Contacts of the strand formed by residues 40 - 47 (chain J) 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 LEU 40 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163F CYS 4.0 2.3 - - - +
164F GLY* 4.6 0.3 - - - -
165F VAL* 3.8 31.4 + - + +
169F ARG* 6.1 0.2 - - - -
31J ILE* 3.7 21.3 - - + -
32J TRP* 3.4 17.9 - - - +
33J ILE* 4.1 6.7 - - + -
38J GLU 3.9 2.0 + - - +
39J GLY* 1.3 72.6 - - - -
41J ARG* 1.3 72.4 + - - +
98J LEU* 5.0 4.0 - - + -
219J TRP* 3.9 39.3 - - + +
222J ARG* 4.2 6.5 - - + -
223J PHE* 3.7 37.7 - - + +
226J HIS* 4.3 11.8 - - + +
238J PHE* 6.2 0.2 - - + -
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Residues in contact with ARG 41 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159F GLY 3.0 29.1 + - - -
160F PRO* 3.4 20.4 + - - +
162F TYR 2.9 35.5 + - - +
163F CYS* 3.1 11.2 - - + +
164F GLY* 4.7 2.2 - - - -
31J ILE* 3.3 3.3 - - - +
32J TRP* 2.8 64.5 + - + +
34J ASP* 3.0 40.5 + - + +
36J THR* 5.4 4.2 - - - +
40J LEU* 1.3 82.5 + - - +
42J CYS* 1.3 65.2 + - - +
66J SER 3.7 6.1 + - - -
67J THR* 3.8 27.5 + - + +
68J LEU* 5.6 1.2 - - - +
223J PHE* 5.0 1.8 - - - -
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Residues in contact with CYS 42 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163F CYS* 3.0 30.6 + - - +
164F GLY 4.5 10.5 - - - -
165F VAL* 5.0 1.1 - - - -
173F ARG* 4.7 9.0 - - - -
194F ASN* 5.0 1.6 - - - +
195F ALA 5.3 0.5 + - - -
29J MET* 3.7 35.7 - - + -
30J TYR 3.0 16.2 - - - +
31J ILE* 4.1 1.8 - - + -
32J TRP* 3.5 6.1 - - - -
41J ARG* 1.3 76.0 - - - +
43J LYS* 1.3 61.2 + - - +
223J PHE* 3.8 23.1 - - + -
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Residues in contact with LYS 43 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162F TYR* 4.7 4.7 + - - +
163F CYS* 3.9 9.9 - - - -
193F THR 3.6 9.9 - - - +
194F ASN* 3.7 19.9 + - + +
205F GLN* 6.1 0.9 - - - +
501F ADP 4.7 18.4 + - - -
706F CL 3.7 10.8 - - - -
28J ALA 3.7 0.7 - - - +
29J MET* 3.3 2.3 - - - -
30J TYR* 2.8 29.0 + - - -
32J TRP* 3.9 12.8 - - + -
42J CYS* 1.3 76.9 - - - +
44J THR* 1.3 62.1 + - - +
60J TRP* 3.6 42.8 - - + +
61J ASN* 2.7 32.0 + - - +
62J PHE* 3.9 15.2 - - - +
79J LEU* 4.6 1.6 - - - -
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Residues in contact with THR 44 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180F TYR* 3.7 15.7 - - + -
192F GLY* 3.0 3.4 - - - -
193F THR* 3.0 43.8 + - - +
205F GLN* 4.3 0.3 - - - +
706F CL 2.9 15.9 - - - +
27J GLN* 3.8 10.5 - - + -
28J ALA 3.3 11.2 - - - +
29J MET* 3.6 3.6 - - - +
43J LYS* 1.3 72.5 - - - +
45J ARG* 1.3 72.9 + - - +
60J TRP* 3.5 10.9 - - - -
90J ARG* 2.9 34.9 + - - +
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Residues in contact with ARG 45 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180F TYR* 3.5 6.7 - - - -
191F ALA 3.3 11.0 - - - +
26J VAL 3.7 0.2 - - - +
27J GLN* 3.5 3.8 - - - -
28J ALA* 2.9 36.0 + - + +
30J TYR* 3.8 16.9 + - + -
44J THR* 1.3 74.9 - - - +
46J THR* 1.3 63.0 + - - +
47J LEU* 4.0 20.9 + - + +
58J PRO* 3.5 23.7 - - - +
59J GLU 3.2 25.7 + - - -
60J TRP* 3.4 51.3 - - + +
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Residues in contact with THR 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180F TYR* 2.6 24.4 + - + -
184F LEU* 4.5 9.4 - - + -
190F ILE 2.7 28.1 + - - +
191F ALA* 2.9 12.8 + - - +
25J LYS* 3.5 37.9 - - + -
26J VAL 3.4 8.1 - - - +
27J GLN* 4.7 0.4 - - + +
45J ARG* 1.3 77.7 + - - +
47J LEU* 1.3 69.9 + - - +
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Residues in contact with LEU 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25J LYS* 3.5 7.6 - - - +
26J VAL* 2.7 37.7 + - + +
28J ALA* 3.6 28.3 - - + -
30J TYR* 5.0 0.2 - - - +
45J ARG* 4.1 20.6 - - + +
46J THR* 1.3 82.1 - - - +
48J ASP* 1.3 64.1 + - - +
49J SER 3.3 11.4 - - - +
51J PRO* 4.2 16.8 - - + -
57J LEU* 3.7 19.3 - - + -
58J PRO* 4.1 24.7 - - + -
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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