Contacts of the helix formed by residues 75 - 81 (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 ASP 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A THR* 3.5 11.7 - - - +
73A PHE 3.0 5.8 + - - +
74A ALA* 1.3 67.1 - - - +
76A LEU* 1.3 74.1 + - - +
78A ALA* 3.1 14.7 + - - +
79A TYR* 3.1 8.5 + - - +
90A LEU* 3.8 22.8 - - + +
91A GLU* 3.4 14.4 - - - +
94A VAL* 3.7 21.5 - - + -
119A LYS* 3.7 7.8 - - - -
120A GLY* 3.1 8.5 + - - -
121A THR* 2.4 52.9 + - - +
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Residues in contact with LEU 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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75A ASP* 1.3 82.8 + - - +
77A HIS* 1.4 58.2 + - - +
79A TYR* 2.7 35.3 + - + +
80A LEU* 2.9 33.2 + - + +
87A TRP* 5.3 8.7 - - + -
90A LEU* 5.2 1.6 - - - -
121A THR* 4.3 14.3 - - + +
124A GLN* 3.4 31.6 + - + +
125A LEU* 4.6 20.2 - - + -
169A LEU* 3.7 27.8 - - + -
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Residues in contact with HIS 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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43A ALA* 4.5 3.8 - - + -
74A ALA* 3.6 17.5 + - + +
75A ASP 3.2 1.2 - - - -
76A LEU* 1.4 77.4 - - - +
78A ALA* 1.3 62.3 + - - +
80A LEU* 3.3 8.2 + - + +
81A ASP* 3.0 27.7 + - - +
124A GLN* 3.5 18.8 + - - -
166A TYR* 3.1 66.2 + + + -
169A LEU* 3.4 18.2 - - + +
170A GLN* 3.2 8.4 + - - -
173A ASP* 3.4 25.1 - - - -
506A TYR* 3.6 18.2 - + + -
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Residues in contact with ALA 78 (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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43A ALA* 4.0 7.9 - - + +
44A THR* 3.5 34.3 - - - +
45A THR* 4.6 7.0 - - - +
74A ALA 3.2 13.7 + - - +
75A ASP 3.1 11.6 + - - +
77A HIS* 1.3 75.5 - - - +
79A TYR* 1.3 60.8 + - - +
81A ASP* 3.6 7.4 + - - +
84A LYS* 3.3 25.9 + - - +
85A ALA* 3.4 13.6 + - + -
90A LEU* 4.1 0.2 - - + -
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Residues in contact with TYR 79 (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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75A ASP 3.1 8.3 + - - +
76A LEU* 2.7 22.8 + - + +
78A ALA* 1.3 74.9 - - - +
80A LEU* 1.3 79.1 + - + +
81A ASP 3.1 2.2 - - - -
83A MET* 3.1 60.4 + - + +
85A ALA 3.3 21.7 + - - +
86A PRO* 4.3 11.0 - - + -
87A TRP* 4.4 17.4 - + + +
90A LEU* 4.1 14.1 - - + -
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Residues in contact with LEU 80 (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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76A LEU* 2.9 30.9 + - + +
77A HIS* 3.3 13.0 + - + +
79A TYR* 1.3 91.6 - - + +
81A ASP* 1.3 57.5 + - - +
82A ASN 3.1 4.7 + - - -
162A SER* 3.1 58.0 + - - +
163A GLY* 4.0 4.5 + - - -
165A LEU* 4.6 16.6 - - + -
166A TYR* 4.6 13.9 - - + -
169A LEU* 4.1 26.0 - - + -
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Residues in contact with ASP 81 (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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77A HIS 3.0 16.9 + - - +
78A ALA* 3.6 4.2 + - - +
79A TYR 3.1 1.8 - - - -
80A LEU* 1.3 74.9 - - - +
82A ASN* 1.3 68.7 + - - +
83A MET 2.9 2.0 + - - -
84A LYS* 3.0 45.2 + - + +
152A VAL 3.9 11.8 - - - +
153A VAL* 3.5 11.5 - - - +
154A LYS* 3.0 28.6 + - - +
163A GLY* 6.0 0.4 - - - -
166A TYR* 3.9 19.1 + - + -
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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