Contacts of the helix formed by residues 9 - 23 (chain P) in PDB entry 2L7F
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 THR 9 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7P HIS* 4.3 11.0 - - + +
8P PHE* 1.3 75.0 - - - +
10P SER* 1.3 60.1 + - - +
11P GLN* 3.4 16.6 + - + +
12P GLN* 2.9 44.5 + - - +
13P LEU* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 10 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9P THR* 1.3 74.2 - - - +
11P GLN* 1.3 57.9 + - - +
13P LEU* 4.0 11.8 + - - +
14P GLN* 2.9 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 11 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9P THR* 3.4 14.9 + - - +
10P SER* 1.3 77.4 - - - +
12P GLN* 1.3 63.7 + - + +
13P LEU 3.4 0.2 - - - -
14P GLN* 3.4 8.2 + - - +
15P GLU* 3.0 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 12 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6P THR* 5.8 2.0 - - - +
7P HIS 3.3 12.7 + - - +
8P PHE* 3.5 5.5 - - + -
9P THR* 2.9 43.0 + - - +
11P GLN* 1.3 78.2 - - + +
13P LEU* 1.3 57.0 + - - +
15P GLU* 3.4 6.4 + - - +
16P LEU* 2.9 36.6 + - - +
38P THR* 2.8 36.4 + - - +
39P ASN* 4.1 6.9 + - - +
40P LEU* 3.5 30.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 13 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8P PHE* 3.6 32.8 - - + +
9P THR 2.9 22.4 + - - +
10P SER* 4.0 10.3 - - - +
12P GLN* 1.3 76.2 - - - +
14P GLN* 1.3 58.9 + - + +
16P LEU* 3.4 4.9 + - - +
17P GLU* 2.9 30.1 + - - +
48P TRP* 3.5 29.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 14 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10P SER* 2.9 30.6 + - - +
11P GLN* 3.4 9.1 + - - +
12P GLN 3.3 0.4 - - - -
13P LEU* 1.3 74.4 - - + +
15P GLU* 1.3 60.9 + - - +
17P GLU* 3.4 8.0 + - + +
18P ALA* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 15 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11P GLN 3.0 17.6 + - - +
12P GLN* 3.8 4.5 - - - +
14P GLN* 1.3 75.3 - - - +
16P LEU* 1.3 53.8 + - - +
18P ALA* 3.5 13.0 + - - +
19P THR* 2.7 40.6 + - - +
37P TRP* 5.9 3.8 - - + +
38P THR* 3.8 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 16 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8P PHE* 4.3 4.0 - - + -
12P GLN 2.9 22.2 + - - +
13P LEU 3.7 1.6 - - - +
15P GLU* 1.3 73.9 - - - +
17P GLU* 1.3 58.7 + - - +
19P THR* 3.3 7.4 + - - +
20P PHE* 2.8 23.4 + - - +
34P ILE* 3.7 29.6 - - + -
38P THR* 4.7 7.4 - - + -
40P LEU* 3.8 27.4 - - + -
45P VAL* 4.4 11.7 - - + -
48P TRP* 3.3 64.2 - - + -
49P PHE* 4.6 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 17 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13P LEU 2.9 18.1 + - - +
14P GLN* 3.4 9.6 + - + +
16P LEU* 1.3 75.8 - - - +
18P ALA* 1.3 56.7 + - - +
20P PHE* 3.2 9.7 + - - +
21P GLN* 2.8 67.4 + - - +
48P TRP* 3.8 7.1 - - + -
52P ARG* 2.8 43.5 + - - +
64P VAL* 5.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 18 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14P GLN 2.9 18.0 + - - +
15P GLU* 3.7 15.7 - - - +
17P GLU* 1.3 74.8 - - - +
19P THR* 1.3 60.6 + - - +
21P GLN* 3.5 12.6 + - - +
22P ARG* 3.1 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 19 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15P GLU* 2.7 31.3 + - - +
16P LEU* 3.4 10.6 - - + +
18P ALA* 1.3 74.9 - - - +
20P PHE* 1.3 56.2 + - - +
22P ARG* 3.2 9.0 + - - +
23P ASN* 2.8 30.5 + - + +
26P PRO* 4.8 6.7 - - + -
30P THR* 6.5 0.2 - - + -
34P ILE* 4.0 37.4 - - + +
49P PHE* 4.0 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 20 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16P LEU 2.8 20.0 + - - +
17P GLU* 3.6 7.0 - - - +
19P THR* 1.3 72.2 - - - +
21P GLN* 1.3 64.7 + - + +
23P ASN* 3.3 12.3 - - - -
24P ARG* 3.3 86.2 - - + +
48P TRP* 3.9 9.9 - + + -
49P PHE* 4.0 15.9 - + + -
52P ARG* 3.5 66.2 - - + -
53P ARG* 5.1 5.6 - - + -
56P TRP* 5.3 9.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 21 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17P GLU* 2.8 49.7 + - - +
18P ALA* 3.8 9.8 - - - +
19P THR 3.4 0.2 - - - -
20P PHE* 1.3 77.1 - - + +
22P ARG* 1.3 59.7 + - - +
24P ARG* 5.6 2.8 - - - +
52P ARG* 6.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 22 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18P ALA 3.1 18.3 + - - +
19P THR* 3.2 8.0 + - - +
21P GLN* 1.3 77.9 - - - +
23P ASN* 1.3 61.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 23 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19P THR* 2.8 21.1 + - + +
20P PHE* 3.3 9.1 + - - -
22P ARG* 1.3 79.8 - - + +
24P ARG* 1.3 61.0 + - - +
25P TYR* 3.1 26.3 + - - +
26P PRO* 3.5 39.2 - - + +
27P ASP 5.0 0.8 - - - +
30P THR* 5.3 4.4 - - + +
49P PHE* 3.9 1.6 - - - -
----------------------------------------------------------
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