Contacts of the helix formed by residues 13 - 27 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C THR* 1.3 83.3 + - - +
14C MSE 1.3 66.7 + - - +
15C TYR* 3.4 28.2 - - + -
16C LYS* 2.9 21.5 + - - +
17C ILE 3.9 0.3 + - - -
133C ILE* 3.0 32.8 - - + +
177C PHE* 4.1 8.1 - - - +
179C THR* 3.5 15.1 + - - -
180C ARG* 3.4 17.9 + - - +
214C SER* 2.7 33.0 + - - +
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Residues in contact with MSE 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C THR 3.7 0.4 + - - -
13C ASP* 1.3 70.5 - - - +
15C TYR* 1.4 57.3 + - - +
17C ILE* 2.9 20.8 + - - +
18C THR* 3.1 24.2 + - + -
76C GLU 5.8 1.3 - - - +
77C ILE* 4.1 26.0 - - + -
79C TYR* 3.3 26.0 - - - +
214C SER 2.7 14.8 + - - +
216C ILE* 3.7 17.9 - - + -
225C LYS* 6.1 0.9 - - - -
226C PRO* 3.3 38.4 - - + +
227C ILE 3.5 15.5 + - - +
228C GLY* 3.7 23.8 - - - +
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Residues in contact with TYR 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ASP* 3.1 37.7 + - + -
14C MSE 1.4 77.5 - - - +
16C LYS* 1.3 77.8 + - + +
17C ILE 3.4 0.2 - - - -
18C THR* 3.6 10.1 - - - -
19C MSE 2.8 40.2 + - + +
132C GLU* 3.0 23.2 + - - -
133C ILE* 3.9 1.4 - - - +
177C PHE* 4.4 14.1 - + - -
180C ARG* 3.2 32.1 + - - -
214C SER* 5.8 0.9 - - - -
228C GLY* 4.2 7.0 - - - -
229C THR 3.1 31.0 - - - +
231C ALA* 3.6 30.7 - - + -
233C GLU* 4.8 1.1 - - - -
294C ARG* 6.1 3.4 - - - +
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Residues in contact with LYS 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C THR* 3.7 13.0 - - + +
13C ASP 2.9 10.9 + - - +
15C TYR* 1.3 92.9 - - + +
17C ILE* 1.3 59.0 + - - +
19C MSE 3.7 2.4 - - - +
20C HIS* 2.9 28.9 + - - +
34C TYR* 4.4 3.0 + - - -
129C ILE* 2.8 38.2 + - - +
130C LEU* 3.6 19.8 - - + +
132C GLU* 2.9 35.2 + - + +
133C ILE* 3.5 30.5 - - + +
233C GLU* 2.6 30.0 + - - -
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Residues in contact with ILE 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU 4.5 9.9 - - - +
10C LEU* 5.3 0.7 - - + -
12C THR* 4.3 8.5 - - + -
14C MSE 2.9 8.4 + - - +
16C LYS* 1.3 74.1 - - - +
18C THR* 1.3 66.0 + - - +
20C HIS* 3.2 4.6 + - - +
21C ALA* 3.0 21.5 + - - +
65C PHE* 4.2 23.3 - - + -
73C LEU* 4.4 14.1 - - + -
77C ILE* 4.7 4.9 - - + -
80C LEU* 4.3 18.2 - - + -
84C TYR* 3.8 27.7 + - + +
130C LEU* 3.9 20.0 - - + -
216C ILE* 3.6 26.0 - - + -
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Residues in contact with THR 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C MSE 3.1 32.1 + - + +
15C TYR* 3.4 18.4 + - - +
17C ILE* 1.3 74.0 - - - +
19C MSE 1.3 61.1 + - - +
21C ALA 3.1 2.1 + - - -
22C ALA* 2.9 24.6 + - - +
77C ILE* 4.3 19.3 - - + -
79C TYR* 4.6 9.2 - - + -
80C LEU* 4.3 7.9 - - + -
228C GLY 5.7 1.4 - - - -
229C THR 4.6 2.4 + - - -
256C TRP* 3.8 19.6 - - + -
260C PHE* 3.3 22.1 - - + -
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Residues in contact with MSE 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C TYR* 2.8 40.1 + - + +
16C LYS* 3.7 4.9 - - - +
18C THR* 1.3 78.2 + - - +
20C HIS* 1.3 56.3 + - - +
22C ALA* 3.1 4.7 + - - +
23C VAL* 2.8 40.2 + - + +
125C TRP* 4.2 7.4 - - + -
129C ILE* 3.8 15.7 - - + -
230C VAL* 4.5 4.0 - - - -
231C ALA* 4.6 6.1 - - + +
233C GLU* 3.5 35.2 - - + +
234C TRP* 3.7 43.5 - - + +
256C TRP* 4.1 15.7 - - + -
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Residues in contact with HIS 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LYS 2.9 19.6 + - - +
17C ILE 3.2 6.7 + - - +
19C MSE 1.3 75.5 - - - +
21C ALA* 1.3 57.3 + - - +
23C VAL* 3.8 1.0 - - - +
24C PHE* 2.8 33.3 + - - +
65C PHE* 5.5 0.2 - + - -
84C TYR* 2.8 21.6 + + - +
87C TYR* 3.0 37.9 + + - -
88C ILE* 3.8 6.5 - - + -
93C TYR* 3.5 24.2 + - - -
126C LYS* 3.0 24.7 + - + -
129C ILE* 3.4 19.7 - - + +
130C LEU* 3.8 19.1 - - + +
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Residues in contact with ALA 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ILE 3.0 12.1 + - - +
18C THR 3.4 8.1 - - - +
20C HIS* 1.3 74.8 - - - +
22C ALA* 1.3 55.8 + - - +
24C PHE* 3.5 1.2 + - - +
25C THR* 2.7 37.9 + - - -
80C LEU* 3.9 19.1 - - + -
81C PRO* 4.2 6.5 - - + -
84C TYR* 3.5 30.2 - - + -
259C THR* 4.5 1.1 - - - -
260C PHE* 4.0 9.4 - - + -
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Residues in contact with ALA 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C THR 2.9 15.2 + - - +
19C MSE 3.7 4.3 - - - +
21C ALA* 1.3 78.5 - - - +
23C VAL* 1.3 57.0 + - - +
26C ASN* 2.9 38.3 + - - +
234C TRP* 3.7 23.9 - - + -
256C TRP* 3.7 23.6 - - + -
259C THR* 4.1 12.1 - - + +
260C PHE* 4.1 7.6 - - + -
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Residues in contact with VAL 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C MSE 2.8 31.2 + - + +
20C HIS* 3.8 4.7 - - - +
22C ALA* 1.3 69.8 - - - +
24C PHE* 1.3 62.7 + - - +
27C PHE* 2.7 43.0 + - - +
125C TRP* 3.5 69.1 - - + +
126C LYS* 3.6 15.9 - - + +
129C ILE* 5.1 2.9 - - + -
234C TRP* 4.0 12.1 - - + -
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Residues in contact with PHE 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C HIS 2.8 18.8 + - - +
21C ALA 3.7 2.2 - - - +
23C VAL* 1.3 80.9 - - - +
25C THR* 1.3 67.5 + - - +
28C PRO* 3.5 23.4 - - + +
83C ALA* 3.6 34.1 - - + -
84C TYR* 3.8 23.6 - - + -
87C TYR* 3.4 55.9 - + + -
126C LYS* 4.1 22.0 - - + +
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Residues in contact with THR 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ALA 2.7 22.0 + - - -
22C ALA 3.9 3.6 - - - -
24C PHE* 1.3 88.7 - - - +
26C ASN* 1.3 66.6 + - - +
28C PRO* 4.4 3.3 - - - +
81C PRO* 3.7 23.0 - - + +
83C ALA* 6.2 0.2 - - - +
84C TYR* 5.0 0.3 + - - +
259C THR* 4.0 22.7 - - + +
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Residues in contact with ASN 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ALA 2.9 25.4 + - - +
25C THR* 1.3 84.3 - - - +
27C PHE* 1.3 87.6 + - + +
28C PRO* 3.3 9.9 - - - +
234C TRP* 3.9 8.9 - - - -
255C CYS* 3.9 24.7 + - - +
258C ASN* 5.4 3.8 + - - +
259C THR* 2.8 27.9 + - - -
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Residues in contact with PHE 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ALA 4.6 0.7 - - - -
23C VAL* 2.7 26.9 + - - +
26C ASN* 1.3 93.8 - - + +
28C PRO* 1.3 61.9 - - - +
29C ASP 3.3 4.1 + - - -
30C VAL* 3.6 26.4 + - + +
125C TRP* 3.9 20.5 - + + +
126C LYS 5.1 0.2 + - - -
234C TRP* 3.5 36.1 - + - -
238C VAL* 3.8 27.4 - - + -
241C ILE* 3.5 27.1 - - + -
255C CYS* 4.4 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
------------------------------------------------------------
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