Contacts of the helix formed by residues 45 - 63 (chain A) in PDB entry 4PZ0
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 VAL 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A LEU* 3.9 32.8 - - + -
43A THR 3.3 0.8 - - - +
44A GLY* 1.3 83.8 - - - +
46A GLY* 1.3 68.2 + - - +
47A PHE* 4.0 8.1 - - + +
48A PHE* 2.9 34.8 + - + +
49A THR* 3.0 12.6 + - - -
200A ASN 4.7 3.4 - - - +
227A ALA* 4.3 18.6 - - + +
228A THR* 4.0 24.0 - - - +
401A PAV 6.0 0.4 - - - -
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Residues in contact with GLY 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLY 4.3 0.2 - - - -
45A VAL* 1.3 73.2 - - - +
47A PHE* 1.3 63.0 + - - +
49A THR* 3.3 7.1 + - - -
50A SER* 2.9 30.6 + - - -
253A THR* 4.2 13.9 - - - -
256A VAL* 4.8 12.8 - - - +
347A PHE* 4.6 1.8 - - - -
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Residues in contact with PHE 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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45A VAL* 3.1 6.0 + - + +
46A GLY* 1.3 74.1 - - - +
48A PHE* 1.3 77.4 + + + +
50A SER* 3.6 0.9 + - - -
51A GLY* 3.0 22.5 + - - -
121A TRP* 3.8 13.9 - + - -
122A ASP* 3.5 39.9 - - - -
227A ALA* 4.0 18.5 - - + +
253A THR* 3.6 17.7 + - + +
271A LEU* 4.0 17.5 - - + -
272A TRP* 3.6 30.5 - + - -
274A VAL* 3.5 31.8 - - + +
277A GLN* 4.1 2.9 - - - -
401A PAV 3.6 20.2 - - + -
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Residues in contact with PHE 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PHE* 4.9 0.7 - - - -
40A PRO* 3.4 14.6 - - + -
41A LYS* 3.6 27.8 - - + -
42A LEU* 3.4 48.2 - - + +
43A THR* 5.0 0.4 - - - -
45A VAL* 2.9 18.8 + - + +
47A PHE* 1.3 87.1 - + - +
49A THR* 1.3 67.0 + - - +
51A GLY* 3.8 0.3 - - - -
52A GLY 2.9 20.3 + - - -
68A TYR* 3.3 18.7 + - - +
97A SER* 3.9 4.0 - - - -
121A TRP* 3.6 18.6 - + - -
122A ASP* 3.5 14.6 - - - -
200A ASN* 5.4 0.9 - - - -
401A PAV 3.4 32.5 - - - -
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Residues in contact with THR 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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44A GLY* 4.3 9.4 + - - -
45A VAL 3.0 19.8 + - - -
46A GLY* 3.8 10.0 - - - -
48A PHE* 1.3 76.2 - - - +
50A SER* 1.3 60.3 + - - +
52A GLY* 3.3 1.4 + - - -
53A GLU* 2.9 46.5 + - + +
68A TYR* 3.5 16.7 + - + -
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Residues in contact with SER 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 GLY* 2.9 15.5 + - - -
49A THR* 1.3 75.4 - - - +
51A GLY* 1.3 66.0 + - - +
53A GLU* 3.2 13.2 + - - +
54A GLY 3.0 18.4 + - - -
255A ASN* 5.4 0.2 + - - -
274A VAL* 3.7 17.0 - - - -
275A LYS* 3.4 15.0 - - - +
347A PHE* 2.7 39.2 + - - -
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Residues in contact with GLY 51 (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 PHE* 3.5 17.8 - - - -
47A PHE 3.0 17.0 + - - -
48A PHE 3.3 2.7 + - - -
50A SER* 1.3 74.4 - - - +
52A GLY* 1.3 57.5 + - - +
54A GLY* 3.2 1.7 + - - -
55A ALA 3.0 23.6 + - - -
121A TRP* 4.3 4.9 - - - -
274A VAL* 3.6 25.2 - - - +
278A GLY* 3.6 6.2 - - - -
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Residues in contact with GLY 52 (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 PHE* 3.5 20.9 - - - -
48A PHE 2.9 14.8 + - - -
49A THR 3.6 4.3 - - - -
51A GLY* 1.3 75.2 - - - +
53A GLU* 1.3 56.1 + - - +
55A ALA* 3.3 1.7 + - - +
56A LYS* 2.9 31.5 + - - +
68A TYR* 3.8 22.3 - - - +
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Residues in contact with GLU 53 (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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49A THR* 2.9 35.2 + - + +
50A SER* 3.2 14.5 + - - +
52A GLY* 1.3 77.1 - - - +
54A GLY* 1.3 57.1 + - - +
56A LYS* 3.8 4.7 - - - +
57A GLU* 2.8 47.6 + - + +
275A LYS* 3.9 18.5 + - - +
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Residues in contact with GLY 54 (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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50A SER 3.0 12.7 + - - -
51A GLY 3.2 1.5 + - - -
53A GLU* 1.3 77.2 - - - +
55A ALA* 1.3 61.8 + - - +
57A GLU* 3.5 6.1 + - - +
58A MSE 3.1 18.2 + - - -
275A LYS* 3.3 31.3 - - - +
279A ALA* 3.5 19.1 - - - +
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Residues in contact with ALA 55 (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 PHE* 3.6 36.1 - - + -
51A GLY 3.0 12.4 + - - +
52A GLY 3.7 3.4 - - - +
54A GLY* 1.3 74.9 - - - +
56A LYS* 1.3 58.2 + - - +
58A MSE 3.5 0.2 + - - -
59A GLY* 3.0 19.4 + - - -
66A VAL* 3.8 6.7 - - + +
278A GLY 3.4 15.7 - - - +
279A ALA* 4.2 0.7 - - - +
282A THR* 2.9 30.8 + - - +
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Residues in contact with LYS 56 (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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52A GLY 2.9 18.7 + - - +
53A GLU* 3.8 5.2 - - - +
55A ALA* 1.3 76.6 - - - +
57A GLU* 1.3 60.9 + - + +
59A GLY* 3.1 2.3 + - - -
60A ASP* 2.9 52.9 + - - +
64A VAL 6.0 0.2 - - - +
65A GLN* 2.7 32.7 + - - +
66A VAL* 3.0 35.7 + - + +
68A TYR* 5.8 4.7 - - + +
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Residues in contact with GLU 57 (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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53A GLU* 2.8 30.3 + - - +
54A GLY* 3.8 6.2 - - - +
56A LYS* 1.3 77.4 - - + +
58A MSE 1.3 57.3 + - - +
60A ASP* 3.3 10.9 + - - +
61A LYS* 3.0 44.0 + - - +
275A LYS* 2.9 35.1 + - - -
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Residues in contact with MSE 58 (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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54A GLY 3.1 17.0 + - - +
55A ALA 3.8 3.4 - - - +
57A GLU* 1.3 73.1 - - - +
59A GLY* 1.3 66.5 + - - +
61A LYS* 3.1 16.9 + - + +
62A LEU* 3.0 51.0 + - + +
279A ALA* 3.4 42.6 - - + +
282A THR* 3.8 6.7 - - + -
283A TYR* 4.0 7.6 - - + +
303A VAL* 3.8 29.2 - - + -
304A LYS 4.9 4.7 - - - +
306A ILE* 4.8 2.2 - - + -
405A EDO 4.2 20.6 - - - +
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Residues in contact with GLY 59 (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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55A ALA 3.0 15.7 + - - -
56A LYS* 3.1 4.5 + - - -
58A MSE 1.3 75.9 - - - +
60A ASP* 1.3 55.9 + - - +
62A LEU 3.1 1.2 + - - -
63A GLY 2.9 25.1 + - - -
64A VAL* 2.9 41.4 + - - -
66A VAL* 3.8 4.7 - - - -
282A THR* 3.6 5.7 - - - +
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Residues in contact with ASP 60 (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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56A LYS* 2.9 44.5 + - - +
57A GLU* 3.6 11.1 - - - +
59A GLY* 1.3 75.5 - - - +
61A LYS* 1.3 62.4 + - + +
62A LEU 3.3 0.5 + - - -
63A GLY* 3.4 10.9 + - - +
64A VAL 4.8 3.2 - - - +
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Residues in contact with LYS 61 (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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57A GLU* 3.0 28.3 + - - +
58A MSE 3.1 23.2 + - + +
60A ASP* 1.3 76.5 - - + +
62A LEU* 1.3 60.2 + - - +
63A GLY 3.5 0.2 - - - -
304A LYS 5.9 0.8 + - - -
405A EDO 3.9 32.7 + - - +
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Residues in contact with LEU 62 (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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31A ALA* 4.0 9.0 - - - +
58A MSE 3.0 40.4 + - + +
59A GLY 3.1 2.9 + - - +
61A LYS* 1.3 77.2 - - - +
63A GLY* 1.3 62.3 + - - +
64A VAL* 3.5 14.4 + - + +
282A THR* 4.5 4.7 - - + -
283A TYR* 4.2 19.7 - - + -
286A ASN* 3.8 41.0 - - + +
405A EDO 4.0 24.9 - - - +
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Residues in contact with GLY 63 (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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31A ALA* 3.4 24.5 - - - +
32A ASP* 4.2 3.5 + - - -
59A GLY 2.9 4.3 + - - -
60A ASP* 3.4 10.8 + - - -
61A LYS 3.5 0.6 - - - -
62A LEU* 1.3 80.0 - - - +
64A VAL* 1.3 59.0 + - - +
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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
------------------------------------------------------------
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