Contacts of the helix formed by residues 36 - 46 (chain D) in PDB entry 4WLE
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D GLY* 1.3 75.3 - - - +
37D GLY* 1.3 66.6 + - - +
39D PRO* 3.3 4.5 - - - +
40D LEU* 3.0 27.2 + - + +
99D PRO* 3.7 34.1 - - + +
140D ILE* 4.4 8.5 - - + -
246D SER* 5.6 2.7 - - - +
247D ALA 3.7 20.2 - - - +
248D THR* 4.0 12.8 - - + -
251D MET* 3.9 30.5 - - + +
252D ALA* 4.0 13.6 - - - +
401D CIT 4.0 15.7 - - - +
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Residues in contact with GLY 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D VAL* 4.4 0.6 - - - +
31D GLY 3.4 24.4 + - - -
32D ALA* 3.2 9.9 - - - -
34D GLY 3.4 5.4 + - - -
36D ILE* 1.3 78.8 - - - +
38D GLN* 1.3 56.7 + - - +
40D LEU* 3.6 2.4 - - - +
41D SER* 2.8 35.0 + - - -
99D PRO* 4.0 13.5 - - - +
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Residues in contact with GLN 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C LYS* 5.2 3.1 + - - -
248C THR* 4.4 7.4 + - - -
249C LEU* 3.7 32.6 - - + +
32D ALA 3.3 15.3 - - - +
33D SER* 3.0 21.5 + - - +
34D GLY 3.1 15.5 + - - +
37D GLY* 1.3 74.5 - - - +
39D PRO* 1.3 70.0 - - + +
41D SER* 3.2 5.9 + - - -
42D LEU* 3.0 21.3 + - - +
60D HIS* 5.6 2.2 - - - +
64D VAL* 3.7 26.3 - - + +
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Residues in contact with PRO 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C PRO* 5.2 6.1 - - + -
42C LEU* 3.9 17.8 - - + +
249C LEU* 4.6 5.6 - - + -
35D GLY* 3.0 28.0 - - - +
36D ILE 3.3 9.4 - - - +
38D GLN* 1.3 92.5 - - + +
40D LEU* 1.3 59.4 + - - +
42D LEU* 3.3 10.3 + - + +
43D LEU* 3.1 27.7 + - - +
248D THR 4.3 2.5 - - - +
249D LEU* 4.0 20.0 - - + -
252D ALA* 3.7 16.8 - - + -
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Residues in contact with LEU 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D VAL* 4.5 5.6 - - + -
36D ILE* 3.0 21.6 + - + +
37D GLY 3.6 4.0 - - - +
39D PRO* 1.3 76.7 - - - +
41D SER* 1.3 61.8 + - - +
43D LEU* 3.2 4.1 + - - +
44D LEU* 3.0 42.7 + - + +
97D VAL* 3.8 28.5 - - + -
99D PRO* 4.0 22.9 - - + -
140D ILE* 4.1 10.8 - - + -
252D ALA* 3.4 31.7 - - + +
255D GLY* 4.0 4.0 - - - -
256D ALA* 3.6 21.5 - - + +
259D VAL* 5.5 0.7 - - + -
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Residues in contact with SER 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D VAL* 3.7 11.4 - - - +
32D ALA* 3.8 5.5 - - - +
37D GLY 2.8 27.2 + - - -
38D GLN* 3.6 6.5 - - - -
40D LEU* 1.3 72.4 - - - +
42D LEU* 1.3 56.8 + - - +
44D LEU* 3.4 8.5 + - - -
45D LYS* 2.9 31.4 + - - +
53D LEU* 3.4 6.6 - - - +
55D LEU* 3.3 26.6 - - - +
64D VAL* 5.1 0.4 - - - -
68D LEU* 3.6 20.9 - - - -
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Residues in contact with LEU 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C PRO* 3.9 28.0 - - + +
42C LEU* 5.5 2.2 - - + -
43C LEU* 4.2 22.9 - - + -
249C LEU* 3.6 22.4 - - + +
253C TYR* 4.4 4.0 - - + -
38D GLN 3.0 12.7 + - - +
39D PRO* 3.4 11.9 - - + +
40D LEU 3.2 0.2 - - - -
41D SER* 1.3 74.3 - - - +
43D LEU* 1.3 62.2 + - + +
45D LYS* 3.3 2.0 + - - +
46D ASN* 3.0 50.0 + - - +
68D LEU* 3.8 14.5 - - + +
71D ILE* 3.6 29.6 - - + -
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Residues in contact with LEU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C LEU* 4.3 12.8 - - + -
43C LEU* 3.8 28.7 - - + -
46C ASN* 3.9 17.0 - - - +
39D PRO 3.1 17.2 + - - +
40D LEU 3.2 6.7 + - - +
42D LEU* 1.3 75.7 - - + +
44D LEU* 1.3 61.6 + - - +
46D ASN* 3.5 9.5 + - + +
47D SER* 3.5 14.6 + - - -
252D ALA* 3.6 25.4 - - + +
253D TYR* 3.6 21.1 - - + +
256D ALA* 3.8 16.4 - - + -
260D PHE* 3.5 14.8 - - + -
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Residues in contact with LEU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D VAL* 3.9 16.4 - - + -
29D VAL* 3.6 31.0 - - + -
40D LEU* 3.0 31.8 + - + +
41D SER* 3.7 4.3 - - - +
43D LEU* 1.3 75.4 - - - +
45D LYS* 1.3 63.1 + - - +
47D SER 3.2 9.7 + - - -
50D VAL* 3.4 30.6 - - + +
53D LEU* 3.9 13.0 - - + -
97D VAL* 4.8 4.9 - - + -
256D ALA* 4.7 7.2 - - - -
259D VAL* 3.8 25.8 - - + -
260D PHE* 3.7 25.6 - - + -
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Residues in contact with LYS 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C THR* 6.1 0.4 - - - +
41D SER 2.9 18.5 + - - +
42D LEU* 3.6 7.6 - - - +
44D LEU* 1.3 76.4 - - - +
46D ASN* 1.3 58.1 + - - +
47D SER 3.3 4.3 + - - +
53D LEU* 3.9 12.7 - - + +
68D LEU* 3.3 32.1 - - + +
69D SER* 4.7 4.9 + - - +
71D ILE* 3.4 29.3 + - + -
73D THR* 2.6 60.0 + - - +
75D ALA* 2.6 37.1 + - + +
77D VAL* 3.7 18.1 - - + +
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Residues in contact with ASN 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C LEU* 3.9 22.0 - - - +
253C TYR* 3.5 30.7 - - + -
42D LEU* 3.0 40.4 + - - +
43D LEU* 3.7 10.3 - - + +
44D LEU 3.2 0.4 - - - -
45D LYS* 1.3 75.5 - - - +
47D SER* 1.3 61.4 + - - +
48D PRO* 3.8 4.7 - - - +
71D ILE* 3.8 10.0 - - - +
73D THR* 3.9 18.0 - - + +
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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