Contacts of the strand formed by residues 61 - 76 (chain A) 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 ASN 61 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A TYR* 3.5 19.2 + - + +
51A SER* 3.5 10.3 - - - +
52A ASN* 2.9 28.8 + - - +
53A GLY 4.4 0.2 + - - -
59A GLY* 4.2 5.2 - - - +
60A ILE* 1.3 102.6 + - - +
62A SER* 1.3 66.2 + - - +
261A TYR* 3.4 9.9 - - - +
262A SER* 3.0 46.0 + - - +
263A GLY* 5.0 3.6 - - - -
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Residues in contact with SER 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A THR 4.3 0.6 + - - -
50A TYR* 3.4 2.4 - - - -
51A SER* 2.9 57.3 + - - +
61A ASN* 1.3 77.9 - - - +
63A ASN* 1.3 72.5 + - - +
64A ALA* 4.1 1.6 - - - -
259A THR* 4.6 8.1 - - - -
260A SER 3.4 7.9 - - - -
261A TYR* 3.7 25.7 - - - +
262A SER* 5.2 0.4 - - - -
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Residues in contact with ASN 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A TYR* 2.7 32.9 + - + +
49A THR 3.7 4.5 - - - -
50A TYR* 3.3 20.7 - - - -
62A SER* 1.3 91.4 - - - +
64A ALA* 1.3 60.7 + - - +
65A THR* 5.1 2.3 - - + +
258A ASP 3.6 2.3 - - - +
259A THR* 3.5 2.1 - - - -
260A SER* 2.9 43.2 + - - +
262A SER* 5.1 5.0 + - - -
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Residues in contact with ALA 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A TYR* 4.2 0.3 - - - -
49A THR* 2.8 41.4 + - - +
62A SER* 4.1 1.1 - - - -
63A ASN* 1.3 73.4 - - - +
65A THR* 1.3 70.8 + - - +
257A SER* 6.5 0.4 - - - -
258A ASP 3.3 5.8 - - - +
259A THR* 3.5 25.6 - - + +
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Residues in contact with THR 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ASP 3.2 11.2 - - - -
48A TYR* 3.2 33.7 - - + -
63A ASN* 5.1 1.8 - - + -
64A ALA* 1.3 84.8 - - - +
66A SER* 1.3 62.7 - - - +
256A ILE* 5.5 1.2 - - - +
257A SER* 3.3 2.5 - - - -
258A ASP* 2.9 42.7 + - - +
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Residues in contact with SER 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ALA* 3.2 3.0 - - - +
47A ASP* 3.0 48.4 + - - +
65A THR* 1.3 74.6 - - - +
67A ALA* 1.3 67.8 + - - +
68A SER* 5.3 0.9 - - - -
256A ILE* 3.4 13.7 - - - -
257A SER* 4.2 9.6 - - - -
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Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 5.3 4.9 - - + -
45A GLY 3.0 17.7 - - - +
46A ALA* 3.8 8.5 - - + +
66A SER* 1.3 81.6 - - - +
68A SER* 1.3 60.7 + - - +
254A THR 4.2 0.7 - - - +
255A GLY* 3.5 4.5 - - - -
256A ILE* 3.2 38.4 + - + +
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Residues in contact with SER 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 3.3 7.1 - - - +
45A GLY* 3.0 34.8 + - - +
66A SER* 5.3 1.1 - - - -
67A ALA* 1.3 74.3 - - - +
69A LEU* 1.3 61.1 + - - +
70A GLN* 3.4 30.6 + - - -
253A SER* 5.2 3.1 - - - -
254A THR 4.3 0.7 - - - -
255A GLY* 3.7 17.0 - - - -
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A LEU* 4.8 18.1 - - + +
43A GLY 3.6 4.3 - - - +
44A LEU* 3.5 21.1 - - + -
68A SER* 1.3 73.7 - - - +
70A GLN* 1.3 62.0 + - - +
71A LEU* 5.4 0.7 - - - +
253A SER* 3.3 19.8 - - - -
254A THR* 3.1 30.5 + - + +
292B ILE* 3.4 32.5 - - + -
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Residues in contact with GLN 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLN 3.8 0.6 - - - +
42A LEU* 3.4 6.3 - - - +
43A GLY 2.9 36.6 + - - +
45A GLY* 5.4 4.9 + - - -
68A SER* 3.4 22.9 + - - +
69A LEU* 1.3 73.9 - - - +
71A LEU* 1.3 62.1 + - - +
72A THR* 6.1 0.4 - - + -
252A ALA 3.6 3.4 - - - +
253A SER* 3.7 17.9 - - - -
1430A PGE 3.9 29.8 - - - +
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PRO* 4.8 14.1 - - + -
41A GLN 3.2 9.9 - - - +
42A LEU* 3.5 22.9 - - + -
69A LEU 5.4 0.7 - - - +
70A GLN* 1.3 75.5 - - - +
72A THR* 1.3 80.9 + - - +
73A GLN* 4.5 4.3 - - + +
250A LEU* 4.3 12.6 - - + -
251A THR* 3.5 3.5 - - - -
252A ALA* 2.8 54.8 + - + +
1430A PGE 5.4 0.2 - - - -
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Residues in contact with THR 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU 4.1 0.7 - - - +
40A PRO* 3.5 3.6 - - - +
41A GLN* 2.9 56.6 + - - +
70A GLN* 6.1 0.9 - - + -
71A LEU* 1.3 78.8 - - - +
73A GLN* 1.3 63.8 + - - +
249A ASP* 6.3 2.2 - - + -
250A LEU 3.5 3.6 - - - +
251A THR* 3.5 27.4 - - + -
1430A PGE 3.8 18.9 + - - +
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Residues in contact with GLN 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU 3.2 21.6 + - - -
39A LEU 4.3 2.0 - - - -
40A PRO* 3.2 40.0 - - + +
71A LEU* 4.6 5.4 - - + -
72A THR* 1.3 77.4 - - - +
74A SER* 1.3 94.1 + - - +
75A ILE* 3.4 11.6 + - + -
249A ASP* 3.7 3.8 - - - +
250A LEU* 2.8 56.1 + - + +
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Residues in contact with SER 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A PRO 4.3 9.0 + - - -
38A LEU* 4.9 9.4 - - - +
39A LEU 5.3 0.4 + - - -
73A GLN* 1.3 100.4 + - - +
75A ILE* 1.3 62.7 + - - +
77A ASP* 3.1 33.3 + - - +
80A LYS* 3.5 27.0 + - - +
249A ASP* 3.8 11.2 + - - -
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Residues in contact with ILE 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A GLN* 4.0 9.0 - - + +
74A SER* 1.3 79.4 - - - +
76A PHE* 1.3 62.1 + - + +
77A ASP 4.2 0.2 - - - -
81A TRP* 5.3 4.6 + - - -
248A LEU* 2.9 43.8 + - + +
249A ASP 4.1 1.6 - - - -
250A LEU* 3.6 45.3 - - + +
286A LEU* 4.8 4.7 - - + -
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Residues in contact with PHE 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ILE* 1.3 82.0 - - + +
77A ASP* 1.3 59.1 + - - +
78A MET* 3.5 40.6 - - + -
81A TRP* 5.6 4.3 - + - +
245A LEU* 4.7 9.4 - - + -
246A PRO* 3.3 29.6 - - + -
247A THR* 3.2 3.2 - - - -
248A LEU* 2.9 38.4 + - + -
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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