Contacts of the helix formed by residues 12 - 30 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B HIS* 2.9 29.0 + - - +
10B ALA 3.5 0.2 + - - -
11B GLY* 1.3 83.6 - - - +
13B HIS* 1.3 73.5 + - + +
14B ALA* 3.4 7.5 + - - +
15B ASP* 3.1 23.6 + - - +
16B VAL* 3.0 17.2 + - - +
60B GLU* 2.7 48.4 + - + +
64B GLY* 4.0 2.9 - - - -
235B MET* 4.0 20.8 - - - +
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Residues in contact with HIS 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ASN* 1.3 82.4 - - + +
14B ALA* 1.3 68.3 + - + +
16B VAL* 3.4 8.7 + - - +
17B LEU* 3.1 26.7 + - - +
60B GLU* 5.6 1.8 + - - -
63B GLU* 4.6 12.0 + - + +
64B GLY* 4.0 7.5 - - - +
224B LEU* 4.6 11.2 + - + +
226B VAL* 3.7 40.8 - - + +
235B MET* 3.6 37.9 + - + +
237B ALA* 4.4 22.2 - - - -
238B SER* 4.5 1.4 + - - -
264B LEU* 4.2 21.7 - - + +
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Residues in contact with ALA 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ASN* 3.1 10.4 + - - +
13B HIS* 1.3 81.7 + - - +
15B ASP* 1.3 61.9 + - - +
17B LEU* 3.4 2.5 + - - +
18B LYS* 2.9 30.7 + - - +
195B TRP* 3.6 27.7 + - + -
235B MET* 3.9 15.0 - - + -
238B SER* 3.4 26.5 - - - +
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Residues in contact with ASP 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B HIS 4.7 0.6 - - - -
10B ALA* 3.4 10.3 - - - +
11B GLY* 2.9 30.1 + - - +
12B ASN* 3.1 20.9 + - - +
14B ALA* 1.3 77.0 - - - +
16B VAL* 1.3 58.6 + - - +
18B LYS* 3.0 29.6 + - - +
19B HIS* 2.8 40.0 + - - +
48B TYR* 5.9 1.0 - - - -
97B TYR* 3.6 22.4 - - - +
195B TRP* 6.1 0.3 - - - -
1281B SAM 6.2 0.2 - - - -
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Residues in contact with VAL 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLY 4.0 1.8 - - - +
12B ASN 3.0 16.8 + - - +
13B HIS* 3.5 9.4 - - - +
15B ASP* 1.3 76.3 - - - +
17B LEU* 1.3 58.6 + - - +
20B THR* 2.8 38.3 + - - +
64B GLY* 3.8 6.3 - - - -
65B ILE* 3.5 31.0 - - + +
68B ILE* 3.6 24.7 - - + -
81B TYR* 3.6 19.6 - - + +
97B TYR* 5.0 0.2 - - - +
260B LEU* 3.7 20.4 - - + -
264B LEU* 4.1 9.4 - - + -
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Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B HIS 3.1 12.4 + - - +
14B ALA 3.8 6.7 - - - +
15B ASP 3.3 0.2 - - - -
16B VAL* 1.3 78.0 - - - +
18B LYS* 1.3 65.7 + - - +
20B THR* 3.3 3.7 + - - -
21B VAL* 3.0 26.1 + - + +
195B TRP* 5.7 0.7 - - - +
222B ILE* 4.1 24.9 - - + +
224B LEU* 3.9 27.4 - - + +
238B SER* 3.4 31.0 - - - +
239B GLY* 3.9 16.8 - - - -
240B MET* 4.5 7.0 - - + +
253B MET* 4.1 9.6 - - + -
257B LEU* 4.1 18.6 - - + -
260B LEU* 4.9 5.6 - - + -
264B LEU* 6.2 0.2 - - - -
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Residues in contact with LYS 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ALA 2.9 16.8 + - - +
15B ASP* 3.0 27.1 + - - +
17B LEU* 1.3 79.0 - - - +
19B HIS* 1.3 72.9 + - + +
21B VAL* 3.4 2.4 + - - +
22B GLN* 2.9 27.8 + - - +
162B LEU* 4.6 11.2 - - + -
164B ASP* 2.6 40.6 + - + +
195B TRP* 3.9 22.7 - - + -
240B MET* 3.9 29.3 - - + +
1281B SAM 3.1 28.3 + - - +
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Residues in contact with HIS 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASP* 2.8 19.9 + - - +
18B LYS* 1.3 90.5 - - + +
20B THR* 1.3 60.0 + - - +
22B GLN* 3.2 24.1 - - - +
23B SER* 2.9 31.7 + - - -
81B TYR* 3.6 25.2 - - + -
97B TYR* 2.6 42.0 + + - -
98B PRO 3.6 11.5 + - - -
99B GLY* 4.1 1.8 - - - -
100B SER* 3.3 12.3 + - - -
103B ILE* 4.2 10.6 - - + +
1281B SAM 3.3 22.3 + - - -
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Residues in contact with THR 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B VAL* 2.8 29.6 + - - +
17B LEU* 3.6 6.1 - - - -
19B HIS* 1.3 75.8 - - - +
21B VAL* 1.3 62.5 + - - +
23B SER* 2.7 21.8 + - - -
24B LEU* 3.1 26.5 + - + +
77B GLU 4.9 0.4 - - - +
78B LEU* 3.4 33.6 - - + +
81B TYR* 3.6 14.0 - - - -
253B MET* 4.4 15.5 - - + -
256B VAL* 4.9 2.0 - - + -
260B LEU* 4.3 7.4 - - + +
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Residues in contact with VAL 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 3.0 22.8 + - + +
18B LYS 3.8 3.1 - - - +
20B THR* 1.3 74.8 - - - +
22B GLN* 1.3 64.7 + - - +
24B LEU* 3.3 7.5 + - - +
25B ILE* 3.1 41.1 + - + +
222B ILE* 4.0 11.2 - - + -
240B MET* 4.0 21.8 - - + -
242B VAL* 4.2 18.2 - - + -
249B LEU* 4.2 9.9 - - + -
253B MET* 3.9 29.6 - - + -
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Residues in contact with GLN 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LYS 2.9 20.1 + - - +
19B HIS* 3.2 29.6 - - - +
21B VAL* 1.3 75.7 - - - +
23B SER* 1.3 62.4 + - - +
25B ILE* 3.3 5.5 + - - +
26B ILE* 3.1 33.5 + - + +
38B TYR* 3.2 25.6 + - + -
100B SER* 3.0 33.0 + - - -
103B ILE* 3.8 11.1 - - - +
104B ALA 3.8 10.9 - - - +
160B LEU* 4.2 14.1 - - + +
162B LEU* 4.5 13.9 - - + +
193B ALA* 6.0 1.3 - - - -
240B MET* 4.8 1.7 - - - +
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Residues in contact with SER 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B HIS 2.9 14.6 + - - -
20B THR* 2.7 20.6 + - - -
22B GLN* 1.3 76.1 - - - +
24B LEU* 1.3 61.0 + - - +
26B ILE* 3.4 3.0 - - - +
27B GLU* 3.0 35.3 - - - -
77B GLU 4.9 3.5 + - - -
80B ALA* 4.9 3.4 - - - -
81B TYR* 3.5 28.3 + - - +
103B ILE* 4.4 3.6 - - - +
107B LEU* 3.7 26.4 - - - +
1291B EDO 5.4 1.1 + - - -
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Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B THR* 3.1 26.2 + - + +
21B VAL 3.9 3.4 - - - +
22B GLN 3.3 0.2 - - - -
23B SER* 1.3 81.5 + - - +
25B ILE* 1.3 62.1 + - - +
27B GLU* 3.4 6.9 + - + +
28B SER* 3.0 25.1 + - - -
77B GLU* 3.4 36.3 - - + +
246B PRO* 5.7 0.2 - - - -
249B LEU* 4.0 9.6 - - + -
252B GLN* 3.7 42.0 + - + +
253B MET* 3.8 28.7 - - - -
256B VAL* 5.1 1.1 - - + -
1291B EDO 4.0 12.1 - - - +
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Residues in contact with ILE 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B VAL* 3.1 35.1 + - + +
22B GLN* 3.8 4.0 - - - +
24B LEU* 1.3 73.1 - - - +
26B ILE* 1.3 68.1 + - - +
28B SER* 3.1 4.5 + - - -
29B LEU* 3.0 25.9 + - + +
160B LEU* 3.9 35.9 - - + -
191B ILE* 4.1 24.5 - - + -
193B ALA* 4.1 7.6 - - + -
242B VAL* 4.0 23.6 - - + -
246B PRO* 4.1 13.7 - - + -
249B LEU* 4.0 16.4 - - + -
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Residues in contact with ILE 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B GLN* 3.1 37.6 + - + +
23B SER 3.7 4.3 - - - -
25B ILE* 1.3 76.9 - - - +
27B GLU* 1.3 63.8 - - - +
29B LEU* 3.1 10.6 + - - +
30B LYS* 3.0 40.5 + - + +
36B PHE* 4.2 7.6 - - + -
38B TYR* 4.6 2.9 - - + -
104B ALA* 4.0 20.4 - - + +
107B LEU* 3.8 26.7 - - + -
108B LEU* 3.8 28.5 - - + -
160B LEU* 3.8 15.7 - - + -
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B SER 3.0 20.9 - - - -
24B LEU* 3.7 7.4 - - + +
25B ILE 3.3 0.2 - - - -
26B ILE* 1.3 76.2 - - - +
28B SER* 1.3 61.4 + - - +
30B LYS* 2.9 45.6 + - - +
31B GLU* 3.5 17.7 + - - +
80B ALA* 4.1 15.4 - - + +
107B LEU* 3.8 17.5 - - + +
252B GLN* 6.2 1.3 - - - +
1291B EDO 4.0 27.4 + - - +
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Residues in contact with SER 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU 3.0 13.6 + - - -
25B ILE 3.5 7.6 - - - -
27B GLU* 1.3 74.8 - - - +
29B LEU* 1.3 65.0 + - - +
31B GLU* 3.1 31.9 + - - +
32B LYS 4.5 0.9 + - - -
158B ARG* 5.0 1.4 + - - -
246B PRO* 3.5 33.4 - - - +
248B LYS* 4.2 23.4 - - - +
252B GLN* 4.6 5.7 + - - -
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ILE* 3.0 22.5 + - + +
26B ILE* 3.5 8.7 - - - +
28B SER* 1.3 76.0 - - - +
30B LYS* 1.3 60.7 + - - +
31B GLU 3.1 1.5 + - - -
32B LYS 3.6 3.3 + - - +
36B PHE* 3.6 40.7 - - + -
158B ARG* 3.1 53.0 + - + +
159B GLY 4.2 12.6 - - - +
160B LEU* 3.8 28.3 - - + +
191B ILE* 4.0 21.5 - - + -
246B PRO* 5.6 0.2 - - + -
1288B EDO 5.4 2.9 - - - -
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Residues in contact with LYS 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ILE* 3.0 28.6 + - + +
27B GLU* 2.9 34.4 + - - +
28B SER 3.1 0.6 - - - -
29B LEU* 1.3 77.6 - - - +
31B GLU* 1.3 59.5 + - - +
32B LYS 3.2 2.0 - - - +
36B PHE* 3.8 11.0 - - + -
107B LEU* 2.8 32.6 + - - +
109B ARG* 3.3 52.5 + - + +
112B ASP* 4.5 0.2 - - - +
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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