Contacts of the helix formed by residues 24 - 33 (chain L) in PDB entry 5U0A
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 GLU 24 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19L LYS* 5.4 3.3 - - - +
20L LEU* 3.1 48.1 + - + +
21L ILE 3.8 4.2 - - - +
23L ASN* 1.3 96.8 + - - +
25L PRO* 1.3 65.5 - - + +
26L ALA* 4.4 6.5 - - + +
27L ALA* 4.5 6.7 - - + +
28L ARG* 3.3 14.9 + - - +
22M C 4.6 19.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 25 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103I GLU* 3.5 24.5 - - - +
23L ASN 3.9 6.3 - - - +
24L GLU* 1.3 84.4 - - + +
26L ALA* 1.3 60.6 + - + +
28L ARG* 3.8 13.9 - - - +
29L ALA* 2.9 33.3 + - - +
25M C 3.7 31.1 - - + +
26M A 3.7 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24L GLU* 3.4 3.7 - - + -
25L PRO* 1.3 83.1 - - + +
27L ALA* 1.3 59.3 + - - +
29L ALA* 3.8 1.9 - - - +
30L ALA* 2.9 26.2 + - - +
24M A 6.2 0.4 - - - +
25M C 3.4 46.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20L LEU* 3.6 34.8 - - + -
24L GLU* 4.2 5.9 + - + +
26L ALA* 1.3 77.5 - - - +
28L ARG* 1.3 60.6 + - - +
30L ALA* 3.1 10.6 + - - +
31L LEU* 2.9 30.8 + - - +
49L ARG* 6.1 3.1 - - - +
50L VAL* 5.0 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20L LEU* 4.3 2.3 + - - +
21L ILE* 3.3 49.7 + - + -
24L GLU 3.3 17.2 + - - +
25L PRO* 4.0 15.1 + - - +
26L ALA 3.3 0.4 - - - -
27L ALA* 1.3 75.9 - - - +
29L ALA* 1.3 60.2 - - - +
31L LEU* 2.9 13.1 + - - +
32L ARG* 2.8 54.3 + - - +
89L ALA* 3.6 19.9 + - + +
91L GLN 5.4 0.6 + - - -
96L ARG* 3.0 41.3 - - - +
26M A 2.6 33.5 + - - -
27M G 5.3 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222E ASN* 5.8 0.4 - - - +
25L PRO 2.9 19.2 + - - +
26L ALA 3.9 2.5 - - - +
28L ARG* 1.3 74.3 - - - +
30L ALA* 1.3 63.9 + - - +
32L ARG* 3.3 40.4 + - - +
33L ARG* 3.4 28.3 + - - +
25M C 4.1 25.8 - - + +
26M A 4.3 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26L ALA 2.9 15.9 + - - +
27L ALA* 3.1 16.8 + - - +
29L ALA* 1.3 79.4 - - - +
31L LEU* 1.3 58.7 + - + +
33L ARG* 4.2 11.6 + - - +
34L GLY 4.8 1.9 + - - -
44L MET* 6.1 1.2 - - - -
46L ALA* 3.6 33.7 - - + +
47L ALA* 4.8 2.3 + - - +
50L VAL* 6.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17L VAL* 3.7 30.1 - - + -
20L LEU* 4.5 7.4 - - + -
21L ILE* 5.0 1.3 - - + -
27L ALA 2.9 14.8 + - - +
28L ARG* 2.9 11.2 + - - +
30L ALA* 1.3 76.6 - - + +
32L ARG* 1.3 64.1 + - - +
33L ARG 3.2 3.0 + - - -
34L GLY* 3.4 5.5 + - - -
46L ALA 4.7 0.9 - - - +
47L ALA* 3.9 33.4 - - + +
50L VAL* 4.4 20.2 - - + -
51L VAL* 4.3 13.2 - - + -
85L ALA* 4.3 12.1 - - + +
86L ALA* 3.3 22.7 - - + +
89L ALA* 3.7 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 32 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222E ASN* 4.3 12.3 - - - +
28L ARG* 2.8 44.7 + - - +
29L ALA* 3.3 22.7 + - - +
31L LEU* 1.3 77.2 - - - +
33L ARG* 1.3 68.5 + - - +
34L GLY 3.2 0.2 - - - -
35L VAL* 3.1 24.4 - - + +
86L ALA 4.4 7.4 - - - -
89L ALA* 3.9 6.7 - - - +
90L ALA* 3.5 36.1 - - + +
26M A 2.8 29.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 33 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203E PHE* 4.7 11.7 - - - -
221E MET* 4.5 0.6 - - - +
222E ASN* 4.0 22.9 - - - +
223E ALA* 3.7 34.2 - - - +
29L ALA* 3.4 25.8 + - - +
30L ALA* 4.6 7.8 - - - +
31L LEU 3.2 1.0 - - - -
32L ARG* 1.3 82.3 - - + +
34L GLY* 1.3 63.1 + - - +
35L VAL* 4.4 2.9 - - - +
25M C 2.8 31.5 + - - -
----------------------------------------------------------
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