Contacts of the strand formed by residues 64 - 71 (chain B) in PDB entry 2QU7
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 SER 64 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A GLN* 3.2 40.1 + - - +
63B ARG* 1.3 72.7 - - - +
65B ASN* 1.3 54.2 + - - +
66B ILE* 3.1 33.7 + - - +
118B GLN 3.9 3.1 + - - -
119B ASN* 3.1 15.5 + - - +
120B VAL* 4.0 5.9 - - - +
121B SER* 2.6 36.8 + - - -
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Residues in contact with ASN 65 (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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114A THR* 3.1 32.6 + - - +
118A GLN* 5.5 0.7 - - - +
63B ARG 3.8 2.1 + - - +
64B SER* 1.3 70.3 + - - +
66B ILE* 1.3 57.6 + - - +
93B HIS* 3.4 25.4 + - - +
94B LEU* 3.5 12.3 - - + +
95B HIS* 2.9 43.6 + - - +
121B SER* 3.9 5.4 - - - -
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Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A THR* 3.6 24.9 - - + -
115A PHE* 3.8 28.0 - - + -
118A GLN* 4.1 13.7 - - + -
64B SER* 3.1 18.8 - - - +
65B ASN* 1.3 78.6 - - - +
67B ILE* 1.3 77.8 + - - +
68B ALA* 4.0 4.7 - - + +
95B HIS* 3.3 8.7 - - + +
97B ALA* 4.0 18.2 - - + -
115B PHE* 5.4 3.6 - - + -
118B GLN* 4.8 12.3 - - - +
120B VAL* 3.3 15.8 - - + +
121B SER* 3.0 25.2 + - - -
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Residues in contact with ILE 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ILE* 1.3 76.7 - - - +
68B ALA* 1.3 64.7 + - - +
85B ILE* 5.7 0.2 - - + -
89B CYS* 3.7 31.2 - - + -
94B LEU* 3.8 27.8 - - + -
95B HIS 2.7 14.0 + - - +
96B VAL* 3.3 15.1 - - + +
97B ALA 2.9 24.6 + - - +
121B SER* 4.5 2.2 - - - -
122B ALA* 3.5 25.8 - - + +
124B ILE* 4.0 32.1 - - + -
309B ILE* 4.0 13.9 - - + -
313B ILE* 4.2 7.9 - - + -
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Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ILE* 4.0 3.8 - - + -
67B ILE* 1.3 71.9 - - - +
69B PHE* 1.3 54.1 + - - +
70B ILE* 3.9 1.7 + - + -
97B ALA 3.5 4.9 - - - -
115B PHE* 3.5 55.0 - - + -
120B VAL* 4.6 4.2 - - + +
122B ALA 3.0 11.6 + - - +
123B ILE* 3.3 7.2 - - + +
124B ILE* 2.8 32.2 + - - +
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Residues in contact with PHE 69 (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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67B ILE 3.7 0.2 + - - -
68B ALA* 1.3 71.4 - - - +
70B ILE* 1.3 59.7 + - - +
71B VAL* 3.8 20.0 - - + -
78B PHE* 3.4 31.0 - + + -
81B VAL* 4.7 1.3 - - + -
82B LEU* 3.7 21.1 - - + -
85B ILE* 4.7 11.4 - - + -
96B VAL* 3.8 14.6 - - + -
97B ALA 2.8 13.9 + - - +
98B VAL* 3.2 25.9 - - + +
99B ALA* 3.1 23.9 + - - +
115B PHE* 5.9 0.2 - - - -
124B ILE* 3.4 35.9 - - + -
126B VAL* 4.0 20.0 - - + -
146B LEU* 4.3 19.1 - - + -
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Residues in contact with ILE 70 (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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68B ALA 4.8 1.1 - - - +
69B PHE* 1.3 72.3 - - - +
71B VAL* 1.3 67.7 + - - +
99B ALA* 3.4 9.9 - - + +
101B SER* 4.7 3.6 - - - +
108B GLN* 4.6 11.4 - - + +
111B LEU* 4.0 18.6 - - + -
112B ILE* 3.7 32.8 - - + +
115B PHE* 3.9 33.9 - - + -
123B ILE* 3.8 21.5 - - + -
124B ILE 2.8 10.5 + - - +
125B LEU* 3.7 20.2 - - + -
126B VAL* 2.9 32.9 + - - +
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Residues in contact with VAL 71 (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 PHE* 3.8 22.0 - - + -
70B ILE* 1.3 77.2 - - - +
72B PRO* 1.4 61.2 - - + +
73B ASP 3.7 18.2 - - - +
78B PHE* 3.8 26.2 - - + -
98B VAL* 3.7 29.8 - - + -
99B ALA 2.9 12.3 + - - +
100B SER* 3.3 13.9 - - - -
101B SER* 2.8 35.8 + - - -
126B VAL* 4.3 2.5 - - + -
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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