Contacts of the helix formed by residues 12 - 30 (chain A) in PDB entry 4BLV
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 ASN 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A HIS* 2.9 19.4 + - - +
10A ALA 3.2 1.2 + - - -
11A GLY* 1.3 83.1 - - - +
13A HIS* 1.3 70.9 + - + +
14A ALA 3.2 2.8 + - - -
15A ASP* 3.0 11.1 + - - +
16A VAL* 3.0 17.7 + - - +
60A GLU* 2.8 51.5 + - + +
64A GLY* 3.9 2.2 - - - -
235A MET* 4.1 7.7 - - - +
1284A EDO 4.8 1.0 - - - -
1285A EDO 5.4 0.4 - - - +
1287A EDO 2.6 47.0 + - - -
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Residues in contact with HIS 13 (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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12A ASN* 1.3 76.5 - - + +
14A ALA* 1.3 72.7 + - + +
16A VAL* 3.4 6.7 + - - +
17A LEU* 3.0 27.0 + - - +
60A GLU 4.9 0.4 + - - -
63A GLU 4.5 10.0 + - - +
64A GLY* 3.9 11.3 - - - +
224A LEU* 4.5 11.5 + - + +
226A VAL* 3.6 29.0 - - + +
235A MET* 3.7 15.4 - - + +
237A ALA* 4.3 24.9 - - - -
238A SER* 4.3 2.5 + - - -
264A LEU* 4.2 20.2 - - + +
1284A EDO 3.0 39.6 + - - -
1285A EDO 3.4 16.4 - - - -
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Residues in contact with ALA 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ASN* 3.1 1.4 + - - +
13A HIS* 1.3 81.5 - - - +
15A ASP* 1.3 61.3 + - - +
17A LEU* 3.4 3.7 + - - +
18A LYS* 2.9 30.5 + - - +
195A TRP* 3.7 6.8 + - - +
235A MET* 3.9 7.2 - - + -
238A SER* 3.1 34.5 - - - +
1287A EDO 3.4 31.9 - - - -
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Residues in contact with ASP 15 (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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6A HIS* 2.9 20.1 + - - -
10A ALA* 3.4 1.2 - - - -
11A GLY* 2.8 28.9 + - - +
12A ASN* 3.0 14.4 + - - +
14A ALA* 1.3 72.3 - - - +
16A VAL* 1.3 61.3 + - - +
18A LYS* 2.9 25.5 + - - -
19A HIS* 2.8 44.8 + - - +
97A TYR* 3.5 18.3 - - - +
1287A EDO 2.7 22.4 + - - -
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Residues in contact with VAL 16 (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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11A GLY 4.1 1.6 - - - +
12A ASN 3.0 13.4 + - - +
13A HIS* 3.5 9.4 - - - +
15A ASP* 1.3 75.8 - - - +
17A LEU* 1.3 63.4 + - - +
20A THR* 2.8 33.5 + - - +
64A GLY* 3.8 5.8 - - - +
65A ILE* 3.4 36.3 - - + +
68A ILE* 3.7 24.5 - - + -
81A TYR* 3.5 20.1 - - - +
260A LEU* 3.8 18.8 - - + -
264A LEU* 4.2 10.8 - - + -
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Residues in contact with LEU 17 (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 HIS 3.0 13.9 + - - +
14A ALA* 3.7 8.3 - - - +
16A VAL* 1.3 78.3 - - - +
18A LYS* 1.3 63.4 + - - +
20A THR* 3.3 5.2 + - - -
21A VAL* 3.1 26.3 + - + +
195A TRP* 5.9 0.4 - - + -
222A ILE* 4.0 25.4 - - + +
223A GLU 4.5 0.4 - - - -
224A LEU* 3.9 25.1 - - + +
238A SER* 3.5 29.6 - - - +
239A GLY* 4.0 15.5 - - - -
240A MET* 4.4 6.3 - - + +
253A MET* 4.1 8.5 - - + -
257A LEU* 4.1 18.4 - - + -
260A LEU* 4.7 8.5 - - + -
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Residues in contact with LYS 18 (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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6A HIS* 4.2 10.5 - - - -
14A ALA 2.9 14.8 + - - +
15A ASP* 2.9 26.6 + - - +
17A LEU* 1.3 76.4 - - - +
19A HIS* 1.3 70.9 + - + +
21A VAL* 3.4 2.9 + - - +
22A GLN* 2.9 25.9 + - - +
100A SER* 4.0 3.1 - - - +
162A LEU* 4.7 7.6 - - + -
164A ASP* 2.7 42.8 + - - +
195A TRP* 3.8 26.0 - - + +
240A MET* 3.8 28.6 - - + +
1281A SAM 3.6 16.4 + - - +
1287A EDO 4.3 5.1 - - - -
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Residues in contact with HIS 19 (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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15A ASP* 2.8 31.8 + - - +
18A LYS* 1.3 79.7 - - + +
20A THR* 1.3 63.6 + - - +
22A GLN* 3.3 16.6 - - - +
23A SER* 3.0 26.0 + - - -
81A TYR* 3.5 23.6 - - + -
97A TYR* 2.6 40.4 + + - -
98A PRO 3.8 8.7 - - - -
100A SER* 2.8 33.2 + - - -
103A ILE* 3.4 14.4 - - + +
1281A SAM 2.9 16.2 + - - -
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Residues in contact with THR 20 (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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16A VAL* 2.8 26.8 + - - +
17A LEU* 3.5 7.0 - - - +
19A HIS* 1.3 75.2 - - - +
21A VAL* 1.3 62.7 + - - +
23A SER* 2.7 22.7 + - - +
24A LEU* 3.0 26.9 + - + +
68A ILE* 5.5 0.2 - - - +
77A GLU 5.2 0.2 - - - +
78A LEU* 3.5 33.1 - - + +
81A TYR* 3.8 14.0 - - - -
253A MET* 4.5 11.4 - - + -
256A VAL* 4.7 2.7 - - + -
260A LEU* 4.2 15.4 - - + +
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Residues in contact with VAL 21 (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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17A LEU* 3.1 18.7 + - + +
18A LYS 3.8 3.8 - - - +
20A THR* 1.3 72.0 - - - +
22A GLN* 1.3 64.9 + - - +
24A LEU* 3.3 7.9 + - - +
25A ILE* 2.9 44.2 + - + +
222A ILE* 3.9 22.7 - - + -
240A MET* 4.0 23.1 - - + -
242A VAL* 4.1 18.6 - - + -
249A LEU* 4.4 4.7 - - + -
253A MET* 4.1 20.9 - - + -
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Residues in contact with GLN 22 (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 LYS* 2.9 16.9 + - + +
19A HIS* 3.3 28.6 - - - +
20A THR 3.4 0.2 - - - -
21A VAL* 1.3 76.2 - - - +
23A SER* 1.3 58.5 + - - +
25A ILE* 3.3 4.1 + - - +
26A ILE* 2.9 44.3 + - + +
38A TYR* 3.1 27.4 + - + -
100A SER* 2.9 33.5 + - - +
103A ILE* 3.9 10.6 - - + +
104A ALA* 3.7 12.7 - - - +
160A LEU* 4.1 16.1 - - + +
162A LEU* 4.5 10.5 - - + +
240A MET* 4.8 2.3 - - - +
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Residues in contact with SER 23 (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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19A HIS 3.0 15.2 + - - -
20A THR* 2.7 21.7 + - - -
22A GLN* 1.3 78.2 - - - +
24A LEU* 1.3 61.3 + - - +
26A ILE* 3.3 1.6 - - - -
27A GLU* 2.9 35.6 - - - -
77A GLU 4.8 4.3 + - - -
80A ALA* 4.8 3.5 - - - +
81A TYR* 3.7 26.5 + - - +
103A ILE* 4.7 2.7 - - - +
107A LEU* 3.8 26.5 - - - +
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Residues in contact with LEU 24 (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 THR* 3.0 26.5 + - + +
21A VAL* 3.8 3.4 - - - +
23A SER* 1.3 81.8 + - - +
25A ILE* 1.3 62.8 + - - +
27A GLU* 3.4 9.1 + - + +
28A SER* 3.1 22.9 + - - -
77A GLU* 3.4 37.9 - - + +
246A PRO* 5.6 0.4 - - - -
249A LEU* 4.1 8.3 - - + -
252A GLN* 3.8 46.7 + - + +
253A MET* 3.9 28.7 - - - -
256A VAL* 5.1 1.6 - - + -
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Residues in contact with ILE 25 (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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21A VAL* 2.9 37.0 + - + +
22A GLN* 3.7 5.2 - - - +
24A LEU* 1.3 77.4 - - - +
26A ILE* 1.3 61.7 + - - +
28A SER* 3.2 4.7 + - - -
29A LEU* 3.0 24.9 + - + +
160A LEU* 3.8 32.1 - - + -
191A ILE* 3.9 28.0 - - + -
193A ALA* 4.4 5.2 - - + -
242A VAL* 3.9 26.0 - - + -
246A PRO* 4.0 20.8 - - + +
249A LEU* 4.2 8.3 - - + -
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Residues in contact with ILE 26 (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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22A GLN* 2.9 48.3 + - + +
23A SER* 3.7 4.9 - - - +
25A ILE* 1.3 75.1 - - - +
27A GLU* 1.3 63.3 + - - +
29A LEU* 3.1 10.3 + - - +
30A LYS* 3.1 31.3 + - + +
36A PHE* 4.2 7.9 - - + -
38A TYR* 4.4 3.6 - - + -
104A ALA* 4.0 12.1 - - + -
107A LEU* 3.8 26.2 - - + -
108A LEU* 3.7 34.5 - - + -
160A LEU* 3.8 15.9 - - + -
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Residues in contact with GLU 27 (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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23A SER 2.9 22.0 - - - -
24A LEU* 3.9 9.9 - - + +
25A ILE 3.3 0.2 - - - -
26A ILE* 1.3 74.4 - - - +
28A SER* 1.3 63.8 + - - +
30A LYS* 2.9 48.5 + - - +
31A GLU* 3.6 15.9 + - - +
80A ALA* 4.1 26.2 - - + +
107A LEU* 4.0 16.0 - - + +
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Residues in contact with SER 28 (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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24A LEU 3.1 14.8 + - - -
25A ILE 3.4 9.2 - - - -
27A GLU* 1.3 77.1 - - - +
29A LEU* 1.3 62.7 + - - +
31A GLU* 3.0 39.5 + - - +
32A LYS* 4.5 0.7 + - - +
158A ARG* 4.8 1.0 + - - -
246A PRO* 3.2 31.6 - - - +
247A TRP* 4.4 8.8 + - - -
248A LYS* 6.1 1.3 - - - +
252A GLN* 6.0 2.0 - - - -
1297A SO4 4.9 2.0 + - - -
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Residues in contact with LEU 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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25A ILE* 3.0 24.4 + - + +
26A ILE* 3.1 8.3 + - - +
28A SER* 1.3 75.8 - - - +
30A LYS* 1.3 58.9 + - - +
31A GLU 3.1 4.6 + - - -
32A LYS 3.4 2.9 + - - +
36A PHE* 3.8 30.2 - - + -
158A ARG* 2.9 39.7 + - - +
159A GLY 4.0 14.6 - - - +
160A LEU* 3.8 37.0 - - + +
191A ILE* 3.9 15.7 - - + -
1297A SO4 3.4 30.5 - - - +
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Residues in contact with LYS 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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26A ILE* 3.1 21.9 + - + +
27A GLU* 2.9 42.6 + - - +
28A SER 3.1 1.0 - - - -
29A LEU* 1.3 72.7 - - - +
31A GLU* 1.3 59.5 + - - +
32A LYS 3.1 8.3 + - - +
33A ASP* 5.2 1.7 - - - +
36A PHE* 3.8 17.3 - - + -
107A LEU* 2.8 30.3 + - - +
109A ARG* 3.5 44.4 + - + +
1282A GOL 3.3 21.5 + - - -
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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