Contacts of the helix formed by residues 13 - 27 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A THR* 1.3 83.6 + - - +
14A MSE 1.3 60.1 + - - +
15A TYR* 3.1 28.0 - - + -
16A LYS* 2.8 26.9 + - - +
17A ILE 3.9 0.5 + - - -
133A ILE* 2.9 29.8 - - + +
177A PHE* 4.2 6.6 - - - +
179A THR* 3.5 18.3 + - - -
180A ARG* 3.5 18.1 + - - +
214A SER* 2.6 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A THR 3.7 0.4 + - - -
13A ASP* 1.3 70.8 - - - +
15A TYR* 1.3 64.3 + - - +
17A ILE* 3.0 15.1 + - - +
18A THR* 3.2 18.3 + - + -
76A GLU 5.3 2.0 - - - +
77A ILE* 4.0 35.7 - - + -
79A TYR* 3.1 27.8 - - + +
214A SER 2.7 15.4 + - - +
216A ILE* 3.8 18.8 - - + +
226A PRO* 3.3 39.5 - - - +
227A ILE 3.5 17.1 + - - +
228A GLY* 3.8 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP* 3.1 37.0 + - + -
14A MSE 1.3 78.0 - - - +
16A LYS* 1.3 77.7 + - + +
18A THR* 3.2 9.0 + - - -
19A MSE 2.9 36.0 + - + +
132A GLU* 2.8 23.5 + - - -
133A ILE* 3.4 8.9 - - + +
177A PHE* 4.6 12.3 - + - -
180A ARG* 3.2 30.4 + - - -
214A SER* 5.9 0.6 - - - -
227A ILE 4.8 0.2 + - - -
228A GLY* 4.3 5.6 - - - -
229A THR 3.2 30.3 - - - +
230A VAL 5.6 0.2 - - - -
231A ALA* 3.5 31.2 - - + +
233A GLU* 4.4 1.3 - - - -
294A ARG* 6.1 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A THR* 3.7 11.4 - - + +
13A ASP 2.8 12.9 + - - +
15A TYR* 1.3 92.5 - - + +
17A ILE* 1.3 55.1 + - - +
19A MSE 3.7 2.8 - - - +
20A HIS* 2.9 29.1 + - - +
34A TYR* 4.5 3.0 + - - -
129A ILE* 2.7 37.8 + - - +
130A LEU* 3.6 19.5 - - + +
132A GLU* 3.0 29.3 + - + +
133A ILE* 3.4 35.4 - - + +
233A GLU* 2.6 33.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU 4.5 7.6 - - - +
10A LEU* 5.2 0.9 - - + -
12A THR* 4.3 8.3 - - + -
14A MSE 3.0 6.8 + - - +
16A LYS* 1.3 73.4 - - - +
18A THR* 1.3 61.7 + - - +
20A HIS* 3.3 4.0 + - - +
21A ALA* 3.0 27.2 + - - +
65A PHE* 4.0 24.9 - - + -
73A LEU* 4.3 22.2 - - + -
77A ILE* 4.6 4.7 - - + -
80A LEU* 4.3 11.7 - - + -
84A TYR* 3.7 27.5 + - + +
130A LEU* 3.9 22.0 - - + -
216A ILE* 3.7 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A MSE 3.2 34.4 + - + +
15A TYR* 3.2 21.0 + - - -
17A ILE* 1.3 75.2 - - - +
19A MSE 1.3 55.5 + - - +
21A ALA* 3.2 3.2 + - - -
22A ALA* 2.8 24.8 + - - +
77A ILE* 4.4 15.5 - - + -
79A TYR* 4.6 9.4 - - + +
80A LEU* 4.4 6.5 - - + -
228A GLY* 5.7 1.5 - - - -
229A THR 4.3 4.2 + - - -
256A TRP* 3.9 23.5 - - + -
260A PHE* 3.3 18.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A TYR* 2.9 34.8 + - + +
16A LYS* 3.7 4.7 - - - +
18A THR* 1.3 74.4 + - - +
20A HIS* 1.3 59.0 + - - +
22A ALA* 3.1 4.1 + - - -
23A VAL* 2.8 38.9 + - + +
125A TRP* 3.7 18.4 - - + -
129A ILE* 3.4 25.1 - - + -
230A VAL* 5.8 0.2 - - - -
231A ALA* 4.5 12.6 - - + +
233A GLU* 3.4 29.4 - - + +
234A TRP* 3.4 44.0 - - + +
256A TRP* 4.2 9.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS 2.9 19.7 + - - +
17A ILE 3.4 6.1 - - - +
18A THR 3.3 0.2 - - - -
19A MSE 1.3 76.3 - - - +
21A ALA* 1.3 57.6 + - - +
23A VAL* 3.9 1.1 - - - +
24A PHE* 2.9 32.4 + - - +
84A TYR* 2.8 22.3 + + - +
87A TYR* 3.0 39.6 + + - -
88A ILE* 3.8 6.9 - - + +
93A TYR* 3.5 23.1 - - - -
126A LYS* 3.0 25.4 + - + -
129A ILE* 3.5 22.6 - - + +
130A LEU* 3.9 16.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE 3.0 13.3 + - - +
18A THR 3.2 8.0 + - - +
20A HIS* 1.3 75.3 - - - +
22A ALA* 1.3 58.2 + - - +
24A PHE* 3.8 0.7 - - - +
25A THR* 2.8 36.2 + - - -
80A LEU* 3.9 15.9 - - + -
81A PRO* 4.2 5.6 - - + -
84A TYR* 3.5 34.0 - - + -
259A THR* 4.8 0.9 - - - -
260A PHE* 4.0 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A THR 2.8 17.3 + - - +
19A MSE 3.6 4.7 - - - +
21A ALA* 1.3 77.9 - - - +
23A VAL* 1.3 56.7 + - - +
25A THR 3.4 0.2 + - - -
26A ASN* 2.9 42.4 + - - +
234A TRP* 3.7 25.0 - - + -
256A TRP* 3.7 23.1 - - + -
259A THR* 4.2 8.1 - - + +
260A PHE* 4.0 5.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A MSE 2.8 28.3 + - + +
20A HIS* 3.9 4.5 - - - +
22A ALA* 1.3 69.2 - - - +
24A PHE* 1.3 62.8 + - - +
27A PHE* 2.8 43.6 + - - +
125A TRP* 3.5 66.6 - - + +
126A LYS* 3.5 16.4 - - - +
129A ILE* 3.9 11.4 - - + -
234A TRP* 4.0 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A HIS 2.9 18.9 + - - +
21A ALA 3.8 1.6 - - - +
23A VAL* 1.3 80.8 - - - +
25A THR* 1.3 70.1 + - - +
28A PRO* 3.6 20.1 - - + +
83A ALA* 3.5 32.3 - - + -
84A TYR* 3.6 28.0 - - + -
87A TYR* 3.5 51.6 - + + -
126A LYS* 4.1 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA* 2.8 22.8 + - - -
22A ALA 3.8 3.4 - - - -
23A VAL 3.2 0.2 - - - -
24A PHE* 1.3 89.3 - - - +
26A ASN* 1.3 72.8 + - - +
28A PRO* 4.4 3.3 - - - +
81A PRO* 3.7 23.6 - - + +
259A THR* 4.1 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA* 2.9 25.7 + - - +
25A THR* 1.3 83.9 - - - +
27A PHE* 1.3 91.6 + - + +
28A PRO* 3.4 9.4 - - - +
29A ASP* 4.6 1.0 - - - +
234A TRP* 4.0 10.5 - - - -
255A CYS* 4.1 17.5 + - - +
258A ASN* 6.0 1.2 - - - +
259A THR* 2.8 29.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA 4.8 0.7 - - - -
23A VAL* 2.8 24.9 + - - +
26A ASN* 1.3 94.1 - - + +
28A PRO* 1.3 57.9 - - - +
29A ASP* 3.0 16.6 + - - -
30A VAL* 3.4 29.0 + - + +
125A TRP* 4.0 21.3 - + + +
234A TRP* 3.6 30.1 - + - -
238A VAL* 4.0 23.3 - - + -
241A ILE* 3.6 28.5 - - + -
255A CYS* 4.3 13.5 - - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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