Contacts of the helix formed by residues 37 - 50 (chain A) in PDB entry 4LXZ
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 PRO 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ILE 3.3 21.2 - - - +
25A GLY* 3.8 9.2 - - - -
27A TYR* 3.3 26.5 - - + +
28A TYR* 5.0 1.6 - - + -
29A TYR* 3.8 21.3 - - + +
35A MET* 3.6 12.8 - - + +
36A LYS* 1.3 81.7 - - - +
38A HIS* 1.3 53.7 + - - +
39A ARG* 3.1 1.8 - - - +
40A ILE* 3.0 40.3 + - + +
114A PHE* 3.8 28.3 - - + -
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Residues in contact with HIS 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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25A GLY* 3.7 18.9 + - - +
27A TYR 4.9 0.2 + - - -
36A LYS* 2.9 10.0 + - + +
37A PRO* 1.3 77.2 - - - +
39A ARG* 1.4 56.6 + - - +
41A ARG* 3.0 39.4 + - - +
42A MET* 3.0 40.5 + - + +
310A ILE* 4.2 9.0 - - + -
338A TYR* 3.4 31.4 - + - -
341A TYR* 3.2 25.6 + - - -
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Residues in contact with ARG 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A MET* 3.5 27.2 - - - +
36A LYS* 2.9 25.3 + - - +
37A PRO* 4.8 1.0 - - - +
38A HIS* 1.4 77.1 - - - +
40A ILE* 1.4 69.7 + - + +
42A MET* 3.5 14.8 + - - +
43A THR* 2.8 36.8 + - - -
140A TRP 4.9 2.2 + - - -
141A ALA 6.0 1.2 + - - -
142A GLY 5.7 0.2 + - - -
144A LEU* 5.1 4.6 - - - +
305A GLY 2.7 31.1 + - - +
306A GLY* 3.3 13.5 + - - -
307A GLY* 3.1 28.7 + - - -
310A ILE* 3.8 27.3 - - + +
313A VAL* 3.9 18.5 - - + +
314A ALA* 4.5 1.0 - - - +
317A TRP* 3.6 17.5 - - + -
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Residues in contact with ILE 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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18A TYR* 5.1 1.0 + - - +
19A TYR 6.0 0.9 - - - +
20A TYR* 4.0 13.5 - - + -
24A ILE* 3.8 29.8 - - + -
37A PRO* 3.0 26.1 + - + +
39A ARG* 1.4 92.1 - - + +
41A ARG* 1.3 59.8 + - - +
43A THR* 3.4 7.7 + - - -
44A HIS* 3.0 27.0 + - - +
114A PHE* 4.9 5.6 - - + -
140A TRP* 4.1 21.1 - - + +
141A ALA* 3.7 40.6 - - + +
317A TRP* 4.4 7.2 - - + -
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Residues in contact with ARG 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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20A TYR* 3.5 25.2 - - - +
22A GLY 4.5 8.3 + - - -
24A ILE* 4.7 0.6 - - - +
25A GLY* 3.1 35.4 + - - +
26A ASN* 2.9 31.3 + - - +
37A PRO 3.8 0.8 + - - -
38A HIS* 3.0 37.5 + - - +
40A ILE* 1.3 77.0 - - - +
42A MET* 1.4 59.2 + - - +
44A HIS* 3.3 1.7 + - - +
45A ASN* 2.9 30.7 + - + +
338A TYR* 3.3 24.6 + - + +
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Residues in contact with MET 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 HIS* 3.0 23.2 + - - +
39A ARG* 3.6 13.7 - - - +
40A ILE 3.4 0.2 - - - -
41A ARG* 1.4 74.7 - - - +
43A THR* 1.3 62.9 + - - +
45A ASN* 3.5 1.2 + - - +
46A LEU* 3.0 26.2 + - - +
310A ILE* 3.6 50.3 - - - +
311A ARG* 4.0 8.3 - - - -
314A ALA* 3.9 6.8 - - + +
336A ASN* 5.6 0.2 - - - +
338A TYR* 3.7 32.2 - - + -
341A TYR* 3.5 32.5 - - + -
342A PHE* 4.0 16.0 - - + -
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Residues in contact with THR 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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18A TYR* 4.9 0.4 - - - +
39A ARG 2.8 18.7 + - - -
40A ILE* 3.4 12.3 - - + +
42A MET* 1.3 75.0 - - - +
44A HIS* 1.3 61.6 + - - +
46A LEU 3.3 1.2 + - - -
47A LEU* 2.9 32.2 + - + +
140A TRP* 3.8 21.3 - - + +
314A ALA* 3.4 22.9 + - - +
317A TRP* 3.6 37.8 - - + -
318A THR* 3.4 11.5 + - - +
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Residues in contact with HIS 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TYR* 2.7 43.9 + + - +
20A TYR* 3.3 45.3 - + + -
40A ILE 3.0 14.6 + - - +
41A ARG 3.3 7.8 + - - +
43A THR* 1.3 75.9 - - - +
45A ASN* 1.3 58.1 + - + +
47A LEU* 3.2 6.0 + - + +
48A LEU* 2.9 69.1 + - + +
58A ILE* 4.3 13.5 - - + -
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Residues in contact with ASN 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 ARG* 2.9 20.5 + - + +
42A MET 4.0 1.3 - - - +
44A HIS* 1.3 76.1 - - + +
46A LEU* 1.3 56.5 + - - +
48A LEU* 3.5 13.2 + - - +
49A ASN* 2.9 46.0 + - - +
336A ASN* 3.3 13.2 - - - +
337A ASP* 2.8 54.4 + - - +
338A TYR* 3.9 14.6 - - + -
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Residues in contact with LEU 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 MET 3.0 18.5 + - - +
45A ASN* 1.3 74.1 + - - +
47A LEU* 1.3 65.4 + - - +
49A ASN* 3.1 3.6 + - - -
50A TYR* 3.1 29.3 + - + -
314A ALA 4.0 12.3 - - - +
315A ARG* 4.4 4.7 - - - -
318A THR* 3.6 28.3 - - + +
333A LEU* 3.8 31.4 - - + -
334A PRO* 4.1 9.0 - - + -
336A ASN* 3.6 31.6 - - + +
342A PHE* 4.1 22.2 - - + -
348A LEU* 4.5 0.7 - - + -
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Residues in contact with LEU 47 (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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18A TYR* 3.6 37.0 - - + +
43A THR* 2.9 31.0 + - + +
44A HIS* 3.5 10.3 - - - +
46A LEU* 1.3 76.4 - - - +
48A LEU* 1.4 71.8 + - + +
50A TYR* 3.2 8.3 + - - +
52A LEU* 3.2 44.3 + - + +
53A TYR 5.1 0.9 - - - +
56A MET* 3.7 26.0 - - + -
58A ILE* 5.1 0.4 - - + -
318A THR* 3.8 16.1 + - + -
321A THR* 3.8 19.1 - - + +
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Residues in contact with LEU 48 (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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44A HIS* 2.9 47.3 + - + +
45A ASN* 3.7 15.5 - - - +
46A LEU 3.3 0.2 - - - -
47A LEU* 1.4 78.3 - - + +
49A ASN* 1.4 61.0 + - - +
51A GLY* 2.9 21.5 + - - -
53A TYR* 3.4 44.9 - - + -
58A ILE* 4.0 15.0 - - + -
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Residues in contact with ASN 49 (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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45A ASN* 2.9 49.1 + - - +
46A LEU 3.1 4.7 + - - +
48A LEU* 1.4 77.0 - - - +
50A TYR* 1.3 58.4 + - - +
51A GLY 3.2 1.4 + - - -
334A PRO* 3.6 21.4 - - + +
335A TYR* 3.1 26.0 - - - +
336A ASN* 3.5 11.9 - - + +
337A ASP* 4.6 0.6 + - - +
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Residues in contact with TYR 50 (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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46A LEU* 3.1 28.6 + - + -
47A LEU 3.6 9.2 - - - +
48A LEU 3.2 0.8 - - - -
49A ASN* 1.3 75.7 - - - +
51A GLY* 1.3 59.9 + - - +
52A LEU* 3.4 16.9 + - + +
54A ARG* 4.8 5.4 + - - -
318A THR* 3.6 26.0 - - + -
329A ILE* 3.8 34.6 - - + +
330A PRO* 2.7 44.8 + - + -
332A GLU 3.7 4.6 + - - -
333A LEU* 3.6 10.5 - - + +
334A PRO* 3.4 28.7 - - + -
348A LEU* 3.4 19.9 - - + +
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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