Contacts of the strand formed by residues 21 - 26 (chain 1) in PDB entry 5DM6
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 21 (chain 1).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111 LYS* 3.2 41.5 - - + -
121 MET 3.5 13.2 - - - +
131 GLU* 3.9 12.6 - - + -
141 SER 4.8 0.2 - - - +
191 GLY 3.8 12.8 - - - -
201 PHE* 1.3 96.3 - - - +
221 TYR* 1.3 79.6 + - - +
231 THR* 4.6 4.3 - - + -
2398X U 4.5 2.5 + - - -
2399X G 3.8 25.8 - - - -
2418X A 2.6 56.6 + - - -
2419X U 3.5 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 22 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111 LYS* 3.1 10.2 - - - +
121 MET* 2.9 40.4 + - + +
201 PHE* 3.3 37.3 - + - -
211 TYR* 1.3 78.3 - - - +
231 THR* 1.3 66.7 + - - +
241 THR* 5.9 0.7 - - - +
391 LYS* 3.7 29.5 - - + +
401 TYR* 3.8 9.3 + - - +
491 PHE* 3.4 34.1 - + - -
363 LYS* 3.8 20.6 - - - +
2347X C 2.7 45.3 + - - -
2348X U 4.0 9.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 23 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91 ILE* 4.6 9.6 - - + -
101 VAL 3.4 7.6 - - - +
111 LYS* 4.0 15.0 - - + -
121 MET* 4.8 0.4 - - - +
211 TYR* 4.6 5.8 - - + -
221 TYR* 1.3 84.6 - - - +
241 THR* 1.3 73.7 + - - +
391 LYS* 5.8 0.7 + - - -
343 THR* 3.8 20.6 + - - +
363 LYS* 3.5 31.8 + - - +
2419X U 3.8 37.0 - - - +
2420X C 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 24 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91 ILE* 3.3 6.9 - - - +
101 VAL* 2.8 31.9 + - - +
121 MET* 4.8 11.6 - - - +
221 TYR* 5.9 0.7 - - - +
231 THR* 1.3 81.2 - - - +
251 THR* 1.3 68.0 + - + +
351 LEU* 5.5 1.4 - - - +
371 LEU* 5.5 0.3 - - - +
391 LYS* 5.2 8.3 + - - +
343 THR* 3.9 11.4 - - + +
363 LYS* 5.7 1.6 - - + +
2286X A 3.3 21.3 + - - -
2346X A 4.0 33.3 + - + +
2347X C 5.8 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 25 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71 ARG* 2.9 29.9 + - + -
81 ILE 3.1 12.3 - - - +
91 ILE* 4.2 19.3 - - + -
101 VAL* 5.1 0.4 - - - -
241 THR* 1.3 90.2 - - - +
261 LYS* 1.3 61.4 + - - +
351 LEU* 5.7 0.7 - - - -
343 THR* 4.5 7.9 - - + +
2285X C 4.3 11.6 + - - -
2286X A 4.2 15.0 + - - +
2346X A 4.7 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 26 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71 ARG* 3.2 7.5 - - - +
81 ILE* 2.9 27.1 + - - -
101 VAL* 3.8 22.0 - - + +
251 THR* 1.3 74.1 - - - +
271 ASN* 1.3 62.2 + - - +
281 ARG* 3.5 29.2 + - - +
311 THR* 3.1 37.7 - - + +
321 GLN 6.0 0.7 - - - -
331 ALA 3.9 8.0 + - - -
341 LYS* 3.8 29.1 - - - +
351 LEU* 4.0 27.5 - - + +
511 ALA* 4.0 13.1 + - - +
2286X A 4.4 3.6 - - - +
----------------------------------------------------------
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