Contacts of the strand formed by residues 83 - 88 (chain B) in PDB entry 1QQG
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 83 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B PRO* 3.8 23.8 - - + -
74B LYS* 3.4 2.6 - - - -
75B ARG* 2.9 36.1 + - + +
76B ALA* 3.8 22.4 - - - +
77B ASP* 3.4 26.7 - - - +
80B ASN* 3.7 25.4 - - + +
82B HIS* 1.3 73.2 - - - +
84B VAL* 1.3 64.0 + - - +
85B ALA* 5.1 0.7 - - + +
94B ALA* 4.4 11.9 - - + -
95B ILE 3.5 13.0 - - - +
96B ALA* 4.2 4.3 - - + -
103B GLN* 2.9 17.8 + - - -
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE* 4.4 7.4 - - + -
73B ASN 3.4 8.5 - - - +
74B LYS* 4.5 0.9 - - + +
82B HIS 4.6 1.1 - - - +
83B LEU* 1.3 79.0 - - - +
85B ALA* 1.3 59.7 - - - +
86B LEU* 3.9 4.6 - - + +
94B ALA* 3.6 2.2 - - - -
95B ILE* 3.1 51.0 + - + +
97B ALA* 5.0 2.9 - - + -
103B GLN* 3.5 36.1 - - + +
106B TRP* 4.6 2.7 - - + -
107B TYR* 4.2 17.9 - - + +
110B LEU* 3.8 28.7 - - + -
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Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ASN 3.9 0.2 - - - +
72B ILE* 3.3 8.0 - - - +
73B ASN 2.8 36.5 + - - +
75B ARG* 4.4 13.9 - - + +
83B LEU 4.1 0.6 - - - -
84B VAL* 1.3 72.5 - - - +
86B LEU* 1.3 64.0 + - - +
87B TYR* 3.7 15.6 - - + +
92B HIS* 3.3 31.6 - - + +
93B PHE 3.6 3.6 - - - +
94B ALA* 4.3 4.7 - - + +
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 3.7 31.6 - - + -
64B ILE* 4.5 12.8 - - + -
66B LEU* 4.9 1.8 - - + -
69B CYS* 3.8 28.0 - - - -
71B ASN 3.6 4.3 - - - -
72B ILE* 4.6 11.9 - - + +
84B VAL* 3.9 11.9 - - + +
85B ALA* 1.3 78.6 - - - +
87B TYR* 1.3 62.1 + - - +
88B THR* 4.0 3.0 - - + +
91B GLU 3.9 0.9 - - - +
92B HIS* 3.5 5.5 - - - -
93B PHE* 2.8 54.9 + - + +
95B ILE* 5.3 2.5 - - + -
110B LEU* 4.2 24.9 - - + -
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Residues in contact with TYR 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B CYS* 3.3 1.8 - - - +
70B PHE* 2.7 53.7 + - + -
71B ASN* 2.8 38.6 + - + +
73B ASN* 4.3 6.3 - - + -
75B ARG* 3.9 13.9 + - - +
85B ALA* 3.7 22.9 - - + +
86B LEU* 1.3 75.4 - - - +
88B THR* 1.3 55.8 + - - +
91B GLU 3.7 2.7 - - - -
92B HIS* 3.4 33.1 + + + -
163B VAL* 3.2 40.9 + - + -
164B TRP* 4.3 2.8 - - - -
165B GLN* 4.0 15.4 + - + -
184B ARG* 3.7 18.6 - - + +
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Residues in contact with THR 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ILE* 4.3 11.4 - - + -
68B SER* 3.2 33.2 - - - +
69B CYS* 3.8 21.1 - - - -
70B PHE* 3.1 10.3 - - - -
86B LEU* 5.1 2.7 - - + +
87B TYR* 1.3 77.7 - - - +
89B ARG* 1.3 53.6 + - - +
90B ASP* 3.1 16.4 + - - +
91B GLU* 3.1 29.8 + - + +
93B PHE* 6.2 1.3 - - + -
184B ARG* 2.4 30.8 + - - -
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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