Contacts of the helix formed by residues 8 - 16 (chain H) in PDB entry 1RQF
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 SER 8 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H VAL* 1.3 81.4 - - - +
9H TRP* 1.3 61.1 + - - +
10H ILE* 4.0 7.4 + - - +
11H SER* 3.1 28.5 + - - -
12H TRP* 2.8 27.4 + - - +
24H GLU* 4.7 1.4 + - - -
55H ASP* 3.5 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 9 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H VAL 3.6 1.0 + - - -
8H SER* 1.3 70.2 - - - +
10H ILE* 1.3 66.4 + - + +
12H TRP* 3.2 34.5 + + - +
13H PHE* 2.7 62.0 + + + +
52H MET* 3.3 46.2 - - + +
53H ILE* 3.8 17.3 - - + +
55H ASP* 3.1 18.7 + - - +
73H GLU* 5.0 3.0 + - - +
76H ALA* 3.6 28.7 - - + -
77H GLU* 4.1 2.7 - - + -
80H TYR* 3.5 46.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 10 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H SER* 3.2 6.9 - - - +
9H TRP* 1.3 88.5 - - + +
11H SER* 1.3 63.7 + - - +
13H PHE* 3.2 1.1 + - - +
14H CYS* 2.9 25.3 + - - -
24H GLU* 3.9 24.0 - - + +
25H VAL 3.6 20.2 - - - +
27H GLU* 5.1 7.9 - - + -
30H ILE* 3.7 24.2 - - + -
53H ILE* 3.8 19.3 + - + +
54H LEU* 5.4 2.5 - - + -
80H TYR* 3.6 33.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 11 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H VAL 4.3 7.7 + - - -
8H SER* 3.1 28.5 + - - -
10H ILE* 1.3 79.0 - - - +
12H TRP* 1.3 62.2 - - - +
14H CYS* 4.1 1.6 - - - +
15H GLY* 3.3 18.2 + - - -
24H GLU* 3.5 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 12 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H VAL 4.7 10.3 - - - +
8H SER 2.8 13.0 + - - +
9H TRP* 3.4 51.8 - + - +
11H SER* 1.3 79.3 - - - +
13H PHE* 1.3 80.9 + + + +
15H GLY* 3.2 11.0 + - - -
16H LEU* 3.4 48.0 + - + +
73H GLU* 5.7 7.0 - - + -
77H GLU* 6.0 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 13 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H TRP* 2.7 45.5 + + + +
10H ILE* 3.2 3.8 + - - +
12H TRP* 1.3 83.4 - + + +
14H CYS* 1.3 64.2 + - - +
15H GLY 2.8 10.4 + - - -
16H LEU* 3.0 18.3 + - + +
19H ASN* 3.0 41.6 + - - -
22H PHE* 4.0 27.1 - + - -
77H GLU* 3.3 46.0 - - + -
80H TYR* 3.4 37.9 - + - -
81H GLY 5.7 0.2 - - - -
158H TYR* 6.2 0.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 14 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H ILE* 2.9 22.1 + - - +
11H SER 4.1 1.8 - - - +
13H PHE* 1.3 75.6 - - - +
15H GLY* 1.3 57.8 + - - +
16H LEU 3.5 0.4 - - - +
19H ASN* 3.4 24.8 - - - +
20H GLU* 4.6 2.3 + - - -
22H PHE* 4.1 12.9 - - + +
23H CYS 3.4 16.2 - - - -
24H GLU* 3.8 22.0 - - + +
80H TYR* 3.3 37.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 15 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H SER 3.3 11.0 + - - -
12H TRP 3.2 9.1 + - - -
13H PHE 2.8 1.8 + - - -
14H CYS* 1.3 77.8 - - - +
16H LEU* 1.3 66.8 + - - +
17H ARG* 3.7 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 16 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H TRP* 3.4 58.0 + - + +
13H PHE* 3.0 19.9 + - + +
14H CYS 4.2 0.3 - - - +
15H GLY* 1.3 82.4 - - - +
17H ARG* 1.3 67.2 + - - +
18H GLY 3.3 0.2 + - - -
19H ASN* 3.1 38.1 + - - +
20H GLU* 4.4 3.8 + - - +
77H GLU* 5.7 3.8 - - - +
----------------------------------------------------------
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