Contacts of the helix formed by residues 36 - 46 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A GLY 3.4 0.2 - - - -
35A GLY* 1.3 73.6 - - - +
37A GLY* 1.3 66.8 + - - +
38A GLN 3.2 0.5 + - - -
39A PRO* 3.3 3.8 - - - +
40A LEU* 3.0 34.5 + - + +
99A PRO* 3.7 34.1 - - + +
140A ILE* 4.4 11.9 - - + -
246A SER* 5.7 2.9 - - - +
247A ALA 3.8 20.9 - - - +
248A THR* 4.0 12.8 - - + -
251A MET* 4.0 28.9 - - + +
252A ALA* 4.1 11.5 - - - +
401A CIT 5.5 3.8 - - + -
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Residues in contact with GLY 37 (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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29A VAL* 4.4 1.0 - - - +
31A GLY 3.5 23.9 + - - -
32A ALA* 3.2 10.5 - - - -
34A GLY* 3.4 5.0 + - - -
36A ILE* 1.3 79.0 - - - +
38A GLN* 1.3 54.2 + - - +
40A LEU* 3.5 3.9 + - - +
41A SER* 2.7 37.1 + - - -
99A PRO* 4.1 13.1 - - - +
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Residues in contact with GLN 38 (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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32A ALA 3.3 15.7 - - - +
33A SER* 3.0 21.2 + - - +
34A GLY 3.1 13.4 + - - +
37A GLY* 1.3 72.1 - - - +
39A PRO* 1.3 68.9 - - + +
41A SER* 3.2 6.0 + - - -
42A LEU* 3.0 22.5 + - - +
60A HIS* 5.7 2.2 - - - +
64A VAL* 3.7 23.5 - - + +
241B LYS* 5.1 4.2 + - - -
248B THR* 4.3 7.4 + - - -
249B LEU* 3.6 37.4 - - + +
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Residues in contact with PRO 39 (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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35A GLY 3.1 29.4 - - - +
36A ILE 3.3 9.0 - - - +
38A GLN* 1.3 87.6 - - + +
40A LEU* 1.3 62.9 + - - +
42A LEU* 3.2 10.6 + - + +
43A LEU* 3.0 27.2 + - - +
248A THR 4.2 3.1 - - - +
249A LEU* 4.1 18.2 - - + -
252A ALA* 3.7 16.6 - - + -
39B PRO* 5.3 6.1 - - + -
42B LEU* 3.8 18.1 - - + +
249B LEU* 4.5 5.8 - - + -
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Residues in contact with LEU 40 (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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29A VAL* 4.4 6.1 - - + -
36A ILE* 3.0 23.3 + - + +
37A GLY 3.6 3.1 - - - +
39A PRO* 1.3 75.3 - - - +
41A SER* 1.3 64.4 + - - +
43A LEU* 3.2 3.5 + - - +
44A LEU* 3.0 41.5 + - + +
97A VAL* 3.9 31.2 - - + -
99A PRO* 4.1 20.6 - - + -
140A ILE* 4.3 8.7 - - + -
252A ALA* 3.4 18.9 - - + +
255A GLY* 4.0 4.9 - - - -
256A ALA* 3.6 33.9 - - + +
259A VAL* 5.6 0.2 - - + -
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Residues in contact with SER 41 (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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29A VAL* 3.9 10.1 - - - +
32A ALA* 3.9 4.8 - - - +
37A GLY 2.7 27.1 + - - -
38A GLN* 3.2 7.4 + - - -
40A LEU* 1.3 75.6 - - - +
42A LEU* 1.3 57.1 + - - +
44A LEU* 3.4 6.6 + - - -
45A LYS* 2.9 30.5 + - - +
53A LEU* 3.4 8.7 - - - +
55A LEU* 3.3 25.6 - - - +
64A VAL* 5.1 0.7 - - - -
68A LEU* 3.6 22.0 - - - -
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Residues in contact with LEU 42 (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 GLN 3.0 13.8 + - - +
39A PRO* 3.4 11.9 - - + +
41A SER* 1.3 76.6 - - - +
43A LEU* 1.3 59.1 + - + +
45A LYS* 3.3 2.3 + - - +
46A ASN* 3.0 49.9 + - - +
68A LEU* 3.8 14.7 - - + +
71A ILE* 3.6 28.9 - - + -
39B PRO* 3.8 29.6 - - + +
42B LEU* 5.7 1.6 - - + -
43B LEU* 4.2 23.1 - - + -
249B LEU* 3.6 22.7 - - + +
252B ALA* 4.3 0.4 - - + -
253B TYR* 4.5 3.8 - - + -
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Residues in contact with LEU 43 (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 PRO 3.0 18.5 + - - +
40A LEU 3.7 6.1 - - - +
42A LEU* 1.3 75.5 - - + +
44A LEU* 1.3 60.9 + - - +
46A ASN* 3.5 8.6 + - + +
47A SER* 3.5 14.4 + - - -
252A ALA 3.6 26.9 - - - +
253A TYR* 3.7 18.4 - - + +
256A ALA* 3.9 14.8 - - + -
260A PHE* 3.7 13.8 - - + -
42B LEU* 4.1 15.7 - - + -
43B LEU* 3.8 28.7 - - + -
46B ASN* 3.9 17.9 - - - +
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Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A VAL* 3.9 11.9 - - + -
29A VAL* 3.6 32.3 - - + -
40A LEU* 3.0 31.2 + - + +
41A SER* 3.7 3.8 - - - +
43A LEU* 1.3 74.4 - - - +
45A LYS* 1.3 65.3 + - - +
47A SER* 3.1 10.4 + - - -
50A VAL* 3.5 32.0 - - + +
53A LEU* 3.8 18.4 - - + -
97A VAL* 5.0 3.6 - - + -
256A ALA* 4.7 6.7 - - + -
259A VAL* 3.9 31.6 - - + -
260A PHE* 3.9 18.6 - - + -
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Residues in contact with LYS 45 (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 SER 2.9 18.8 + - - +
42A LEU 3.3 5.1 + - - +
44A LEU* 1.3 76.8 - - - +
46A ASN* 1.3 58.0 + - - +
47A SER 3.4 3.5 + - - +
53A LEU* 3.9 12.2 - - + +
68A LEU* 3.4 33.9 - - + +
69A SER* 4.8 3.7 + - - +
71A ILE* 3.4 30.6 + - + -
73A THR* 2.6 61.0 + - - +
75A ALA* 2.6 37.6 + - + +
77A VAL* 3.6 19.9 - - + +
179B THR* 6.1 0.2 - - - +
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Residues in contact with ASN 46 (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* 3.0 41.0 + - - +
43A LEU* 3.7 9.8 - - + +
44A LEU 3.2 0.4 - - - -
45A LYS* 1.3 75.7 - - - +
47A SER* 1.3 60.9 + - - +
48A PRO* 3.8 5.9 - - - +
71A ILE* 3.8 9.9 - - - +
73A THR* 4.0 16.1 - - - +
43B LEU* 3.8 23.2 - - - +
253B TYR* 3.6 30.3 - - + -
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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