - - +
59A ARG* 1.3 70.9 + - - -
74A GLY 3.2 14.1 - - - -
75A TRP* 3.8 4.5 - - - -
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Residues in contact with ARG 59 (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 ASP* 3.1 26.7 + - - +
37A GLY* 3.2 15.9 - - - -
38A ALA* 3.4 27.1 - - - +
39A LEU* 3.6 4.8 - - - +
58A GLY* 1.3 84.4 - - - -
60A TYR* 1.3 63.2 + - - +
73A LEU* 3.3 2.9 - - - +
74A GLY 2.9 30.4 + - - +
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Residues in contact with TYR 60 (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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13A ASP 4.7 5.2 - - - -
14A GLU* 3.8 25.4 + - - +
17A ILE* 3.6 27.8 - - + -
33A ALA* 3.6 17.9 - - + +
34A GLY 2.7 31.6 + - - -
35A ALA* 4.5 1.7 - - - -
37A GLY* 2.9 38.7 + - - +
38A ALA 3.6 2.0 - - - -
39A LEU* 3.6 19.1 - - + -
59A ARG* 1.3 79.4 + - - +
61A ASP* 1.3 75.0 + - - +
62A SER* 3.2 30.6 + - - -
71A THR* 4.2 3.1 - - + -
72A ALA 3.4 5.8 - - - +
73A LEU* 3.6 17.9 - - + +
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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