Contacts of the strand formed by residues 26 - 33 (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 VAL 26 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22J GLN* 4.0 0.2 - - - +
24J GLU 3.8 7.4 - - - +
25J LYS* 1.3 80.3 - - - +
27J GLN* 1.3 72.5 + - - +
45J ARG 3.7 0.2 - - - +
46J THR* 3.4 3.6 - - - -
47J LEU* 2.7 42.5 + - + +
49J SER 3.4 32.5 - - - +
50J GLU* 3.5 8.1 - - + +
51J PRO* 4.2 15.5 - - + -
93J PRO* 3.1 42.4 - - + +
94J ASN* 3.8 3.8 - - - -
95J LYS* 4.8 2.0 - - + -
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Residues in contact with GLN 27 (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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177F GLU* 4.9 2.2 + - - -
180F TYR* 3.3 57.0 - - + +
181F ARG* 4.1 13.6 + - - +
184F LEU* 4.4 12.1 - - + -
22J GLN* 4.5 2.9 + - - +
26J VAL* 1.3 75.1 - - - +
28J ALA* 1.3 59.8 + - - +
29J MET 4.2 0.2 - - - -
44J THR* 3.8 9.2 - - + -
45J ARG 3.5 4.5 - - - -
46J THR* 5.5 0.9 - - + -
90J ARG* 3.4 37.4 + - - +
94J ASN* 2.8 33.2 + - + +
95J LYS 2.9 25.8 + - - +
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Residues in contact with ALA 28 (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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26J VAL 3.9 0.6 + - - -
27J GLN* 1.3 72.4 - - - +
29J MET* 1.3 60.4 + - - +
30J TYR* 3.7 24.5 - - + -
43J LYS 3.7 1.0 - - - +
44J THR* 3.3 5.7 - - - -
45J ARG* 2.9 32.6 + - + +
47J LEU* 3.6 26.9 - - + -
57J LEU* 4.3 7.9 - - + -
95J LYS* 3.6 9.2 - - + -
97J VAL* 4.5 5.6 - - + -
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Residues in contact with MET 29 (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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173F ARG* 4.5 9.2 - - - +
177F GLU* 4.5 5.8 - - - +
706F CL 3.8 12.1 - - + -
27J GLN 4.2 0.4 - - - -
28J ALA* 1.3 71.1 - - - +
30J TYR* 1.3 63.1 + - - +
31J ILE* 3.9 4.1 + - + +
42J CYS* 3.7 24.5 - - + -
43J LYS 3.3 7.6 - - - +
44J THR* 3.6 6.9 - - - +
87J ASP* 4.6 1.8 - - - +
89J PHE* 6.0 2.5 - - - -
90J ARG* 3.6 39.0 - - - +
95J LYS 2.9 14.4 + - - +
96J LEU* 3.5 15.0 - - + -
97J VAL 2.9 26.2 + - - -
223J PHE* 3.6 30.5 - - - -
227J ARG* 5.5 7.2 - - - +
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Residues in contact with TYR 30 (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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28J ALA* 3.7 32.3 - - + -
29J MET* 1.3 74.1 - - - +
31J ILE* 1.3 59.8 + - - +
32J TRP* 3.4 4.8 - - + -
42J CYS* 3.0 26.5 - - - +
43J LYS 2.8 12.5 + - - +
45J ARG* 3.8 17.0 + - - -
47J LEU* 5.0 0.3 - - - +
57J LEU* 3.8 10.5 - - + +
58J PRO* 2.7 49.4 + - - +
60J TRP* 3.8 37.0 - + + -
79J LEU* 4.3 13.7 - - + -
81J PRO* 4.3 11.7 - - + -
97J VAL* 3.3 13.2 - - + -
99J CYS* 3.5 20.9 - - - -
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Residues in contact with ILE 31 (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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29J MET* 3.9 6.1 - - + +
30J TYR* 1.3 78.8 - - - +
32J TRP* 1.3 66.5 + - - +
40J LEU* 3.7 24.7 - - + -
41J ARG 3.3 4.9 - - - +
42J CYS* 4.1 4.0 - - + -
96J LEU* 3.9 33.9 - - + -
97J VAL 2.6 16.4 + - - +
98J LEU* 3.6 17.1 - - + +
99J CYS* 2.8 27.7 + - - +
219J TRP 5.7 0.4 - - - +
220J VAL* 4.8 7.2 - - + -
223J PHE* 3.7 51.1 - - + -
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Residues in contact with TRP 32 (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* 3.8 26.9 - - + -
30J TYR* 3.4 22.4 - - + -
31J ILE* 1.3 79.7 - - - +
33J ILE* 1.3 76.6 + - - +
40J LEU* 3.4 8.5 - - - -
41J ARG* 2.8 72.9 + - + +
42J CYS* 3.5 12.3 - - - -
43J LYS* 3.8 13.9 - - + -
62J PHE* 3.3 58.8 - + + -
67J THR* 4.1 4.6 - - + +
69J GLN* 4.5 2.2 - - - -
79J LEU* 3.7 35.0 - - + -
98J LEU* 4.9 2.0 - - - -
99J CYS 4.1 8.5 - - - +
101J VAL* 3.8 11.0 - - + -
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Residues in contact with ILE 33 (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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32J TRP* 1.3 77.0 - - - +
34J ASP* 1.3 71.8 + - - +
37J GLY* 3.7 29.6 - - - +
39J GLY 3.5 7.0 - - - +
40J LEU* 4.1 13.7 - - + -
69J GLN* 3.2 12.1 - - - +
98J LEU* 5.3 6.7 - - + -
99J CYS 4.9 3.8 + - - +
101J VAL* 3.6 16.2 - - + +
111J THR* 4.2 18.9 + - - +
219J TRP* 3.3 48.9 - - + +
347J ASP* 4.7 6.1 - - - +
349J PHE* 4.5 9.4 - - + -
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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