Contacts of the helix formed by residues 36 - 47 (chain B) in PDB entry 4WLU
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 ILE 36 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B GLY* 1.3 76.0 - - - +
37B GLY* 1.3 66.3 + - - +
38B GLN 3.3 0.3 + - - -
39B PRO* 3.3 4.0 - - - +
40B LEU* 3.0 33.5 + - + +
99B PRO* 4.0 16.2 - - + -
140B ILE* 4.1 7.2 - - + -
247B ALA 3.9 13.9 - - - +
248B THR* 3.9 11.4 - - - -
251B MET* 3.6 19.7 - - + +
252B ALA* 4.1 9.1 - - - +
402B NAD 3.0 73.4 + - + +
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Residues in contact with GLY 37 (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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29B VAL* 4.3 1.5 - - - +
31B GLY 3.6 17.7 + - - -
32B ALA* 3.0 15.9 - - - -
34B GLY* 3.3 5.6 + - - -
36B ILE* 1.3 78.4 - - - +
38B GLN* 1.3 54.0 + - - +
40B LEU* 3.8 3.8 - - - +
41B SER* 2.6 37.8 + - - -
99B PRO* 4.2 11.3 - - - +
402B NAD 4.4 0.8 + - - -
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Residues in contact with GLN 38 (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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241A LYS* 5.0 3.5 + - - +
248A THR* 4.1 9.4 + - - -
249A LEU* 3.6 37.2 - - + +
32B ALA 3.0 16.7 + - - +
33B SER* 2.9 21.7 + - - +
34B GLY 3.1 12.6 + - - +
37B GLY* 1.3 72.7 - - - +
39B PRO* 1.3 67.8 - - + +
41B SER* 3.3 5.7 + - - -
42B LEU* 3.0 22.7 + - - +
60B HIS* 5.7 2.4 - - - +
64B VAL* 3.8 25.2 - - + +
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Residues in contact with PRO 39 (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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39A PRO* 5.2 6.7 - - + -
42A LEU* 3.9 16.9 - - + +
249A LEU* 4.6 4.9 - - + -
35B GLY* 3.1 28.3 - - - +
36B ILE* 3.3 9.9 - - - +
38B GLN* 1.3 90.5 - - + +
40B LEU* 1.3 62.7 + - - +
42B LEU* 3.4 10.6 + - + +
43B LEU* 3.0 27.9 + - - +
248B THR 4.4 1.3 - - - +
249B LEU* 4.2 17.9 - - + -
252B ALA* 3.7 17.9 - - + -
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Residues in contact with LEU 40 (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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29B VAL* 4.3 18.8 - - + -
36B ILE* 3.0 21.9 + - + +
37B GLY 3.8 2.7 - - - +
39B PRO* 1.3 75.8 - - - +
41B SER* 1.3 59.1 + - - +
43B LEU* 3.1 4.5 + - - +
44B LEU* 3.0 46.1 + - + +
97B VAL* 3.9 28.5 - - + -
99B PRO* 4.5 7.6 - - + -
140B ILE* 4.2 11.9 - - + -
252B ALA* 3.5 18.9 - - + +
255B GLY* 3.9 6.1 - - - +
256B ALA* 3.5 33.7 - - + +
259B VAL* 5.5 0.9 - - + -
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Residues in contact with SER 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 3.8 11.3 - - - +
32B ALA* 4.0 3.9 - - - +
37B GLY 2.6 23.3 + - - -
38B GLN* 3.6 5.6 - - - -
40B LEU* 1.3 75.8 - - - +
42B LEU* 1.3 57.2 + - - +
44B LEU* 3.4 9.8 + - - -
45B LYS* 2.9 30.3 + - - +
53B LEU* 3.4 6.1 - - - +
55B LEU* 3.3 26.9 - - - +
64B VAL* 5.4 0.4 - - - -
68B LEU* 3.6 20.8 - - - +
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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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39A PRO* 3.8 29.6 - - + +
42A LEU* 5.7 1.6 - - + -
43A LEU* 4.2 21.3 - - + -
249A LEU* 3.7 22.7 - - + +
252A ALA* 4.4 0.2 - - + -
253A TYR* 4.5 3.8 - - + -
38B GLN 3.0 14.3 + - - +
39B PRO* 3.4 11.7 - - + +
41B SER* 1.3 76.3 - - - +
43B LEU* 1.3 64.5 + - + +
45B LYS* 3.3 2.1 + - - +
46B ASN* 3.0 44.7 + - - +
68B LEU* 3.6 13.1 - - + +
71B ILE* 3.6 29.8 - - + -
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Residues in contact with LEU 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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42A LEU* 4.2 14.1 - - + -
43A LEU* 3.9 28.5 - - + -
46A ASN* 3.9 17.9 - - - +
39B PRO 3.0 17.8 + - - +
40B LEU 3.1 6.5 + - - +
42B LEU* 1.3 76.5 - - + +
44B LEU* 1.3 62.6 + - - +
46B ASN* 3.3 15.6 + - + +
47B SER 3.4 8.7 + - - -
252B ALA 3.5 33.0 - - - +
253B TYR* 3.7 12.3 - - + +
256B ALA* 3.8 16.4 - - + -
260B PHE* 3.5 13.7 - - + -
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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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27B VAL* 4.0 11.4 - - + -
29B VAL* 3.6 31.0 - - + -
40B LEU* 3.0 33.6 + - + +
41B SER* 3.7 4.0 - - - +
43B LEU* 1.3 73.7 - - - +
45B LYS* 1.3 64.5 + - - +
47B SER* 3.1 17.2 + - - +
50B VAL* 3.6 24.4 - - + +
53B LEU* 4.0 17.7 - - + -
97B VAL* 5.0 3.1 - - + -
256B ALA* 4.6 7.0 - - - -
259B VAL* 3.9 26.0 - - + -
260B PHE* 3.8 24.9 - - + -
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Residues in contact with LYS 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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179A THR* 6.0 0.4 - - - +
41B SER 2.9 19.0 + - - +
42B LEU 3.6 5.6 - - - +
44B LEU* 1.3 76.1 - - - +
46B ASN* 1.3 57.6 + - - +
47B SER 3.4 4.0 + - - +
53B LEU* 4.0 12.0 - - + +
68B LEU* 3.3 34.1 - - + +
69B SER* 4.7 4.8 + - - +
71B ILE* 3.3 31.4 + - + +
73B THR* 2.7 57.4 + - - +
75B ALA* 2.6 36.7 + - + +
77B VAL* 3.6 18.8 - - + +
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Residues in contact with ASN 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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43A LEU* 3.8 23.0 - - - +
253A TYR* 3.5 31.0 - - + -
42B LEU* 3.0 40.9 + - - +
43B LEU* 3.7 10.0 - - + +
44B LEU 3.2 0.6 - - - -
45B LYS* 1.3 77.4 - - - +
47B SER* 1.3 59.9 + - - +
48B PRO* 3.9 5.2 - - - +
71B ILE* 3.9 9.0 - - - +
73B THR* 3.9 16.6 - - - +
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Residues in contact with SER 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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43B LEU 3.4 1.4 + - - -
44B LEU 3.1 13.2 + - - +
45B LYS 4.1 4.2 - - - +
46B ASN* 1.3 78.8 - - - +
48B PRO* 1.3 68.5 - - - +
49B LEU* 3.1 25.2 + - - +
50B VAL* 3.4 18.1 + - - +
73B THR* 5.5 2.7 - - - -
74B LYS* 5.5 1.0 - - - +
75B ALA* 5.1 0.3 + - - +
260B PHE* 3.3 42.1 - - - -
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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