Contacts of the strand formed by residues 76 - 86 (chain B) in PDB entry 2QC8
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 76 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B ASN* 4.4 16.8 + - + -
62B PHE 3.5 8.5 - - - +
74B ASN 4.4 0.7 - - - +
75B SER* 1.3 75.5 - - - +
77B MET* 1.3 62.8 + - - +
104B TYR* 4.5 4.5 + - - +
317C ALA* 3.5 14.2 - - - -
319C ARG* 3.0 7.7 + - - +
324C ARG* 2.9 40.5 + - - -
326C PRO* 3.7 2.1 - - - +
327C ARG* 2.9 62.5 + - + +
328C THR 4.9 0.5 + - - -
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Residues in contact with MET 77 (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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61B ASN* 2.9 26.7 - - - +
62B PHE* 3.0 34.6 + - + +
64B GLY* 3.7 11.9 - - - -
69B GLN* 3.4 45.5 - - + +
70B SER* 3.7 7.0 - - - +
75B SER 3.5 11.0 - - - +
76B ASP* 1.3 79.3 - - - +
78B TYR* 1.3 65.8 + - - +
101B VAL* 4.0 12.8 - - + -
102B PHE 3.5 7.6 - - - +
103B LYS* 3.7 39.3 - - + +
104B TYR 5.1 1.3 - - - +
109B ALA* 4.3 4.9 - - + -
110B GLU* 5.5 0.7 - - - +
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Residues in contact with TYR 78 (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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59B GLU* 3.9 17.5 - - - -
60B TRP 3.5 8.1 - - - +
61B ASN* 4.3 2.9 - - + +
62B PHE* 4.8 0.2 - - - -
77B MET* 1.3 74.1 - - - +
79B LEU* 1.3 65.3 + - - +
80B VAL* 4.8 4.0 - - + -
100B GLU 3.5 0.6 - - - +
101B VAL* 3.4 10.6 - - - +
102B PHE* 2.9 47.8 + - + +
103B LYS 3.4 26.5 - - - -
104B TYR 4.0 2.8 + - - -
106B ARG* 3.6 47.0 + - + +
327C ARG* 3.3 37.7 - - + +
328C THR* 5.3 10.1 - - - -
331C GLN* 4.1 15.9 - - + +
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Residues in contact with LEU 79 (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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30B TYR* 4.3 12.3 - - + -
32B TRP* 3.6 60.3 - - + -
43B LYS* 4.6 0.4 - - - -
59B GLU* 3.4 9.0 - - - +
60B TRP* 2.8 50.5 + - + +
61B ASN 4.0 22.4 - - - +
62B PHE* 3.7 20.9 - - + -
78B TYR* 1.3 74.3 - - - +
80B VAL* 1.3 62.2 + - - +
81B PRO* 4.0 1.4 - - - +
99B CYS* 4.0 17.9 - - + -
100B GLU 3.6 1.6 - - - -
101B VAL* 4.3 3.6 - - + -
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Residues in contact with VAL 80 (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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59B GLU* 4.0 24.7 - - + +
78B TYR* 4.8 5.4 - - + -
79B LEU* 1.3 76.5 - - - +
81B PRO* 1.3 80.5 - - + +
82B ALA* 4.2 0.3 - - - +
99B CYS* 3.4 3.1 - - - +
100B GLU* 3.0 30.0 + - + +
102B PHE* 3.7 35.2 - - + -
106B ARG* 5.6 4.3 - - - +
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Residues in contact with PRO 81 (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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30B TYR* 4.2 10.3 - - + -
54B VAL* 3.8 19.1 - - + +
57B LEU* 3.7 29.4 - - + +
58B PRO 3.7 18.4 - - - +
59B GLU* 4.2 7.2 - - + +
79B LEU 4.0 5.2 - - - +
80B VAL* 1.3 97.2 - - + +
82B ALA* 1.3 59.3 + - - +
97B VAL* 3.7 15.3 - - + -
99B CYS* 3.9 10.5 - - - -
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Residues in contact with ALA 82 (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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54B VAL* 3.7 15.8 - - - +
80B VAL 4.2 4.9 - - - +
81B PRO* 1.3 75.0 - - - +
83B ALA* 1.3 61.4 + - + +
98B LEU* 2.9 21.1 + - + +
99B CYS 4.5 0.4 - - - -
100B GLU* 4.3 7.9 - - + +
114B ARG* 3.7 46.7 + - - +
216B ASP* 5.1 0.4 - - - +
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Residues in contact with ALA 83 (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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54B VAL* 4.1 6.1 - - - -
82B ALA* 1.3 80.3 - - - +
84B MET* 1.3 61.1 + - - +
85B PHE* 3.7 23.4 - - + -
96B LEU 3.9 0.5 - - - +
97B VAL* 3.4 3.3 - - - -
98B LEU* 2.8 38.0 + - + +
216B ASP* 3.8 28.7 - - + +
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Residues in contact with MET 84 (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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51B PRO* 4.0 18.8 - - - +
52B LYS 4.1 2.9 - - - +
53B CYS* 3.6 35.4 - - - +
54B VAL* 4.1 18.4 - - + +
57B LEU* 3.7 24.2 - - + -
83B ALA* 1.3 73.3 - - - +
85B PHE* 1.3 82.5 + - - +
95B LYS* 4.0 30.3 - - + +
96B LEU 3.4 10.1 - - - +
97B VAL* 4.5 1.1 - - - +
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Residues in contact with PHE 85 (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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83B ALA* 3.7 27.8 - - + -
84B MET* 1.3 83.9 - - - +
86B ARG* 1.3 67.7 + - - +
95B LYS* 3.4 11.4 - - - +
96B LEU* 2.8 37.9 + - + +
186B ALA* 3.5 19.5 - - + +
187B GLY* 3.8 23.3 - - - -
188B VAL* 4.0 11.4 - - + -
216B ASP 4.5 0.9 - - - -
217B HIS* 3.8 38.4 - + - -
220B VAL* 3.5 42.2 - - + -
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Residues in contact with ARG 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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21A PRO* 4.9 5.5 + - - +
22A GLN 6.0 1.4 + - - -
85B PHE* 1.3 76.2 - - - +
87B ASP* 1.3 59.3 + - - +
88B PRO* 3.2 7.8 - - - +
92B ASP* 2.6 42.3 + - - +
94B ASN 4.1 4.0 - - - -
95B LYS* 4.7 11.9 - - - +
96B LEU* 4.2 2.4 - - - +
184B LEU 5.0 0.6 + - - -
185B TYR* 2.9 73.6 + - + +
186B ALA* 3.0 33.2 + - - +
187B GLY* 5.7 1.1 - - - -
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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