Contacts of the strand formed by residues 71 - 77 (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 ALA 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ILE 3.4 13.7 - - - +
64A PRO* 3.9 22.2 - - + +
69A GLY 4.0 1.2 + - - -
70A GLU* 1.3 77.3 - - - +
72A VAL* 1.3 59.9 + - - +
94A LEU* 3.4 5.2 - - - -
95A LEU* 2.8 41.2 + - + +
96A PRO 3.9 12.2 + - - +
99A ALA* 4.6 1.1 - - + -
101A LEU* 4.0 22.4 - - + -
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Residues in contact with VAL 72 (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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25A PHE* 3.6 32.8 - - + -
60A PHE* 4.0 10.8 - - + -
61A ALA* 3.4 2.3 - - - -
62A ILE* 2.7 48.5 + - + +
63A ALA 6.0 0.2 - - - +
67A LEU* 4.2 16.4 - - + +
70A GLU* 3.9 9.2 - - + +
71A ALA* 1.3 81.5 - - - +
73A THR* 1.3 62.3 + - - +
92A ALA* 4.0 15.0 - - + -
93A CYS 3.5 10.3 - - - +
94A LEU* 3.7 20.0 - - + -
95A LEU* 5.3 1.8 - - - -
101A LEU* 5.0 2.1 - - - +
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Residues in contact with THR 73 (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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60A PHE* 2.8 25.4 + - - -
61A ALA* 4.3 1.6 - - - +
72A VAL* 1.3 73.1 - - - +
74A GLY* 1.3 57.6 + - - +
92A ALA* 3.4 2.4 - - - +
93A CYS* 2.8 39.5 + - + +
95A LEU* 4.1 7.6 - - + +
101A LEU* 5.5 0.4 - - - -
104A LEU* 3.5 21.1 - - + +
111A TRP* 3.8 9.4 - - + -
112A PHE* 3.2 21.2 - - + -
142A PRO* 3.7 30.3 - - + -
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Residues in contact with GLY 74 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A ARG* 3.5 0.7 - - - -
60A PHE* 3.0 37.5 + - - +
73A THR* 1.3 81.0 + - - +
75A VAL* 1.3 67.3 + - - +
91A VAL 3.0 14.1 - - - -
111A TRP* 3.9 14.4 - - - -
112A PHE* 3.8 3.8 - - - -
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Residues in contact with VAL 75 (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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57A LEU* 4.0 11.7 - - + -
58A TRP 3.3 18.2 - - - +
59A ARG* 4.1 7.6 - - + +
60A PHE* 3.7 2.9 - - - -
74A GLY* 1.3 78.4 - - - +
76A VAL* 1.3 63.9 + - - +
90A THR* 3.4 2.4 - - - +
91A VAL 3.0 30.4 + - - +
112A PHE* 3.9 26.2 - - + +
115A VAL* 3.8 24.5 - - + +
116A GLU* 3.8 19.3 - - + +
119A LEU* 3.6 26.6 - - + +
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Residues in contact with VAL 76 (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 TRP* 4.4 8.3 - - + -
32A TRP* 6.1 0.7 - - + -
33A LEU* 4.7 7.6 - - + -
56A PRO 4.4 1.9 - - - +
57A LEU* 3.5 2.3 - - - -
58A TRP* 2.9 54.6 + - + +
60A PHE* 3.9 14.8 - - + -
75A VAL* 1.3 75.1 - - - +
77A MSE 1.3 62.5 + - - +
78A PRO* 4.5 0.7 - - - +
88A PRO* 3.5 26.0 - - + -
89A LEU 3.4 3.1 - - - +
90A THR* 3.1 24.0 - - - +
183A TRP* 4.6 9.4 - - + -
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Residues in contact with MSE 77 (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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57A LEU* 3.6 22.7 - - + -
76A VAL* 1.3 73.8 - - - +
78A PRO* 1.3 90.2 - - + +
79A SER* 3.9 12.7 - - - +
88A PRO* 3.2 6.3 - - - +
89A LEU* 2.8 48.5 + - + +
119A LEU* 3.5 43.5 - - + +
120A LEU* 4.0 17.0 - - - -
122A THR* 3.7 11.9 - - - +
123A LEU* 3.7 28.7 - - + -
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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