Contacts of the helix formed by residues 256 - 268 (chain L) in PDB entry 5MQF
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 256 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816 C 5.0 14.3 - - - +
254L GLU* 5.1 0.2 - - - +
255L LYS* 1.3 79.0 - - - +
257L GLY* 1.3 57.2 - - - +
259L ASP* 3.8 8.9 - - - +
260L ARG* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 257 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254L GLU* 4.8 8.5 - - - +
255L LYS 3.1 3.6 - - - +
256L GLU* 1.3 78.8 - - - +
258L ARG* 1.3 56.7 + - - +
260L ARG* 3.4 4.8 + - - +
261L LYS* 2.9 30.5 + - - +
208O PRO* 6.2 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 258 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254L GLU* 5.6 5.3 - - - +
255L LYS* 3.4 10.2 + - - +
257L GLY* 1.3 74.9 - - - +
259L ASP* 1.3 58.0 + - - +
261L LYS* 4.0 5.6 - - - +
262L LYS* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 259 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816 C 6.1 2.2 - - - +
255L LYS 3.4 10.4 + - - +
256L GLU* 3.4 12.0 + - - +
257L GLY 3.2 0.4 - - - -
258L ARG* 1.3 77.2 - - - +
260L ARG* 1.3 59.8 + - - +
262L LYS* 3.4 6.2 + - - +
263L ASP* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 260 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256L GLU 2.9 18.2 + - - +
257L GLY* 3.9 4.3 - - - +
259L ASP* 1.3 74.1 - - - +
261L LYS* 1.3 61.0 + - - +
263L ASP* 3.3 7.5 + - - +
264L LYS* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 261 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257L GLY 2.9 18.1 + - - +
258L ARG* 4.0 6.5 - - - +
260L ARG* 1.3 76.7 - - - +
262L LYS* 1.3 58.2 + - - +
264L LYS* 3.3 6.7 + - - +
265L GLN* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 262 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258L ARG 2.9 21.4 + - - +
259L ASP* 3.7 5.8 - - - +
261L LYS* 1.3 75.2 - - - +
263L ASP* 1.3 59.0 + - - +
265L GLN* 3.8 5.9 - - - +
266L HIS* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 263 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259L ASP 2.9 18.4 + - - +
260L ARG* 3.3 7.8 + - - +
262L LYS* 1.3 75.9 - - - +
264L LYS* 1.3 59.2 + - - +
266L HIS* 3.9 4.9 - - - +
267L LEU* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 264 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260L ARG 2.9 16.5 + - - +
261L LYS* 3.7 7.4 - - - +
263L ASP* 1.3 75.5 - - - +
265L GLN* 1.3 59.8 + - - +
267L LEU* 3.4 5.4 + - - +
268L LYS* 2.9 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 265 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261L LYS 2.9 17.8 + - - +
262L LYS* 3.9 6.5 - - - +
264L LYS* 1.3 76.2 - - - +
266L HIS* 1.3 61.7 + - - +
268L LYS* 3.8 6.1 - - - +
269L ARG* 3.2 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 266 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262L LYS 2.9 18.8 + - - +
263L ASP* 3.9 6.1 - - - +
265L GLN* 1.3 77.0 - - - +
267L LEU* 1.3 62.8 + - - +
269L ARG 3.4 18.9 - - - +
270L LYS* 3.7 13.6 + - + +
215N ASN* 4.9 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 267 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263L ASP 2.9 19.4 + - - +
264L LYS* 3.4 5.6 + - - +
266L HIS* 1.3 74.8 - - - +
268L LYS* 1.3 65.4 + - - +
217N LYS* 6.3 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 268 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264L LYS 2.9 17.7 + - - +
265L GLN* 3.8 7.6 - - - +
266L HIS 3.3 0.2 - - - -
267L LEU* 1.3 80.9 - - - +
269L ARG* 1.3 62.3 + - + +
----------------------------------------------------------
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