Contacts of the helix formed by residues 18 - 29 (chain A) in PDB entry 1VI9
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 GLY 18 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN* 3.9 18.4 - - - -
10A SER* 3.8 10.1 - - - -
17A ALA* 1.3 71.5 - - - +
19A ASN* 1.3 64.7 + - - -
21A ALA* 2.9 11.1 + - - +
22A ALA* 3.0 14.7 + - - +
83A TYR* 6.4 1.8 - - - -
224A ASP* 2.8 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ALA* 3.0 40.4 + - - +
9A GLN* 3.0 41.6 + - - +
10A SER 2.7 17.5 + - - +
11A HIS* 5.1 1.3 - - + +
18A GLY* 1.3 72.5 - - - -
20A SER* 1.3 54.3 + - - +
22A ALA* 4.4 1.8 - - - +
23A GLU* 2.8 38.7 + - + +
33A VAL* 5.4 0.2 - - - +
35A PRO* 3.8 9.8 - - + +
36A LEU 3.7 6.3 + - - +
37A ASN* 3.0 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A SER 3.6 0.2 + - - -
11A HIS* 3.1 19.4 + - - -
12A VAL* 2.9 45.9 + - - -
15A GLY 4.0 4.7 - - - -
16A HIS* 2.7 29.7 + - - -
17A ALA 3.0 13.7 + - - -
19A ASN* 1.3 77.6 - - - +
21A ALA* 1.3 54.6 + - - +
23A GLU* 4.7 5.0 - - - +
24A PHE* 5.4 2.4 + - - +
268A VAL* 5.0 1.2 - - - +
27B ARG* 5.1 9.9 + - - +
35B PRO* 6.5 0.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
16A HIS* 3.7 14.4 - - + +
17A ALA* 3.4 23.0 - - - +
18A GLY 2.9 9.4 + - - +
20A SER* 1.3 81.3 - - - +
22A ALA* 1.3 57.4 + - - +
25A PRO* 3.1 26.4 - - - +
221A GLY* 4.1 12.8 - - - +
224A ASP* 4.3 2.5 - - + -
225A VAL* 3.5 22.1 - - + +
266A LEU* 4.8 2.7 - - + -
268A VAL* 3.9 4.7 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
9A GLN* 4.1 15.5 - - - +
18A GLY 3.0 14.6 + - - +
19A ASN* 4.4 1.3 - - - +
21A ALA* 1.3 77.9 - - - +
23A GLU* 1.3 65.1 + - - +
25A PRO* 3.2 5.3 - - - +
26A MSE 3.2 40.3 + - - +
80A LEU* 5.1 0.2 - - + -
224A ASP 3.7 23.6 - - - +
225A VAL* 4.7 4.3 - - - +
228A GLY* 4.7 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASN* 2.8 26.7 + - + +
20A SER* 5.3 2.9 - - - +
21A ALA 3.8 0.4 - - - -
22A ALA* 1.3 72.1 - - - +
24A PHE* 1.3 78.8 + - - +
26A MSE 3.3 2.0 + - - +
27A ARG* 2.9 68.4 + - + +
33A VAL* 4.2 23.3 - - + -
35A PRO* 4.6 9.9 - - + -
23B GLU* 2.5 24.1 - - - +
24B PHE* 4.4 1.9 - - - +
27B ARG* 3.0 24.4 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
16A HIS* 6.2 0.2 - - + -
20A SER 5.4 2.5 + - - +
21A ALA 4.7 0.6 + - - -
23A GLU* 1.3 88.6 + - - +
25A PRO* 1.3 71.1 - - + +
27A ARG* 3.2 4.0 + - - +
28A ARG* 2.8 38.4 + - + +
268A VAL* 3.6 26.5 - - + -
269A VAL* 4.0 7.6 - - + -
272A GLN* 3.5 50.7 - - + -
275A ILE* 5.0 0.7 - - + -
23B GLU* 4.4 0.9 - - - -
24B PHE* 3.7 32.3 - + - -
27B ARG* 3.5 50.5 - - + +
28B ARG* 4.0 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A SER 5.7 0.2 - - - +
21A ALA 3.1 26.5 - - - +
22A ALA* 3.2 6.7 - - - +
24A PHE* 1.3 94.7 - - + +
26A MSE 1.3 59.0 + - - +
28A ARG* 3.2 16.4 + - + +
29A LEU* 3.3 11.1 + - - +
225A VAL* 4.1 14.1 - - + -
229A LEU* 3.5 26.8 - - + +
268A VAL* 3.9 24.2 - - + -
275A ILE* 4.0 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 3.7 41.7 - - + -
7A ALA* 5.4 1.3 - - - -
22A ALA* 3.2 22.3 + - - +
23A GLU 3.7 0.2 - - - +
25A PRO* 1.3 77.6 - - - +
27A ARG* 1.3 63.3 + - - +
29A LEU* 3.4 11.4 + - - +
30A GLY 3.4 0.3 + - - -
31A ALA* 3.2 22.2 + - + +
33A VAL* 3.6 22.9 - - + -
80A LEU* 4.1 12.6 - - + -
228A GLY* 3.5 42.0 - - - +
229A LEU* 4.1 4.5 - - + +
231A LEU* 4.6 3.4 - - + -
232A VAL* 3.5 26.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU* 2.9 43.7 + - - +
24A PHE 3.8 2.0 - - - +
26A MSE 1.3 75.7 - - - +
28A ARG* 1.3 58.5 + - - +
30A GLY 2.9 16.6 + - - -
31A ALA 3.4 17.3 - - - +
32A ASN* 5.3 0.2 - - - +
33A VAL* 2.8 39.3 + - + +
35A PRO* 3.7 15.6 - - - +
15B GLY 5.5 2.0 + - - -
16B HIS* 4.4 20.0 + - - -
20B SER* 5.0 12.4 + - - +
23B GLU* 2.9 29.1 + - - -
24B PHE* 3.7 28.7 - - + +
269B VAL* 3.5 24.8 - - + +
272B GLN* 2.9 14.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 2.8 28.6 + - + +
25A PRO* 3.5 10.5 - - + +
26A MSE 3.2 0.2 - - - -
27A ARG* 1.3 75.2 - - - +
29A LEU* 1.3 58.4 + - - +
30A GLY 3.3 0.2 - - - -
272A GLN* 3.0 49.6 + - + +
273A ASP* 3.0 33.7 + - - +
275A ILE* 4.7 6.5 - - + -
276A ALA* 3.6 20.1 - - + +
277A LYS* 4.3 8.5 - - - +
24B PHE* 4.1 2.2 - - - -
28B ARG* 3.1 31.9 - - - +
272B GLN* 3.2 29.4 + - - +
273B ASP* 4.4 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PRO 3.3 11.0 + - - +
26A MSE 3.5 10.5 - - - +
27A ARG 3.2 0.6 - - - -
28A ARG* 1.3 73.5 - - - +
30A GLY* 1.3 57.3 + - - +
31A ALA 3.7 0.7 - - - -
229A LEU* 3.7 23.6 - - + +
232A VAL* 3.8 17.0 - - + -
233A LYS* 3.8 31.4 - - + -
236A GLN* 3.0 19.2 + - - +
246A HIS* 3.8 15.3 - - + +
247A VAL* 6.1 0.2 - - + -
275A ILE* 3.6 28.5 - - + +
276A ALA* 3.7 15.5 - - + -
----------------------------------------------------------
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