Contacts of the strand formed by residues 22 - 28 (chain F) in PDB entry 5HMG
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 TYR 22 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E GLY 3.4 6.5 - - - +
17E HIS* 4.0 2.2 - - + -
320E MET* 3.5 19.6 - - + +
6F ILE* 4.5 0.9 - - + -
17F MET* 3.9 4.7 - - - -
21F TRP* 1.3 87.9 - - + +
23F GLY* 1.3 58.8 + - - +
36F ALA* 3.6 8.1 - - - +
37F ASP* 2.8 23.0 + - - +
40F SER* 3.2 50.9 - - - +
41F THR* 3.3 3.3 + - - -
44F ALA* 3.5 19.4 - - + +
111F THR* 2.9 47.2 + - - +
114F GLU* 3.5 9.2 - - + +
115F MET* 3.8 34.1 - - + -
118F LEU* 3.7 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 23 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E LEU* 3.4 9.2 - - - +
16E GLY 2.9 31.9 + - - +
14F TRP* 3.8 6.2 - - - -
17F MET* 3.7 8.4 - - - -
22F TYR* 1.3 76.9 - - - +
24F PHE* 1.3 68.5 + - - -
35F ALA 3.5 10.1 - - - -
37F ASP* 3.6 8.7 - - - -
118F LEU* 4.2 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 24 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E LEU* 3.8 28.9 - - + -
14E CYS 3.4 3.4 - - - -
15E LEU* 3.8 22.7 - - + -
14F TRP* 4.0 3.1 - - - -
17F MET* 4.0 0.4 - - - +
23F GLY* 1.3 75.2 - - - -
25F ARG* 1.3 59.2 + - - +
34F GLN* 3.2 6.8 - - - +
35F ALA 2.8 42.4 + - - +
36F ALA 5.2 0.4 - - - -
37F ASP* 4.1 23.8 - - + -
118F LEU* 3.6 20.0 - - + -
122F THR* 3.6 25.6 - - + -
152F ILE* 5.2 2.5 - - + -
153F ARG* 3.5 53.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 25 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E THR 3.9 0.2 - - - +
13E LEU* 3.5 2.7 - - - +
14E CYS* 2.7 39.3 + - + +
325E GLU* 4.3 11.9 + - - -
14F TRP* 3.5 60.8 - - + +
16F GLY* 4.7 9.3 - - - -
24F PHE* 1.3 68.9 - - - +
26F HIS* 1.3 58.5 + - - +
33F GLY 3.4 7.6 - - - +
34F GLN* 2.8 46.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 26 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E THR 3.0 14.4 - - - +
13E LEU* 4.1 7.4 - - + -
14E CYS* 6.1 0.2 - - - -
24F PHE 6.0 0.2 - - - -
25F ARG* 1.3 76.3 - - - +
27F GLN* 1.3 60.2 + - - +
28F ASN* 3.7 31.2 + - + -
32F THR* 3.1 32.4 + - - +
33F GLY* 2.9 50.0 + - - -
146F ASN* 3.3 21.4 + - - -
149F ILE* 3.9 36.4 - - + +
153F ARG* 4.8 9.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 27 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E ALA* 3.6 1.4 - - - +
12E THR* 2.8 45.0 + - - +
26F HIS* 1.3 75.2 - - - +
28F ASN* 1.3 65.3 + - - +
31F GLY 3.6 4.3 - - - +
32F THR* 3.6 22.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 28 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E THR 4.7 1.1 - - - -
11E ALA* 4.1 13.9 - - + +
26F HIS* 3.7 13.5 - - + -
27F GLN* 1.3 79.4 - - - +
29F SER* 1.3 61.3 + - - +
30F GLU* 2.9 12.6 + - - +
31F GLY* 2.8 49.6 + - - +
144F CYS 3.1 28.1 + - - +
145F ASP* 3.2 16.1 - - - +
146F ASN* 3.1 24.0 + - - +
149F ILE* 4.0 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