Contacts of the helix formed by residues 21 - 32 (chain U) in PDB entry 5A0Q
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 PHE 21 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8U ASP* 3.4 23.9 + - + +
15U SER* 3.2 25.6 + - - +
17U ASP* 4.0 11.0 - - - -
19U ARG* 3.4 32.3 + - + -
20U VAL* 1.3 69.9 - - - +
22U GLN* 1.3 64.4 + - - +
23U VAL 3.3 0.2 - - - -
24U GLU* 3.1 23.8 + - - +
25U TYR* 3.1 52.9 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 22 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11T THR* 4.7 4.0 - - + +
12T VAL* 3.8 7.8 - - - +
13T TRP* 2.4 71.0 + - - +
8U ASP 4.3 4.0 + - - -
9U LEU* 2.5 31.6 - - - +
10U SER 4.6 1.3 - - - +
11U ALA* 4.1 17.5 - - + +
20U VAL* 3.3 14.6 - - + +
21U PHE* 1.3 76.0 - - - +
23U VAL* 1.3 62.0 + - - +
25U TYR* 3.2 7.2 + - - +
26U ALA* 3.1 20.3 + - - +
130U PRO* 3.8 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 23 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83O MET* 6.2 2.2 - - + -
132O ARG* 5.5 2.2 - - - +
11U ALA* 5.7 0.4 - - + -
20U VAL* 3.7 29.6 - - + +
21U PHE 3.3 0.6 - - - -
22U GLN* 1.3 75.7 - - + +
24U GLU* 1.3 58.4 + - + +
26U ALA* 3.5 4.3 + - - +
27U MET* 3.0 34.9 + - + +
123U THR* 4.1 37.5 - - + +
130U PRO* 4.1 17.7 - - + -
153U PRO* 5.1 1.9 - - + +
154U SER* 4.5 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 24 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19U ARG* 3.5 26.9 + - + +
20U VAL 3.8 10.8 - - - +
21U PHE* 3.1 45.5 - - - +
22U GLN 3.2 0.4 - - - -
23U VAL* 1.3 76.6 - - + +
25U TYR* 1.4 61.6 + - + +
27U MET* 3.2 17.3 + - - +
28U LYS* 3.0 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 25 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12T VAL* 6.0 0.2 - - + -
13T TRP* 3.2 34.2 - - + -
14T SER 3.3 15.0 - - - +
15T PRO* 3.7 41.3 - - + +
17T GLY 3.3 20.6 - - - +
8U ASP 3.9 20.8 + - - -
9U LEU* 5.0 6.5 - - + -
21U PHE* 3.1 41.8 + + + -
22U GLN* 3.2 12.8 + - - +
24U GLU* 1.4 77.2 - - + +
26U ALA* 1.3 61.9 + - - +
28U LYS* 3.4 19.5 + - - +
29U ALA 3.8 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13T TRP* 3.6 33.3 - - + +
22U GLN 3.1 7.3 + - - +
23U VAL 3.5 8.7 - - - +
25U TYR* 1.3 73.6 - - - +
27U MET* 1.3 60.9 + - - +
28U LYS 3.3 0.2 - - - -
29U ALA* 3.4 8.3 - - - +
130U PRO* 3.6 16.4 - - + -
131U PHE 3.2 21.9 - - - +
132U GLY* 3.4 23.6 - - - +
153U PRO* 5.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 27 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23U VAL* 3.0 22.1 + - + +
24U GLU* 3.2 19.9 + - - +
26U ALA* 1.3 73.8 - - - +
28U LYS* 1.3 57.6 + - - +
30U VAL* 3.1 26.5 + - + +
31U GLU* 3.4 11.1 - - + +
152U ASP* 3.9 12.8 - - + +
153U PRO* 3.4 31.4 - - + -
154U SER* 3.4 34.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 28 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15T PRO 3.3 26.0 - - - +
16T GLN* 4.3 16.2 - - - +
17T GLY 4.8 3.1 - - - +
24U GLU* 3.0 14.6 + - - +
25U TYR* 3.5 19.3 - - - +
26U ALA 3.3 0.6 - - - -
27U MET* 1.3 74.2 - - - +
29U ALA* 1.4 62.3 + - - +
30U VAL 3.4 0.2 - - - -
31U GLU* 3.2 23.1 + - + +
32U ASN* 3.1 28.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13T TRP* 3.7 27.4 - - + -
17T GLY 4.6 3.5 + - - +
18T ARG* 4.6 7.8 + - + +
25U TYR 3.8 2.6 + - - -
26U ALA 3.4 15.1 + - - +
27U MET 3.2 0.2 - - - -
28U LYS* 1.4 79.1 - - - +
30U VAL* 1.4 58.0 + - - +
32U ASN* 3.5 23.7 + - - +
33U SER* 3.6 5.7 + - - -
79U GLY* 4.0 7.1 - - - -
80U LEU* 4.4 13.7 + - + +
132U GLY* 3.8 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 30 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27U MET* 3.1 22.0 - - + +
29U ALA* 1.4 74.0 - - - +
31U GLU* 1.3 67.8 + - - +
32U ASN 3.1 6.3 + - - -
33U SER 3.5 5.2 - - - +
78U ALA* 3.5 21.1 - - + +
79U GLY* 3.4 25.4 - - - +
132U GLY 3.5 17.0 + - - +
133U CYS 4.7 1.3 - - - +
134U SER* 4.1 24.0 - - - +
152U ASP* 6.0 0.4 - - - +
153U PRO* 5.0 4.0 - - + -
165U ILE* 4.6 3.4 - - + -
166U GLY* 3.3 23.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 31 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27U MET* 3.4 17.7 - - + +
28U LYS* 3.2 21.6 + - + +
30U VAL* 1.3 89.2 - - - +
32U ASN* 1.4 59.8 - - - +
165U ILE* 5.9 1.2 - - - +
166U GLY 3.8 7.8 + - - +
167U LYS* 3.5 20.8 - - - +
169U ARG* 3.0 42.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 32 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16T GLN 4.8 10.7 + - - -
17T GLY 5.3 1.2 + - - -
18T ARG* 3.2 41.8 - - - +
28U LYS* 3.1 24.7 + - - +
29U ALA* 3.6 10.8 - - - +
30U VAL 3.1 0.4 - - - -
31U GLU* 1.4 80.1 - - - +
33U SER* 1.4 67.1 + - - +
34U SER 3.8 0.2 + - - -
167U LYS* 3.4 26.7 + - - +
----------------------------------------------------------
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