Contacts of the strand formed by residues 41 - 53 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B SER* 3.5 18.0 + - - +
37B PRO* 4.0 12.1 - - + +
39B LEU 3.5 10.2 - - - +
40B PRO* 1.3 73.6 - - - +
42B LEU* 1.3 58.9 + - - +
70B GLN 3.8 1.2 - - - +
71B LEU* 3.1 6.2 - - - +
72B THR* 2.8 54.8 + - - +
1431B PGE 3.9 13.6 + - - +
293C TYR 3.5 0.4 - - - -
294C GLN* 3.0 57.4 + - - +
297C MET* 5.7 3.5 - - - +
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Residues in contact with LEU 42 (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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40B PRO* 3.9 2.1 - - + -
41B GLN* 1.3 73.4 - - - +
43B GLY* 1.3 59.9 + - - +
69B LEU* 4.8 17.7 - - + -
70B GLN 3.4 15.0 - - - +
71B LEU* 3.5 29.6 - - + -
1431B PGE 3.7 6.5 + - - +
292C ILE* 2.9 55.7 + - + -
293C TYR* 2.7 33.7 + - + +
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Residues in contact with GLY 43 (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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42B LEU* 1.3 75.8 - - - +
44B LEU* 1.3 60.8 + - - -
69B LEU* 3.7 7.1 - - - +
70B GLN* 2.9 35.4 + - - +
1431B PGE 3.2 30.8 - - - -
290C LEU 3.7 5.6 - - - -
292C ILE* 3.8 5.6 - - - -
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Residues in contact with LEU 44 (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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43B GLY* 1.3 73.6 - - - -
45B GLY* 1.3 68.1 + - - +
46B ALA* 5.8 1.6 - - + -
67B ALA* 5.2 4.3 - - + -
68B SER 3.3 20.4 - - - +
69B LEU* 3.5 16.4 - - + -
1431B PGE 5.0 4.3 + - - -
288C PHE* 4.0 11.6 - - + +
289C SER* 3.6 5.6 + - - -
290C LEU* 2.9 57.8 + - + +
292C ILE* 3.6 17.7 - - + -
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Residues in contact with GLY 45 (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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43B GLY 4.3 0.4 + - - -
44B LEU* 1.3 80.3 - - - +
46B ALA* 1.3 62.0 + - - +
47B ASP* 5.2 1.1 - - - -
67B ALA* 3.0 22.9 - - - +
68B SER* 3.0 23.0 + - - +
70B GLN* 5.4 4.5 + - - -
1431B PGE 5.8 1.1 - - - -
288C PHE* 3.5 8.1 - - - -
289C SER* 4.8 1.8 - - - -
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Residues in contact with ALA 46 (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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44B LEU* 5.8 1.3 - - + -
45B GLY* 1.3 77.0 - - - +
47B ASP* 1.3 67.3 + - - +
66B SER 3.2 14.4 - - - +
67B ALA* 3.8 9.2 - - + +
286C LEU 4.2 0.2 - - - +
287C SER 3.9 0.2 - - - -
288C PHE* 2.9 49.9 + - + +
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Residues in contact with ASP 47 (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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45B GLY* 5.2 0.9 - - - -
46B ALA* 1.3 81.1 + - - +
48B TYR* 1.3 61.1 + - - +
49B THR* 4.6 9.2 - - - +
65B THR* 3.2 7.0 - - - -
66B SER* 3.0 44.7 + - - +
286C LEU 3.4 6.5 - - - +
287C SER* 2.9 34.1 + - - -
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Residues in contact with TYR 48 (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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47B ASP* 1.3 77.4 - - - +
49B THR* 1.3 63.2 + - - +
50B TYR* 3.9 24.2 - - + +
63B ASN* 2.7 36.3 + - + -
64B ALA 3.5 4.5 - - - -
65B THR* 3.3 26.9 - - + -
284C VAL* 5.3 3.4 - - + -
285C GLY* 3.0 29.0 - - - -
286C LEU* 3.1 24.0 + - + +
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Residues in contact with THR 49 (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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47B ASP* 4.6 7.4 - - - +
48B TYR* 1.3 84.9 + - - +
50B TYR* 1.3 69.9 + - - +
51B SER* 3.7 13.2 + - - +
62B SER 3.7 1.2 - - - +
63B ASN* 3.8 0.4 - - - -
64B ALA* 2.8 41.5 + - - +
283C LYS* 4.6 16.4 - - + -
284C VAL 3.7 11.4 - - - +
285C GLY* 4.8 2.6 - - - -
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Residues in contact with TYR 50 (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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48B TYR* 3.9 19.0 - - + +
49B THR* 1.3 73.0 - - - +
51B SER* 1.3 74.9 - - - +
52B ASN* 3.4 28.2 - - + +
61B ASN* 3.6 21.3 + - + -
62B SER 3.4 4.9 - - - -
63B ASN* 3.3 27.8 - - - +
262B SER* 5.9 0.4 - - - -
282C ASN* 4.9 2.0 - - + -
283C LYS* 3.5 21.5 - - - -
284C VAL* 3.2 29.9 + - + +
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Residues in contact with SER 51 (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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49B THR* 3.7 9.3 + - - +
50B TYR* 1.3 88.4 - - - +
52B ASN* 1.3 60.8 + - - +
53B GLY 4.3 0.4 - - - -
60B ILE 5.8 0.4 - - - -
61B ASN* 3.5 1.7 - - - -
62B SER* 2.8 45.9 + - - -
281C GLN* 3.8 13.5 - - - -
282C ASN 3.6 4.7 - - - -
283C LYS* 4.3 17.9 + - - +
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Residues in contact with ASN 52 (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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50B TYR* 3.4 24.6 + - + +
51B SER* 1.3 77.5 - - - +
53B GLY* 1.3 72.2 + - - +
54B TYR* 3.7 0.3 + - - +
59B GLY 5.6 0.6 - - - +
60B ILE 4.0 0.2 - - - -
61B ASN* 2.9 25.0 + - - +
281C GLN* 3.5 4.3 - - - +
282C ASN* 3.0 52.0 + - + +
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Residues in contact with GLY 53 (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 SER* 5.4 0.2 - - - -
52B ASN* 1.3 87.7 + - - +
54B TYR* 1.3 59.5 + - - +
57B ALA* 3.4 22.2 - - - +
58B ASN* 3.7 8.5 - - - -
59B GLY 4.2 3.1 + - - -
60B ILE 2.8 14.7 + - - -
280C GLY 3.2 13.0 - - - -
281C GLN* 3.5 13.1 + - - -
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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