Contacts of the helix formed by residues 13 - 27 (chain B) in PDB entry 1VLP
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 ASP 13 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B THR* 1.3 82.2 + - - +
14B MSE 1.3 66.3 + - - +
15B TYR* 3.4 29.4 - - + -
16B LYS* 2.9 20.6 + - - +
17B ILE 4.0 0.5 + - - -
133B ILE* 2.9 31.5 - - + +
177B PHE* 4.1 8.7 - - - +
179B THR* 3.6 17.7 + - - -
180B ARG* 3.6 12.9 + - - +
214B SER* 2.4 33.3 + - - +
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Residues in contact with MSE 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B THR 3.7 0.8 + - - -
13B ASP* 1.3 71.4 - - - +
15B TYR* 1.3 63.8 + - - +
17B ILE* 3.0 14.7 + - - +
18B THR* 3.2 23.2 + - + -
76B GLU 5.3 2.9 - - - +
77B ILE* 4.0 28.9 - - + -
79B TYR* 3.2 27.4 - - - +
214B SER* 2.7 16.4 + - - +
216B ILE* 3.7 19.7 - - + +
225B LYS* 6.5 0.7 - - - -
226B PRO* 3.3 36.6 - - + +
227B ILE 3.6 15.3 - - - +
228B GLY* 3.9 23.1 - - - +
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Residues in contact with TYR 15 (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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13B ASP* 3.1 41.0 + - + -
14B MSE 1.3 80.1 - - - +
16B LYS* 1.3 74.8 + - + +
18B THR* 3.2 9.1 + - - -
19B MSE 2.9 39.9 + - + +
132B GLU* 3.1 18.9 + - - -
133B ILE* 3.3 16.1 - - + +
177B PHE* 4.6 12.1 - + - -
180B ARG* 3.4 24.7 + - - -
214B SER* 5.9 0.7 - - - -
227B ILE 4.8 0.2 + - - -
228B GLY* 4.3 5.3 - - - -
229B THR 3.0 29.8 - - - +
231B ALA* 3.4 31.4 - - + -
233B GLU* 3.9 5.4 - - - -
294B ARG* 6.2 1.8 - - - -
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Residues in contact with LYS 16 (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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12B THR* 3.6 12.1 - - + +
13B ASP 2.9 12.4 + - - +
15B TYR* 1.3 88.5 - - + +
17B ILE* 1.3 57.2 + - - +
19B MSE 3.8 1.9 - - - +
20B HIS* 2.9 28.9 + - - +
34B TYR* 4.5 2.6 + - - -
129B ILE* 2.9 38.7 + - - +
130B LEU* 3.6 19.2 - - + +
132B GLU* 2.8 26.4 + - + +
133B ILE* 3.3 39.9 - - + +
233B GLU* 2.7 34.0 + - - -
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Residues in contact with ILE 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU 4.6 8.7 - - - +
10B LEU* 5.6 0.2 - - + -
12B THR* 4.4 6.1 - - + -
14B MSE 3.0 7.5 + - - +
16B LYS* 1.3 75.6 - - - +
18B THR* 1.3 59.5 + - - +
20B HIS* 3.3 4.1 + - - +
21B ALA* 2.9 27.7 + - - +
65B PHE* 4.2 23.1 - - + -
73B LEU* 4.1 21.3 - - + -
77B ILE* 4.6 4.7 - - + -
80B LEU* 4.3 11.4 - - + +
84B TYR* 3.7 28.4 + - + +
130B LEU* 3.9 21.3 - - + -
216B ILE* 3.5 27.8 - - + -
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Residues in contact with THR 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B MSE 3.2 34.8 + - + +
15B TYR* 3.2 23.2 + - - +
17B ILE* 1.3 75.3 - - - +
19B MSE 1.3 57.6 + - - +
21B ALA* 3.1 4.1 + - - +
22B ALA* 2.9 23.4 + - - +
77B ILE* 4.2 18.4 - - + -
79B TYR* 4.5 9.9 - - + +
80B LEU* 4.6 5.4 - - + -
228B GLY 5.6 1.1 - - - -
229B THR 4.5 3.6 + - - -
256B TRP* 4.0 21.6 - - + -
260B PHE* 3.3 17.8 - - + -
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Residues in contact with MSE 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TYR* 2.9 22.4 + - + +
16B LYS* 3.8 4.5 - - - +
18B THR* 1.3 73.1 - - - +
20B HIS* 1.3 56.0 + - - +
22B ALA* 3.1 4.6 + - - +
23B VAL* 2.7 43.0 + - + +
125B TRP* 5.7 0.4 - - - -
129B ILE* 4.1 13.9 - - + -
230B VAL* 5.2 0.4 - - - -
231B ALA* 3.1 44.9 - - + +
233B GLU* 3.3 25.4 - - + -
234B TRP* 3.7 37.5 - - - -
256B TRP* 4.1 14.1 - - + -
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Residues in contact with HIS 20 (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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16B LYS 2.9 19.8 + - - +
17B ILE 3.4 6.7 - - - +
19B MSE 1.3 76.1 - - - +
21B ALA* 1.3 56.4 + - - +
23B VAL* 3.7 1.1 - - - -
24B PHE* 2.8 33.1 + - - +
84B TYR* 2.8 21.5 + + - +
87B TYR* 3.1 29.9 + + - -
88B ILE* 3.9 6.9 - - + +
93B TYR* 3.5 22.9 + - - -
126B LYS* 3.0 33.7 + - + -
129B ILE* 3.4 22.5 - - + +
130B LEU* 4.0 15.8 - - + +
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ILE 2.9 13.5 + - - +
18B THR 3.1 8.9 + - - +
20B HIS* 1.3 75.8 - - - +
22B ALA* 1.3 57.2 + - - +
24B PHE* 3.8 0.7 - - - +
25B THR* 2.8 35.8 + - - -
80B LEU* 3.8 22.2 - - + -
81B PRO* 4.1 6.7 - - + -
84B TYR* 3.6 26.3 - - + -
259B THR* 4.6 0.7 - - - -
260B PHE* 4.0 10.8 - - + -
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Residues in contact with ALA 22 (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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18B THR 2.9 15.2 + - - +
19B MSE 3.7 2.7 - - - +
21B ALA* 1.3 76.1 - - - +
23B VAL* 1.3 58.5 + - - +
26B ASN* 2.9 42.6 + - - +
234B TRP* 3.6 25.5 - - + -
256B TRP* 3.7 23.3 - - + -
259B THR* 4.0 7.6 - - + +
260B PHE* 4.0 7.4 - - + -
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B MSE 2.7 24.2 + - + +
20B HIS* 3.8 4.3 - - - +
22B ALA* 1.3 74.5 - - - +
24B PHE* 1.3 60.0 + - - +
27B PHE* 2.8 42.7 + - - +
125B TRP* 3.6 53.4 - - + +
126B LYS* 3.5 32.1 - - + +
129B ILE* 4.9 4.7 - - + -
234B TRP* 3.9 15.9 - - + -
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Residues in contact with PHE 24 (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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20B HIS 2.8 22.7 + - - +
21B ALA 3.8 1.3 - - - +
23B VAL* 1.3 74.0 - - - +
25B THR* 1.3 70.9 + - - +
28B PRO* 3.8 20.0 - - + +
83B ALA* 3.5 35.4 - - + -
84B TYR* 3.7 22.4 - - + -
87B TYR* 3.4 54.3 - + + -
126B LYS* 4.1 24.6 - - + +
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Residues in contact with THR 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 ALA* 2.8 22.2 + - - -
22B ALA 3.9 3.1 - - - -
24B PHE* 1.3 89.2 - - - +
26B ASN* 1.3 61.4 + - - +
28B PRO* 4.6 2.5 - - - +
81B PRO* 3.8 22.5 - - + +
83B ALA* 6.1 0.3 - - - +
84B TYR* 5.1 0.3 - - - +
259B THR* 3.9 26.0 - - + +
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Residues in contact with ASN 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 ALA 2.9 26.8 + - - +
25B THR* 1.3 83.7 - - - +
27B PHE* 1.3 90.9 + - + +
28B PRO* 3.4 9.8 - - - +
234B TRP* 3.9 6.1 - - - -
255B CYS* 3.9 25.9 + - - +
258B ASN* 5.6 2.4 - - - +
259B THR* 2.7 30.2 + - - -
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Residues in contact with PHE 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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22B ALA 4.7 0.7 - - - -
23B VAL* 2.8 26.4 + - - +
26B ASN* 1.3 92.6 - - + +
28B PRO* 1.4 62.9 - - - +
29B ASP 3.3 3.7 + - - -
30B VAL* 3.4 29.6 + - + +
125B TRP* 3.8 27.5 - + + +
126B LYS 5.1 0.3 + - - -
234B TRP* 3.5 29.2 - + - -
238B VAL* 3.8 26.5 - - + -
241B ILE* 3.6 26.9 - - + -
255B CYS* 4.2 13.5 - - - -
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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
------------------------------------------------------------
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