Contacts of the strand formed by residues 41 - 53 (chain C) in PDB entry 2WMZ
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 GLN 41 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A TYR 3.3 2.5 - - - -
294A GLN* 2.9 58.8 + - - +
297A MET* 5.6 4.1 - - - +
36C SER* 3.4 17.7 + - - +
37C PRO* 3.9 12.9 - - - +
39C LEU 3.4 11.2 - - - +
40C PRO* 1.3 70.9 - - - +
42C LEU* 1.3 59.3 + - - +
71C LEU* 3.1 6.6 - - - +
72C THR* 2.9 55.6 + - - +
1431C PGE 3.7 14.8 + - - +
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Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A PRO* 4.2 0.2 - - - +
292A ILE* 2.8 60.4 + - + -
293A TYR* 2.6 31.1 + - + +
40C PRO* 4.0 1.9 - - + -
41C GLN* 1.3 73.0 - - - +
43C GLY* 1.3 60.7 + - - +
69C LEU* 4.8 17.9 - - + +
70C GLN 3.4 15.0 - - - +
71C LEU* 3.5 29.2 - - + -
1431C PGE 3.8 6.4 + - - +
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Residues in contact with GLY 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A LEU 3.6 7.4 - - - -
292A ILE* 3.8 5.4 - - - -
42C LEU* 1.3 74.6 - - - +
44C LEU* 1.3 60.7 + - - -
69C LEU* 3.7 7.6 - - - +
70C GLN* 2.9 33.6 + - - +
1431C PGE 3.5 29.9 - - - -
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Residues in contact with LEU 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A PHE* 3.9 20.1 - - + +
289A SER* 3.4 4.5 - - - -
290A LEU* 2.8 57.0 + - + +
292A ILE* 3.7 13.7 - - + -
43C GLY* 1.3 74.1 - - - -
45C GLY* 1.3 65.3 + - - +
46C ALA* 5.8 1.1 - - + -
67C ALA* 5.2 4.5 - - + -
68C SER 3.2 20.6 - - - +
69C LEU* 3.5 18.2 - - + -
1431C PGE 3.9 5.8 - - - -
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Residues in contact with GLY 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A PHE* 3.4 8.5 - - - -
289A SER* 4.7 0.7 - - - -
43C GLY 4.3 0.2 + - - -
44C LEU* 1.3 79.1 - - - +
46C ALA* 1.3 62.9 + - - +
47C ASP* 5.2 1.1 - - - -
67C ALA* 3.0 22.7 - - - +
68C SER* 3.0 23.4 + - - +
70C GLN* 5.4 2.3 + - - -
1431C PGE 4.6 8.4 + - - -
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Residues in contact with ALA 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A LEU 4.1 0.3 - - - +
287A SER* 3.9 0.2 - - - -
288A PHE* 2.9 49.9 + - + +
44C LEU* 5.8 1.6 - - + -
45C GLY* 1.3 75.8 - - - +
47C ASP* 1.3 67.4 + - - +
66C SER 3.1 14.1 - - - +
67C ALA* 3.8 9.6 - - + +
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Residues in contact with ASP 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A LEU 3.3 6.7 - - - +
287A SER* 2.9 33.3 + - - -
288A PHE 5.0 0.2 - - - +
45C GLY 5.2 0.3 - - - -
46C ALA* 1.3 80.0 + - - +
48C TYR* 1.3 62.0 + - - +
49C THR* 4.6 9.2 - - - +
65C THR* 3.2 7.0 - - - -
66C SER* 3.0 44.5 + - - +
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Residues in contact with TYR 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A VAL* 5.1 3.6 - - + -
285A GLY* 2.9 31.0 - - - -
286A LEU* 3.0 24.6 + - + +
47C ASP* 1.3 76.1 - - - +
49C THR* 1.3 63.7 + - - +
50C TYR* 4.0 24.2 - - + +
63C ASN* 2.6 36.6 + - + -
64C ALA 3.5 4.3 - - - -
65C THR* 3.2 26.9 - - + -
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Residues in contact with THR 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A LYS* 4.4 19.5 - - + -
284A VAL 3.6 11.9 - - - +
285A GLY* 4.8 2.3 - - - -
47C ASP* 4.6 7.3 - - - +
48C TYR* 1.3 85.8 + - - +
50C TYR* 1.3 68.9 - - - +
51C SER* 3.7 11.2 + - - +
62C SER 3.7 1.2 - - - +
64C ALA* 2.8 41.2 + - - +
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Residues in contact with TYR 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A ASN* 4.7 3.4 - - + -
283A LYS* 3.3 21.8 - - - +
284A VAL* 3.0 32.2 + - + +
48C TYR* 4.0 16.8 - - + +
49C THR* 1.3 73.0 - - - +
51C SER* 1.3 73.7 + - - +
52C ASN* 3.4 28.1 - - + +
61C ASN* 3.5 21.7 + - + -
62C SER 3.4 4.7 - - - -
63C ASN* 3.3 26.7 - - - -
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Residues in contact with SER 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A GLN* 3.7 15.0 - - - -
282A ASN 3.5 4.7 - - - -
283A LYS* 4.1 18.7 + - - +
49C THR* 3.7 9.1 + - - +
50C TYR* 1.3 87.0 - - - +
52C ASN* 1.3 61.7 + - - +
53C GLY 4.3 0.2 - - - -
60C ILE 5.8 0.2 - - - -
61C ASN* 3.5 1.8 - - - -
62C SER* 2.8 48.4 + - - -
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Residues in contact with ASN 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A GLN* 3.4 4.7 - - - +
282A ASN* 2.8 55.2 + - + +
50C TYR* 3.4 24.7 + - + +
51C SER* 1.3 78.9 - - - +
53C GLY* 1.3 71.5 + - - +
54C TYR* 5.5 0.3 - - - +
59C GLY 5.6 0.6 - - - +
61C ASN* 2.9 24.9 + - - +
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Residues in contact with GLY 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A GLY 3.0 12.1 - - - -
281A GLN* 3.5 13.5 + - - -
52C ASN* 1.3 88.1 + - - +
54C TYR* 1.3 59.4 + - - +
57C ALA* 3.4 23.0 - - - +
58C ASN* 3.7 9.0 - - - -
59C GLY 4.2 2.1 + - - -
60C ILE 2.9 14.1 + - - -
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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