Contacts of the helix formed by residues 28 - 50 (chain A) in PDB entry 4HE2
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 GLY 28 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLY* 3.1 6.6 + - - -
27A THR* 1.3 79.9 - - - +
29A GLU* 1.3 57.5 + - - +
30A LEU 3.5 2.0 - - - -
31A THR* 3.4 15.1 + - - -
32A ARG* 2.9 43.6 + - - +
401A AMP 3.5 2.3 + - - -
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Residues in contact with GLU 29 (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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27A THR* 3.4 12.4 + - - +
28A GLY* 1.3 77.7 - - - +
30A LEU* 1.3 61.5 + - - +
32A ARG* 3.4 17.5 + - - +
33A LEU 3.1 9.9 + - - -
89A TYR 4.4 2.5 - - - -
90A SER* 2.8 41.8 + - - +
111A GLY* 3.1 12.7 - - - -
112A LYS* 2.7 59.5 + - - +
113A TYR* 3.9 3.6 - - + -
401A AMP 2.9 12.6 + - - +
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Residues in contact with LEU 30 (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 GLU* 1.3 70.0 - - - +
31A THR* 1.3 60.5 + - - +
33A LEU* 3.1 8.8 + - + +
34A LEU* 2.8 51.9 + - + +
113A TYR* 3.8 22.8 - - + +
138A ILE* 4.0 31.2 - - + -
160A VAL* 3.7 15.0 - - + +
161A ALA* 4.7 6.3 - - + -
177A THR* 5.0 0.7 - - + -
401A AMP 2.8 65.6 + - + +
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Residues in contact with THR 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 4.2 11.0 - - + +
18A MET* 3.8 36.7 - - + -
21A GLY* 3.7 9.5 - - - -
28A GLY* 3.4 17.7 + - - +
29A GLU 3.3 0.4 - - - -
30A LEU* 1.3 78.5 - - - +
32A ARG* 1.3 59.2 + - + +
34A LEU* 3.4 1.6 + - - +
35A ASN* 3.0 30.9 + - + +
401A AMP 2.9 32.8 + - - -
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Residues in contact with ARG 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A THR 4.7 4.0 + - - -
28A GLY* 2.9 30.6 + - - +
29A GLU* 3.7 14.9 - - - +
31A THR* 1.3 78.1 - - + +
33A LEU* 1.3 62.4 + - - +
35A ASN* 3.5 7.3 + - - +
36A SER* 3.0 27.9 + - - -
88A SER* 3.0 21.9 + - - +
89A TYR* 3.5 20.9 + - - +
90A SER* 3.5 16.3 + - - +
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLU 3.1 13.9 + - - +
30A LEU* 3.1 11.0 + - + +
32A ARG* 1.3 77.2 - - - +
34A LEU* 1.3 58.9 + - - +
36A SER* 3.1 4.4 + - - -
37A MET* 2.9 28.3 + - + +
85A LEU* 4.1 13.2 - - + +
88A SER* 4.3 9.4 - - - +
90A SER* 3.8 9.6 + - - +
91A THR* 4.0 11.4 - - + -
113A TYR* 3.4 37.5 - - + -
115A VAL* 3.8 21.8 - - + -
138A ILE* 3.4 36.6 - - + -
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 3.8 28.3 - - + -
30A LEU* 2.8 39.2 + - + +
31A THR 3.8 3.4 - - - +
33A LEU* 1.3 72.8 - - - +
35A ASN* 1.3 58.5 + - - +
37A MET* 3.3 5.6 + - + +
38A LEU* 2.9 42.7 + - + +
136A PHE* 4.5 6.1 - - + -
138A ILE* 3.7 26.5 - - + -
161A ALA* 4.4 3.8 - - + -
175A LEU* 4.2 25.8 - - + -
177A THR* 4.3 18.4 - - + -
401A AMP 4.2 8.5 - - - +
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Residues in contact with ASN 35 (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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14A THR* 3.8 29.7 + - + +
17A VAL* 5.0 3.4 - - + +
18A MET* 5.8 4.9 - - + -
31A THR* 3.0 19.8 + - + +
32A ARG* 3.8 7.0 + - - +
34A LEU* 1.3 77.6 - - - +
36A SER* 1.3 57.2 + - - +
38A LEU* 3.3 8.5 + - - +
39A THR* 2.8 48.2 + - - -
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Residues in contact with SER 36 (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 ARG* 3.0 18.1 + - - +
33A LEU 3.1 4.7 + - - -
35A ASN* 1.3 77.2 + - - +
37A MET* 1.3 65.6 + - - +
39A THR* 3.3 6.6 + - - -
40A ALA 3.1 17.5 + - - -
84A MET* 3.4 42.4 + - - +
85A LEU* 4.5 2.5 - - - -
87A SER* 5.3 0.2 + - - -
88A SER* 3.4 19.0 - - - -
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Residues in contact with MET 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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33A LEU* 2.9 17.4 + - + +
34A LEU* 3.6 11.7 - - + +
36A SER* 1.3 76.8 - - - +
38A LEU* 1.3 56.8 + - + +
40A ALA* 3.2 7.7 + - - +
41A ILE* 3.0 34.9 + - + +
81A VAL* 4.0 34.5 - - + -
85A LEU* 4.0 20.0 - - + +
115A VAL* 4.9 3.8 - - - -
117A PHE* 4.8 3.1 - - + -
134A THR* 3.7 30.3 - - + -
136A PHE* 4.0 48.2 - - + -
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Residues in contact with LEU 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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13A LEU* 3.5 46.7 - - + -
14A THR* 5.7 2.9 - - - +
17A VAL* 4.2 12.8 - - + -
34A LEU* 2.9 31.1 + - + +
35A ASN* 3.9 7.9 - - - +
36A SER 3.3 0.2 - - - -
37A MET* 1.3 72.4 - - + +
39A THR* 1.3 60.7 + - - +
41A ILE* 3.3 15.9 + - + +
42A LYS* 3.0 33.2 + - - +
136A PHE* 5.2 8.3 - - + -
173A VAL* 4.1 26.9 - - + -
175A LEU* 5.1 5.8 - - + -
193A PHE* 4.6 4.3 - - + -
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Residues in contact with THR 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ASN* 2.8 35.6 + - - -
36A SER* 3.6 7.9 - - - -
38A LEU* 1.3 74.5 - - - +
40A ALA* 1.3 65.6 + - - +
42A LYS* 3.2 17.4 + - - +
43A ALA* 3.1 22.4 + - + +
84A MET* 4.4 16.6 - - - -
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Residues in contact with ALA 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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36A SER 3.1 12.6 + - - +
37A MET* 3.2 11.4 + - + +
39A THR* 1.3 74.8 - - - +
41A ILE* 1.3 59.3 + - - +
43A ALA* 3.1 8.7 + - - +
44A ILE* 2.9 33.6 + - - +
80A LEU* 4.2 5.8 - - + +
81A VAL* 3.9 35.2 - - + +
84A MET* 3.9 19.0 - - + +
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Residues in contact with ILE 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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37A MET* 3.0 33.8 + - + +
38A LEU* 3.5 22.4 - - + +
39A THR 3.2 0.2 - - - -
40A ALA* 1.3 75.3 - - - +
42A LYS* 1.3 57.9 + - - +
44A ILE* 3.3 1.7 + - + -
45A SER* 2.8 28.1 + - - -
134A THR* 4.3 6.5 - - + -
136A PHE* 4.0 26.9 - - + -
165A ALA* 3.5 31.4 - - + -
167A TYR* 3.7 20.5 + - + +
171A THR* 5.2 0.2 - - + -
173A VAL* 4.2 3.6 - - + -
193A PHE* 3.9 24.9 - - + -
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Residues in contact with LYS 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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14A THR* 5.9 0.8 + - - -
38A LEU 3.0 15.4 + - - +
39A THR* 3.2 19.0 + - + +
41A ILE* 1.3 75.1 - - - +
43A ALA* 1.3 61.7 + - - +
45A SER* 3.4 8.0 + - - -
46A SER* 3.1 22.7 + - - -
186A LEU* 4.0 20.1 - - + +
191A GLY 2.8 30.4 + - - +
192A GLU* 4.2 11.4 - - - +
193A PHE* 3.6 26.0 - - + -
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Residues in contact with ALA 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 THR* 3.1 13.8 + - + +
40A ALA* 3.5 8.3 - - - +
42A LYS* 1.3 74.5 - - - +
44A ILE* 1.3 64.8 + - - +
46A SER* 3.3 8.1 + - - -
47A ALA* 3.1 21.7 + - - +
80A LEU* 3.9 29.7 - - + +
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Residues in contact with ILE 44 (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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40A ALA* 2.9 23.8 + - + +
41A ILE* 3.7 1.8 - - + +
43A ALA* 1.3 76.0 - - - +
45A SER* 1.3 62.7 + - - +
47A ALA* 3.1 7.0 + - - +
48A VAL* 2.8 31.5 + - + +
73A LEU* 5.6 1.3 - - + -
77A SER* 3.7 39.9 - - - +
80A LEU* 3.9 14.1 - - + -
81A VAL* 4.0 22.7 - - + -
119A PRO 3.9 2.2 - - - +
120A LEU* 4.2 4.3 - - + -
134A THR* 3.9 15.3 - - + +
167A TYR* 3.5 32.3 - - + +
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Residues in contact with SER 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 ILE 2.8 17.3 + - - -
42A LYS* 3.6 7.4 - - - -
43A ALA 3.3 0.2 - - - -
44A ILE* 1.3 75.3 - - - +
46A SER* 1.3 57.6 + - - +
48A VAL* 3.3 4.1 + - - +
49A ARG* 2.9 40.1 + - - +
167A TYR* 3.7 22.8 - - - +
171A THR* 3.1 29.9 + - - +
186A LEU* 3.9 14.0 - - - +
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Residues in contact with SER 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 LYS 3.1 10.5 + - - -
43A ALA* 3.6 10.5 - - - -
44A ILE 3.2 0.2 - - - -
45A SER* 1.3 79.2 - - - +
47A ALA* 1.3 62.5 + - - +
49A ARG* 3.4 10.7 + - - +
50A LYS* 3.3 40.7 + - - +
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Residues in contact with ALA 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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43A ALA 3.1 11.8 + - - +
44A ILE* 3.1 11.0 + - - +
46A SER* 1.3 73.9 - - - +
48A VAL* 1.3 60.5 + - - +
50A LYS* 3.2 9.1 + - - +
51A ALA* 2.8 32.3 + - - +
54A ALA* 5.5 1.1 - - - +
73A LEU* 4.2 8.9 - - + +
76A LEU* 3.8 29.6 - - + -
80A LEU* 5.8 0.2 - - + -
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Residues in contact with VAL 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 ILE* 2.8 34.9 + - + +
45A SER* 3.7 6.5 - - - +
47A ALA* 1.3 75.8 - - - +
49A ARG* 1.3 65.1 + - + +
50A LYS 3.1 1.0 + - - -
51A ALA* 3.3 18.8 + - - +
73A LEU* 4.1 14.6 - - + -
120A LEU* 4.3 4.3 - - + -
129A LEU* 5.9 2.8 - - - +
132A ILE* 3.8 33.2 - - + -
167A TYR* 4.1 21.3 - - + +
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Residues in contact with ARG 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A SER* 2.9 27.1 + - - +
46A SER* 3.9 8.0 - - - +
47A ALA 3.3 0.2 - - - -
48A VAL* 1.3 80.0 - - + +
50A LYS* 1.3 58.7 + - - +
53A LEU* 5.6 0.9 - - - +
167A TYR* 6.6 0.2 - - + -
168A GLY 5.6 1.6 + - - -
169A SER 5.4 2.0 + - - -
170A ALA* 4.9 6.1 - - - +
171A THR* 3.3 25.4 + - - +
186A LEU* 3.5 28.9 + - - +
188A PRO* 4.3 26.4 - - - +
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Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A SER* 3.3 31.6 + - - +
47A ALA* 3.2 6.9 + - - +
48A VAL 3.1 0.6 - - - -
49A ARG* 1.3 80.5 - - - +
51A ALA* 1.3 56.0 + - - +
52A GLY 3.5 2.5 - - - -
53A LEU* 3.3 23.4 + - + +
54A ALA* 3.0 35.3 + - + +
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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
------------------------------------------------------------
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