Contacts of the strand formed by residues 61 - 76 (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 ASN 61 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B TYR* 3.6 19.2 + - + +
51B SER* 3.5 10.8 - - - +
52B ASN* 2.9 27.7 + - - +
53B GLY 4.4 0.8 + - - -
59B GLY* 4.2 3.9 - - - -
60B ILE* 1.3 105.7 + - - +
62B SER* 1.3 66.2 + - - +
261B TYR* 3.2 9.1 - - - +
262B SER* 2.8 47.7 + - - +
263B GLY* 5.1 3.4 - - - -
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Residues in contact with SER 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B THR 3.7 0.8 + - - +
50B TYR* 3.4 2.9 - - - -
51B SER* 2.8 55.9 + - - +
61B ASN* 1.3 80.1 - - - +
63B ASN* 1.3 71.6 + - - +
64B ALA* 4.1 1.8 - - - -
259B THR* 4.5 9.0 - - - -
260B SER 3.1 11.9 - - - -
261B TYR* 3.8 22.0 - - - +
262B SER* 5.2 0.4 - - - -
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Residues in contact with ASN 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TYR* 2.7 31.8 + - + +
49B THR 3.8 4.5 - - - -
50B TYR* 3.3 21.4 - - - -
62B SER* 1.3 84.6 + - - +
64B ALA* 1.3 60.6 + - - +
65B THR* 5.0 2.8 - - + +
258B ASP 3.4 5.9 - - - +
259B THR 3.7 0.2 - - - -
260B SER* 2.8 43.1 + - - +
262B SER* 5.3 3.1 + - - -
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Residues in contact with ALA 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ASP 4.8 0.2 - - - -
48B TYR* 4.3 0.9 - - - -
49B THR* 2.8 41.1 + - - +
62B SER* 4.1 1.1 - - - -
63B ASN* 1.3 74.3 - - - +
65B THR* 1.3 70.2 + - - +
257B SER* 6.4 0.9 - - - -
258B ASP 3.2 5.2 - - - +
259B THR* 3.7 26.7 - - + +
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Residues in contact with THR 65 (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 3.2 12.1 - - - -
48B TYR* 3.3 33.0 - - + -
63B ASN* 5.0 2.2 - - + +
64B ALA* 1.3 82.2 - - - +
66B SER* 1.3 60.1 + - - +
256B ILE* 4.2 2.3 - - - +
257B SER* 3.4 2.3 - - - -
258B ASP* 3.0 41.2 + - - +
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Residues in contact with SER 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ALA* 3.2 3.2 - - - +
47B ASP* 3.0 49.4 + - - +
65B THR* 1.3 74.7 - - - +
67B ALA* 1.3 67.1 + - - +
68B SER* 5.3 0.9 - - - -
256B ILE* 3.3 13.0 - - - -
257B SER* 4.3 10.3 - - - -
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Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 5.2 4.8 - - + +
45B GLY 3.0 17.7 - - - +
46B ALA* 3.8 9.4 - - + +
66B SER* 1.3 83.9 - - - +
68B SER* 1.3 60.8 + - - +
254B THR 4.2 1.2 - - - +
255B GLY* 3.6 14.9 - - - -
256B ILE* 3.2 24.8 + - + +
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Residues in contact with SER 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 3.3 7.7 - - - +
45B GLY* 3.0 33.5 + - - -
66B SER* 5.3 0.6 - - - -
67B ALA* 1.3 76.2 - - - +
69B LEU* 1.3 60.8 + - - +
70B GLN* 3.4 29.1 + - - -
253B SER* 5.2 3.8 - - - -
254B THR 3.6 7.0 - - - -
255B GLY* 3.8 11.0 - - - -
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 4.8 18.5 - - + +
43B GLY 3.7 4.3 - - - +
44B LEU* 3.5 20.0 - - + -
68B SER* 1.3 73.7 - - - +
70B GLN* 1.3 61.8 + - - +
71B LEU* 5.4 0.5 - - - +
253B SER* 3.2 21.2 - - - -
254B THR* 3.1 30.3 + - + +
292C ILE* 3.3 33.2 - - + -
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Residues in contact with GLN 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLN 3.8 0.8 - - - +
42B LEU* 3.4 6.3 - - - +
43B GLY 2.9 35.9 + - - +
44B LEU 6.0 0.2 - - - -
45B GLY* 5.4 4.5 + - - -
68B SER* 3.4 22.9 + - - +
69B LEU* 1.3 75.1 - - - +
71B LEU* 1.3 62.0 + - - +
72B THR* 6.1 0.9 - - + -
252B ALA 3.6 3.6 - - - +
253B SER* 3.8 18.1 - - - -
1431B PGE 4.1 29.8 + - - +
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Residues in contact with LEU 71 (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* 4.8 14.8 - - + -
41B GLN 3.1 9.9 - - - +
42B LEU* 3.5 22.7 - - + -
69B LEU 5.4 0.4 - - - +
70B GLN* 1.3 76.0 - - - +
72B THR* 1.3 80.5 + - - +
73B GLN* 4.7 4.5 - - + -
250B LEU* 4.2 12.6 - - + -
251B THR* 3.5 3.8 - - - -
252B ALA* 2.9 54.4 + - + +
1431B PGE 5.2 0.4 - - - -
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Residues in contact with THR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU 4.2 0.7 - - - +
40B PRO* 3.5 4.3 - - - +
41B GLN* 2.8 56.8 + - - +
70B GLN* 6.1 1.3 - - + -
71B LEU* 1.3 77.7 - - - +
73B GLN* 1.3 63.7 + - - +
249B ASP* 6.2 2.9 - - + -
250B LEU 3.6 3.1 - - - +
251B THR* 3.6 26.9 - - + -
1431B PGE 3.9 15.5 - - - +
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Residues in contact with GLN 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU 3.3 21.8 + - - -
39B LEU 4.3 1.8 - - - -
40B PRO* 3.2 40.2 - - + +
71B LEU* 4.7 4.9 - - + -
72B THR* 1.3 76.8 - - - +
74B SER* 1.3 92.3 + - - +
75B ILE* 3.4 11.8 + - + -
249B ASP* 3.6 3.7 - - - +
250B LEU* 2.9 55.2 + - + +
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Residues in contact with SER 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PRO 4.3 10.1 + - - -
38B LEU* 4.9 9.5 - - - +
39B LEU 5.2 0.8 + - - -
73B GLN* 1.3 95.7 + - - +
75B ILE* 1.3 61.9 + - - +
76B PHE 4.5 0.2 + - - -
77B ASP* 3.0 34.3 + - - +
80B LYS* 3.4 24.8 + - - +
249B ASP* 3.6 12.8 + - - -
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Residues in contact with ILE 75 (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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73B GLN* 4.0 11.0 - - + +
74B SER* 1.3 79.6 - - - +
76B PHE* 1.3 59.7 + - + +
77B ASP 4.2 0.2 - - - -
81B TRP* 5.4 4.0 + - - -
248B LEU* 2.8 48.5 + - + +
249B ASP 4.0 2.0 - - - -
250B LEU* 3.8 41.5 - - + +
286B LEU* 4.9 3.8 - - + -
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Residues in contact with PHE 76 (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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75B ILE* 1.3 81.5 - - + +
77B ASP* 1.3 59.6 - - - +
78B MET* 3.5 41.3 - - + -
81B TRP* 5.6 4.3 - + - +
245B LEU* 4.5 12.1 - - + -
246B PRO* 3.1 29.8 - - + -
247B THR* 3.1 4.5 - - - -
248B LEU* 2.9 39.5 + - + -
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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