Contacts of the helix formed by residues 18 - 27 (chain B) in PDB entry 5M64
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 18 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PHE* 3.1 31.5 + - - -
17B ARG* 1.3 73.4 - - - +
19B LEU* 1.3 62.5 + - - +
20B GLU 3.5 0.2 - - - -
21B ARG* 3.7 15.4 + - - +
22B GLU* 2.9 30.5 + - + +
18J TRP* 5.8 4.9 - - + -
21J TYR* 4.5 25.4 + - + -
22J LEU* 4.7 15.3 - - + -
25J LEU* 5.3 11.9 - - + -
55J ASP* 5.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B THR* 1.3 76.4 - - - +
20B GLU* 1.3 72.8 + - + +
22B GLU* 3.3 9.4 + - + +
23B SER* 2.9 31.2 + - - -
25J LEU* 5.3 16.1 - - + +
26J GLN* 3.3 30.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ARG* 3.8 35.4 - - + +
18B THR 3.5 1.0 - - - +
19B LEU* 1.3 88.2 - - + +
21B ARG* 1.3 57.0 + - - +
23B SER* 3.2 7.8 + - - -
24B ARG* 2.9 45.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PHE* 3.8 14.6 - - - -
17B ARG* 3.2 35.0 + - + +
18B THR* 3.7 29.3 + - - +
19B LEU 3.3 0.4 - - - -
20B GLU* 1.3 78.2 - - - +
22B GLU* 1.3 59.2 + - - +
24B ARG* 3.2 14.6 - - + +
25B PHE* 3.0 57.9 + - + -
749B THR* 4.7 4.4 - - - +
763B ASP* 3.3 45.0 + - - +
18J TRP* 6.0 1.0 - - - -
51J LEU 5.2 0.6 + - - -
53J HIS 3.7 14.9 + - - -
54J VAL* 3.4 28.3 - - - +
55J ASP* 4.0 11.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B THR* 2.9 23.1 + - + +
19B LEU* 3.7 10.4 - - + +
20B GLU 3.3 0.2 - - - -
21B ARG* 1.3 81.9 - - - +
23B SER* 1.3 62.2 + - - +
25B PHE* 3.4 6.7 + - + +
26B ILE* 3.0 47.6 + - + +
18J TRP* 6.5 0.4 - - + -
22J LEU* 5.1 22.1 - - + +
26J GLN* 4.7 11.0 - - - +
55J ASP* 5.0 9.2 - - - +
58J GLU* 5.8 3.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 2.9 21.2 + - - -
20B GLU* 3.2 11.0 + - - -
22B GLU* 1.3 80.1 + - - +
24B ARG* 1.3 65.2 + - - +
26B ILE* 3.1 5.1 + - - +
27B ASN* 3.0 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ARG* 5.3 7.3 - - - +
20B GLU* 2.9 32.3 + - - +
21B ARG* 3.2 23.0 - - - +
23B SER* 1.3 75.7 - - - +
25B PHE* 1.3 66.0 + - + +
26B ILE 3.4 0.2 - - - -
27B ASN 3.8 18.6 - - - +
28B PRO* 4.1 5.2 - - - +
29B PRO* 5.5 13.2 - - + +
34B ALA* 3.5 21.8 - - - +
35B PHE* 3.5 29.8 - - - -
187B SER* 5.4 0.2 + - - -
758B ASP* 5.8 2.7 + - - -
763B ASP* 6.0 0.2 - - - -
764B ASN* 4.3 17.3 - - - +
59J LYS* 3.1 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ARG* 3.0 32.5 + - + +
22B GLU* 3.7 6.1 - - - +
23B SER 3.1 0.4 - - - -
24B ARG* 1.3 83.3 - - + +
26B ILE* 1.3 63.8 + - - +
763B ASP* 3.5 22.0 - - - -
764B ASN* 3.2 25.6 - - - -
54J VAL* 3.2 22.9 - - + -
55J ASP* 3.5 27.8 - - - +
56J LEU* 4.1 17.0 - - + -
58J GLU* 3.5 35.8 - - + +
59J LYS* 3.2 34.7 + - + +
62J ARG* 4.6 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLU* 3.0 43.7 + - + +
23B SER* 3.1 6.5 + - - +
25B PHE* 1.3 77.8 - - - +
27B ASN* 1.3 61.1 + - + +
150C SER* 3.5 32.3 - - - +
151C THR 4.4 14.1 - - - +
153C PRO* 5.2 12.1 - - + -
195C LYS* 5.3 0.7 - - - +
58J GLU* 3.5 29.2 - - + +
62J ARG* 2.8 21.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B SER* 3.0 23.6 + - - +
24B ARG* 3.8 8.8 - - - +
25B PHE 3.5 0.6 - - - -
26B ILE* 1.3 82.2 - - + +
28B PRO* 1.3 78.7 + - + +
29B PRO* 3.8 1.9 - - - +
178B TYR* 4.6 9.9 - - + -
150C SER* 3.1 37.3 + - - +
62J ARG* 3.6 2.9 - - - +
----------------------------------------------------------
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