Contacts of the helix formed by residues 11 - 20 (chain D) in PDB entry 1I8F
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 11 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D PHE* 2.7 24.5 - - - +
10D ALA* 1.4 82.1 - - - +
12D LEU* 1.3 94.5 + - + +
13D GLY 4.8 0.4 - - - +
15D THR* 4.1 4.5 + - - -
40E SER* 3.8 14.3 + - - -
41E PHE* 3.8 10.4 + - - -
42E ASP* 3.3 25.6 + - - +
46E ASN* 3.5 27.0 + - + +
47E LEU* 3.9 3.5 + - - -
48E LEU* 4.2 11.3 - - - +
67E VAL* 3.0 18.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 12 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D THR* 1.3 98.4 - - + +
13D GLY* 1.3 66.0 + - - +
14D ALA 3.3 0.7 + - - -
15D THR* 3.4 3.1 + - - -
16D LEU* 3.1 31.5 + - + +
43D GLN 5.7 1.6 - - - +
45D VAL* 3.4 36.8 - - + -
46E ASN* 3.9 37.0 - - + +
67E VAL* 2.6 49.9 - - + +
68E VAL 4.6 5.2 - - - +
69E ARG* 4.6 5.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 13 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D PHE 3.8 6.1 + - - -
11D THR* 4.8 0.4 - - - +
12D LEU* 1.3 76.0 - - - +
14D ALA* 1.3 57.2 + - - +
16D LEU* 3.7 0.4 - - - +
17D GLN* 2.5 42.3 + - - +
41D PHE* 4.0 20.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 14 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D PHE 3.4 5.4 + - - +
10D ALA* 2.7 40.5 + - - +
12D LEU 3.3 1.2 + - - -
13D GLY* 1.3 77.2 - - - +
15D THR* 1.3 56.3 + - - +
17D GLN* 3.2 7.1 + - - +
18D ASP* 3.0 24.5 + - - +
48E LEU* 5.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 15 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ALA 3.6 4.0 + - - -
11D THR 4.1 1.7 + - - -
12D LEU 3.4 6.7 + - - -
13D GLY 3.3 0.2 - - - -
14D ALA* 1.3 72.8 - - - +
16D LEU* 1.3 68.0 + - + +
18D ASP* 3.1 8.6 + - + +
19D SER* 2.5 41.7 + - - +
76D ILE 6.2 0.2 - - - -
78D PRO* 4.1 16.8 - - + -
48E LEU* 3.2 29.9 - - + +
65E THR* 3.8 22.6 - - + +
67E VAL* 4.8 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 16 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D LEU* 3.1 30.1 - - + +
13D GLY* 3.2 0.8 + - - +
15D THR* 1.3 78.7 - - + +
17D GLN* 1.3 67.6 + - - +
19D SER* 2.8 14.5 + - - +
20D ILE* 3.3 12.1 + - - +
38D LEU* 3.6 15.6 - - + +
41D PHE* 3.5 46.2 - - + -
42D ASP 5.4 0.2 - - - +
45D VAL* 4.6 19.5 - - + -
47D LEU* 4.9 0.7 - - + -
76D ILE* 4.1 25.8 - - + -
67E VAL* 4.1 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 17 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D GLY 2.5 24.2 + - - +
14D ALA* 3.3 7.6 - - - +
16D LEU* 1.3 75.1 - - - +
18D ASP* 1.3 62.4 + - - +
20D ILE* 3.1 23.0 + - - +
41D PHE* 3.6 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 18 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ALA 3.0 13.2 + - - +
15D THR* 3.1 10.5 + - + +
17D GLN* 1.3 78.0 - - - +
19D SER* 1.3 58.2 + - - +
20D ILE 3.5 1.7 + - - +
22D LYS* 3.1 32.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 19 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D THR* 2.5 33.7 + - - +
16D LEU* 2.8 8.3 + - - +
18D ASP* 1.3 77.1 + - - +
20D ILE* 1.3 68.4 + - - +
21D GLY 3.2 0.5 + - - -
22D LYS* 2.8 35.4 + - - +
24D VAL* 5.3 7.6 - - - -
38D LEU* 4.0 15.8 - - - +
78D PRO* 3.9 22.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D LEU 3.3 4.4 + - - +
17D GLN* 3.1 28.1 + - - +
18D ASP 3.5 2.5 - - - +
19D SER* 1.3 78.2 - - - +
21D GLY* 1.3 63.8 + - - +
22D LYS* 3.4 6.6 + - - +
38D LEU* 3.4 15.0 - - + +
39D ARG* 3.8 23.8 - - - +
40D SER* 4.1 6.3 - - - -
41D PHE* 3.5 32.8 - - + -
----------------------------------------------------------
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