Contacts of the helix formed by residues 8 - 19 (chain C) in PDB entry 3DVA
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 PRO 8 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLN* 6.1 0.7 - - - +
231A ILE* 6.1 0.2 - - + -
5C PHE* 5.7 2.0 - - + -
6C GLN 4.0 3.6 - - - +
7C PHE* 1.3 87.7 - - + +
9C PHE* 1.3 63.8 + - - +
10C ALA 3.4 2.7 - - - -
11C GLU* 3.7 28.0 - - + +
12C GLN* 3.0 25.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 9 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A PRO* 3.1 29.8 - - + -
231A ILE* 3.2 36.8 - - + -
247A ALA* 4.8 15.3 - - + -
248A ALA* 5.5 0.7 - - + -
251A ARG* 3.6 42.2 - - + +
259A THR* 4.4 11.4 - - + -
6C GLN* 5.7 4.5 - - - -
7C PHE* 2.7 47.5 + + + +
8C PRO* 1.3 73.8 - - - +
10C ALA* 1.3 59.1 + - - +
12C GLN* 3.2 8.2 + - - +
13C LEU* 3.0 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 10 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C PRO 3.4 0.4 - - - -
9C PHE* 1.3 73.8 - - - +
11C GLU* 1.3 66.8 + - - +
13C LEU* 3.2 9.1 + - - +
14C GLU* 3.0 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 11 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLN* 4.8 7.6 + - - +
8C PRO* 3.5 28.1 + - + +
9C PHE 3.4 0.4 - - - -
10C ALA* 1.3 77.2 - - - +
12C GLN* 1.3 57.4 + - - +
14C GLU* 3.9 8.0 - - - +
15C LYS* 2.9 67.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 12 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLN* 3.2 35.4 + - + +
20A PHE* 3.4 22.4 - - + -
224A VAL* 5.4 1.7 - - + +
228A ILE 4.3 1.9 - - - +
229A PRO* 3.4 10.7 - - - +
230A GLY 2.7 46.4 + - - +
231A ILE* 4.4 8.5 - - - +
8C PRO* 3.0 17.0 + - + +
9C PHE* 3.3 13.5 - - - +
10C ALA 3.2 0.2 - - - -
11C GLU* 1.3 76.1 - - - +
13C LEU* 1.3 65.8 + - + +
15C LYS* 4.1 0.5 - - - +
16C VAL* 3.1 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 13 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A GLY* 4.0 20.0 - - - +
228A ILE 4.3 3.4 - - - +
229A PRO* 4.0 35.4 - - + -
251A ARG* 4.9 9.6 - - - +
9C PHE 3.0 24.2 + - - +
10C ALA* 3.2 7.4 + - - +
12C GLN* 1.3 84.5 - - + +
14C GLU* 1.3 62.3 + - + +
16C VAL* 4.2 3.3 - - - +
17C ALA* 3.3 25.1 + - - +
217C LYS* 5.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 14 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ALA* 3.0 28.1 + - - +
11C GLU* 3.9 6.4 - - - +
13C LEU* 1.3 76.9 - - + +
15C LYS* 1.3 68.2 + - + +
17C ALA* 3.4 4.3 + - - +
18C GLU* 2.9 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 15 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLN* 3.4 34.1 - - + +
11C GLU* 2.9 44.0 + - + +
14C GLU* 1.3 82.4 + - - +
16C VAL* 1.3 65.1 + - - +
18C GLU* 3.2 40.3 + - - +
19C GLN* 3.5 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 16 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 4.8 12.8 - - + +
19A GLN* 4.1 22.7 - - + -
20A PHE* 4.7 5.2 - - + -
224A VAL* 3.4 45.5 - - + -
12C GLN* 3.1 22.3 + - + +
13C LEU* 4.2 3.6 - - - +
15C LYS* 1.3 74.1 - - - +
17C ALA* 1.3 61.0 + - - +
19C GLN* 2.9 29.5 + - - +
20C PHE* 3.3 17.1 - - + -
221C GLN* 4.8 4.9 - - + +
224C VAL* 4.7 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 17 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU 3.3 17.7 + - - +
14C GLU* 3.9 4.0 - - - +
16C VAL* 1.3 79.8 - - - +
18C GLU* 1.3 61.5 + - - +
20C PHE* 3.1 24.4 + - - +
21C PRO* 5.3 0.3 - - - +
217C LYS* 3.7 50.1 + - + -
218C THR* 4.6 1.2 - - - +
221C GLN* 4.2 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C GLU* 2.9 17.7 + - - +
15C LYS* 3.2 39.4 + - - +
17C ALA* 1.3 78.2 - - - +
19C GLN* 1.3 66.7 + - - +
20C PHE 3.1 5.0 + - - -
21C PRO* 3.5 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PRO 5.4 0.2 - - - +
11A GLU* 4.4 11.3 + - - +
12A GLN* 3.6 38.6 + - + +
15A LYS* 3.3 43.3 - - + +
16A VAL* 4.7 7.9 - - + -
15C LYS 3.7 13.8 + - - +
16C VAL* 2.9 15.1 + - - +
18C GLU* 1.3 88.7 + - - +
20C PHE* 1.3 76.8 + - + +
21C PRO* 3.4 7.7 - - - +
----------------------------------------------------------
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