Contacts of the strand formed by residues 89 - 95 (chain A) in PDB entry 2QNU
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 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A PHE* 4.4 14.4 - - + -
7A TYR 4.0 10.1 - - - +
8A GLY 4.1 4.9 - - - +
9A MLZ 3.6 25.8 - - - +
10A LEU* 3.8 25.8 - - + -
76A VAL* 3.4 0.9 - - - -
77A MSE 2.8 42.8 + - + +
79A SER* 3.6 9.0 - - - +
88A PRO* 1.3 74.1 - - - +
90A THR* 1.3 66.4 + - - +
119A LEU* 3.5 27.2 - - + +
122A THR* 3.7 23.1 - - - +
132A PHE* 4.0 9.2 - - + -
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Residues in contact with THR 90 (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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6A PHE* 3.0 6.5 - - - +
7A TYR* 2.8 45.1 + - - +
21A LEU* 5.2 0.2 - - - +
25A PHE* 4.7 2.5 - - + -
29A TRP* 3.2 39.5 + - + +
33A LEU* 4.4 3.8 - - - +
60A PHE* 3.9 10.3 - - + -
75A VAL 3.4 10.5 - - - +
76A VAL* 3.1 23.0 - - - +
89A LEU* 1.3 73.0 - - - +
91A VAL* 1.3 74.0 + - - +
92A ALA* 4.2 8.3 - - + -
119A LEU* 4.6 0.2 - - - -
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Residues in contact with VAL 91 (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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4A VAL* 3.3 31.0 - - + -
5A GLY 3.4 5.4 - - - +
6A PHE* 4.0 5.6 - - + -
74A GLY* 3.0 4.6 - - - -
75A VAL 3.0 32.3 + - - +
90A THR* 1.3 72.9 - - - +
92A ALA* 1.3 62.3 + - - +
111A TRP* 5.2 1.1 - - + -
115A VAL* 3.4 30.1 - - + +
118A LEU* 5.6 1.8 - - + -
119A LEU* 3.7 23.2 - - + +
132A PHE* 4.0 19.5 - - + -
136A VAL* 4.1 9.2 - - + -
139A LEU* 4.4 7.6 - - + -
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Residues in contact with ALA 92 (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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4A VAL* 3.5 4.7 - - - -
5A GLY 2.9 33.4 + - - +
6A PHE* 4.7 0.2 - - - +
21A LEU* 3.6 16.3 - - + +
25A PHE* 4.0 23.6 - - + -
60A PHE* 4.4 2.0 - - + -
72A VAL* 4.0 18.2 - - + -
73A THR 3.4 9.0 - - - +
74A GLY* 4.2 0.4 - - - -
90A THR* 4.1 7.4 - - + -
91A VAL* 1.3 75.6 - - - +
93A CYS* 1.3 60.3 + - - +
111A TRP* 5.2 0.2 - - - -
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Residues in contact with CYS 93 (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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4A VAL* 4.1 17.5 - - + +
72A VAL* 3.5 3.3 - - - -
73A THR* 2.8 38.7 + - + +
92A ALA* 1.3 73.4 - - - +
94A LEU* 1.3 74.4 - - - +
95A LEU* 3.8 9.0 + - - +
111A TRP* 4.1 20.4 - - + -
141A ALA* 3.8 17.5 - - - -
142A PRO* 3.7 23.8 - - + -
229A PGE 5.7 0.7 - - - -
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Residues in contact with LEU 94 (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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4A VAL 5.8 0.2 - - - +
21A LEU* 4.5 11.1 - - + +
22A PRO* 3.7 34.8 - - + -
25A PHE* 4.1 20.9 - - + -
67A LEU 5.7 1.3 - - - +
70A GLU* 3.7 34.1 - - + +
71A ALA 3.4 4.9 - - - +
72A VAL* 3.7 33.7 - - + -
92A ALA 4.2 0.6 + - - -
93A CYS* 1.3 81.0 - - - +
95A LEU* 1.3 62.1 + - - +
96A PRO* 4.8 0.7 - - - +
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Residues in contact with LEU 95 (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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70A GLU* 3.2 10.6 - - - +
71A ALA* 2.8 35.1 + - + +
73A THR* 4.1 24.0 - - + +
93A CYS* 3.9 21.3 - - - +
94A LEU* 1.3 80.6 - - - +
96A PRO* 1.3 74.2 - - + +
99A ALA* 3.9 9.9 - - + -
101A LEU* 4.2 11.9 - - + -
104A LEU* 4.2 9.0 - - + -
141A ALA* 4.8 6.3 - - + -
142A PRO* 4.6 8.1 - - + +
144A CYS* 4.1 32.3 - - + +
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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