Contacts of the helix formed by residues 24 - 33 (chain B) in PDB entry 5U07
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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 3.4 19.0 - - + +
169A ASP* 4.3 30.7 - - + +
187A ALA* 5.2 7.6 - - + +
20B LEU* 2.7 35.9 + - + +
21B ILE 4.4 1.8 - - - -
23B ASN* 1.3 73.8 - - + +
25B PRO* 1.3 65.9 - - + +
26B ALA* 2.7 32.4 + - - +
27B ALA* 2.3 40.7 + - + +
28B ARG* 3.3 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A TYR* 5.2 15.3 - - + +
166A GLN* 6.1 6.7 - - + -
169A ASP 5.7 2.7 - - - +
187A ALA 6.1 1.3 - - - +
21B ILE 5.2 0.7 - - - +
23B ASN 3.4 9.4 - - - +
24B GLU* 1.3 87.3 - - + +
26B ALA* 1.3 59.9 + - - +
28B ARG* 3.1 3.8 + - + +
29B ALA* 2.9 28.8 + - - +
22I LEU* 3.4 52.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 4.1 18.8 - - + +
105A ARG* 5.0 10.1 - - - +
107A VAL* 6.3 1.3 - - + -
164A TYR* 5.6 5.6 + - - +
189A ARG* 5.8 6.1 - - + -
24B GLU* 2.7 25.1 + - - +
25B PRO* 1.3 75.1 - - - +
27B ALA* 1.3 55.1 + - - +
29B ALA* 3.5 5.4 + - - +
30B ALA* 2.9 29.0 + - - +
49B ARG* 5.3 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 5.5 0.2 - - - +
20B LEU* 4.9 16.6 - - + -
24B GLU* 2.3 37.5 + - + +
26B ALA* 1.3 66.8 - - - +
28B ARG* 1.3 59.7 + - - +
30B ALA* 3.1 3.8 + - - +
31B LEU* 2.9 35.6 + - + +
49B ARG* 4.1 22.4 - - - +
50B VAL* 4.5 16.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU 4.9 0.6 + - - -
21B ILE* 3.9 31.0 - - + +
24B GLU 3.3 13.4 + - - +
25B PRO* 3.4 11.7 - - + +
27B ALA* 1.3 77.4 - - - +
29B ALA* 1.3 57.4 + - - +
31B LEU* 3.1 25.8 - - - +
32B ARG* 3.1 22.3 + - - +
89B ALA* 4.6 3.7 - - - +
96B ARG* 5.3 1.3 - - - +
22I LEU* 4.1 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PRO 2.9 16.3 + - - +
26B ALA* 3.9 4.5 - - - +
28B ARG* 1.3 78.3 - - - +
30B ALA* 1.3 57.8 + - - +
32B ARG* 3.3 20.3 - - - +
33B ARG* 3.0 24.2 - - - +
20I ASP* 6.0 0.7 - - - +
22I LEU* 4.0 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA 2.9 19.0 + - - +
27B ALA* 3.1 7.4 + - - +
29B ALA* 1.3 78.2 - - - +
31B LEU* 1.3 57.1 + - - +
33B ARG* 3.3 22.7 + - - +
34B GLY 5.2 0.3 + - - -
43B ARG 5.3 0.9 - - - +
44B MET* 5.3 1.2 - - - +
46B ALA* 4.0 34.6 - - + +
47B ALA* 4.1 5.7 + - - +
49B ARG* 5.3 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 4.2 13.0 - - + -
20B LEU* 6.4 0.7 - - + -
21B ILE* 4.0 20.2 - - + -
27B ALA* 2.9 28.4 + - + +
28B ARG* 3.1 27.6 - - - +
30B ALA* 1.3 75.4 - - - +
32B ARG* 1.3 64.9 + - - +
33B ARG 3.2 3.3 + - - -
34B GLY* 3.4 6.8 + - - -
47B ALA* 4.0 24.2 - - + +
50B VAL* 4.8 12.6 - - + -
51B VAL* 4.6 17.3 - - + -
85B ALA* 4.3 6.7 - - + +
86B ALA* 3.4 23.1 - - + +
89B ALA* 3.4 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ARG 3.1 12.8 + - - +
29B ALA* 3.3 28.9 - - - +
31B LEU* 1.3 74.2 - - - +
33B ARG* 1.3 61.1 + - + +
34B GLY 3.0 10.1 + - - -
35B VAL* 3.7 19.1 + - - +
86B ALA* 4.2 10.5 - - - -
89B ALA 4.1 4.9 + - - +
90B ALA* 3.8 37.0 + - + +
91B GLN 5.5 0.6 + - - -
201E VAL* 3.6 21.6 + - - +
203E PHE* 2.9 46.7 - - - -
20I ASP* 4.6 6.3 + - - -
21I ASP* 4.2 11.3 + - - -
22I LEU* 4.6 7.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ALA 3.0 22.2 - - - +
30B ALA* 3.3 21.1 - - - +
32B ARG* 1.3 74.5 - - + +
34B GLY* 1.3 56.6 + - - +
35B VAL* 3.7 2.2 + - - -
43B ARG* 2.5 54.9 + - - +
46B ALA* 4.9 10.7 - - - +
----------------------------------------------------------
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