Contacts of the strand formed by residues 76 - 86 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317A ALA* 3.6 11.1 - - - +
319A ARG* 3.0 16.9 + - - +
324A ARG* 3.1 31.2 + - - -
326A PRO* 3.7 3.6 - - - +
327A ARG* 2.9 67.9 + - + +
328A THR 5.0 0.2 + - - -
61E ASN* 4.3 17.5 + - + +
62E PHE 3.5 8.3 - - - -
74E ASN 4.4 1.0 - - - +
75E SER* 1.3 75.8 - - - +
77E MET* 1.3 60.8 + - - +
104E TYR* 4.5 5.0 + - - +
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Residues in contact with MET 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E ASN* 3.0 8.0 - - - +
62E PHE* 2.9 54.0 + - + +
64E GLY* 3.8 9.0 - - - -
69E GLN* 3.4 48.9 - - + +
70E SER* 3.8 7.0 - - - +
75E SER 3.4 14.1 - - - +
76E ASP* 1.3 74.8 - - - +
78E TYR* 1.3 65.0 + - - +
101E VAL* 4.1 11.4 - - + -
102E PHE 3.7 6.5 - - - +
103E LYS* 3.6 41.5 - - + +
104E TYR 5.2 1.1 - - - +
109E ALA* 4.4 5.4 - - + -
110E GLU* 5.5 0.7 - - - +
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Residues in contact with TYR 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A ARG* 3.5 32.4 - - + +
328A THR* 5.4 8.9 - - - -
331A GLN* 4.1 19.6 - - + +
59E GLU* 3.8 16.6 - - + -
60E TRP 3.5 9.0 - - - -
61E ASN* 4.3 3.6 - - + -
77E MET* 1.3 74.7 - - - +
79E LEU* 1.3 64.7 + - - +
80E VAL* 4.1 3.4 - - + -
101E VAL* 3.4 10.6 - - - +
102E PHE* 3.0 46.2 + - + +
103E LYS 3.5 25.6 - - - -
104E TYR 4.1 3.7 + - - -
106E ARG* 3.5 47.0 + - + +
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Residues in contact with LEU 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E TYR* 4.3 19.7 - - + -
32E TRP* 3.6 60.1 - - + -
43E LYS* 4.7 3.8 - - - -
59E GLU* 3.5 5.9 - - - +
60E TRP* 2.7 40.3 + - + +
61E ASN* 4.1 18.6 - - - +
62E PHE* 3.6 25.6 - - + -
78E TYR* 1.3 73.2 - - - +
80E VAL* 1.3 62.5 + - - +
81E PRO* 3.9 2.3 - - - +
99E CYS* 4.1 17.3 - - + -
100E GLU 3.4 1.6 - - - -
101E VAL* 4.3 4.3 - - + -
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Residues in contact with VAL 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E GLU* 3.9 27.6 - - + +
78E TYR* 4.8 5.4 - - + -
79E LEU* 1.3 77.2 - - - +
81E PRO* 1.3 81.5 - - + +
82E ALA* 4.2 0.3 - - - -
99E CYS* 4.0 2.9 - - - -
100E GLU* 2.9 31.1 + - + +
102E PHE* 3.8 34.5 - - + -
106E ARG* 5.3 5.2 - - - +
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Residues in contact with PRO 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E TYR* 4.2 11.4 - - + -
54E VAL* 3.6 28.0 - - + +
57E LEU* 3.7 18.6 - - + +
58E PRO 3.4 27.4 - - - +
59E GLU* 4.1 6.7 - - + +
79E LEU 3.9 6.3 - - - +
80E VAL* 1.3 98.6 - - + +
82E ALA* 1.3 58.6 + - - +
97E VAL* 3.8 8.3 - - + -
99E CYS* 4.0 10.5 - - - -
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Residues in contact with ALA 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E VAL* 3.8 18.0 - - - +
80E VAL 4.3 4.7 - - - +
81E PRO* 1.3 74.8 - - - +
83E ALA* 1.3 62.7 + - + +
98E LEU* 2.9 20.4 + - + +
99E CYS* 4.3 3.6 - - - -
100E GLU* 4.4 5.4 - - + +
114E ARG* 3.7 46.2 + - - +
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Residues in contact with ALA 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E VAL* 4.2 6.1 - - - -
82E ALA* 1.3 80.7 - - - +
84E MET* 1.3 60.3 + - - +
85E PHE* 3.8 23.9 - - + -
96E LEU 3.9 0.3 - - - +
97E VAL* 3.4 2.8 - - - -
98E LEU* 2.8 37.3 + - + +
216E ASP* 3.8 28.5 - - + +
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Residues in contact with MET 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E PRO* 3.9 24.5 - - - +
52E LYS 4.2 3.4 - - - +
53E CYS* 3.7 32.1 - - - +
54E VAL* 3.9 17.8 - - + +
57E LEU* 3.6 25.6 - - + -
83E ALA* 1.3 72.0 - - - +
85E PHE* 1.3 78.5 + - - +
95E LYS* 3.9 31.0 - - + +
96E LEU 3.4 10.3 - - - +
97E VAL* 4.5 1.1 - - - +
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Residues in contact with PHE 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E ALA* 3.8 28.0 - - + -
84E MET* 1.3 82.0 - - - +
86E ARG* 1.3 64.3 - - - +
95E LYS* 3.3 11.4 - - - +
96E LEU* 2.8 42.2 + - + +
186E ALA* 3.4 22.9 - - + +
187E GLY* 3.7 21.8 - - - -
188E VAL* 4.1 11.7 - - + -
216E ASP 4.6 1.1 - - - -
217E HIS* 3.8 35.0 - + - -
220E VAL* 3.5 39.7 - - + -
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Residues in contact with ARG 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D PRO* 5.0 4.6 + - - +
22D GLN 6.2 0.8 - - - -
85E PHE* 1.3 75.8 - - - +
87E ASP* 1.3 58.6 + - - +
88E PRO* 3.3 3.3 - - - +
92E ASP* 2.8 40.0 + - - +
94E ASN 3.9 4.9 - - - -
95E LYS* 4.6 11.2 - - - +
96E LEU* 4.2 2.0 - - - +
184E LEU 5.0 1.0 + - - -
185E TYR* 2.9 77.2 + - + +
186E ALA* 3.2 32.8 + - - +
187E GLY* 5.8 0.7 - - - -
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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