Contacts of the strand formed by residues 216 - 221 (chain B) in PDB entry 1P5Q
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 HIS 216 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ILE 3.8 0.2 - - - -
155B GLN* 2.8 28.7 + - + -
156B THR* 3.0 52.4 + - + +
214B GLY 3.5 11.1 + - - -
215B GLU* 1.3 71.4 - - - +
217B SER* 1.3 64.5 + - - +
247B LEU 3.9 4.2 + - - +
248B HIS* 3.1 47.7 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ARG* 3.7 24.9 - - - -
153B ARG 3.8 6.1 - - - -
154B ILE* 3.8 3.7 - - - +
155B GLN* 4.1 2.2 - - - +
211B MSE 4.0 12.0 - - - +
215B GLU* 2.5 36.8 + - - +
216B HIS* 1.3 72.7 + - - +
218B ILE* 1.3 65.6 + - - +
246B GLU* 3.6 6.1 - - - +
247B LEU* 3.1 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ILE 3.9 0.2 - - - +
152B ARG* 3.2 3.4 - - - +
153B ARG* 2.6 49.3 + - + +
155B GLN* 3.6 35.7 - - + +
217B SER* 1.3 76.0 - - - +
219B VAL* 1.3 61.4 + - - +
220B TYR* 3.4 36.1 - - + +
244B LYS* 3.8 22.0 - - + +
245B TYR 3.4 5.4 - - - +
246B GLU* 3.5 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B ILE* 3.9 26.5 - - + -
151B ILE 3.3 7.9 - - - +
152B ARG* 4.2 7.2 - - + +
204B LEU* 3.9 10.8 - - + -
207B ALA* 3.9 15.7 - - + -
218B ILE* 1.3 75.6 - - - +
220B TYR* 1.3 66.0 + - - +
221B LEU* 4.1 14.7 - - + +
243B LEU 3.9 1.0 - - - +
244B LYS* 3.5 5.5 - - - +
245B TYR* 3.0 56.9 + - + +
247B LEU* 3.9 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A GLN* 5.6 3.8 - - - +
149B GLY 3.3 4.3 - - - +
150B ILE* 3.6 1.2 - - - -
151B ILE* 2.5 67.0 + - + +
153B ARG* 3.6 44.5 + - + +
218B ILE* 3.4 27.9 - - + +
219B VAL* 1.3 73.1 - - - +
221B LEU* 1.3 61.3 + - - +
222B LYS* 6.0 1.3 - - + -
242B GLU* 6.2 0.4 - - - +
243B LEU 3.8 3.8 - - - +
244B LYS* 3.1 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B GLY 3.4 1.1 - - - -
150B ILE* 3.1 44.9 - - + -
201B PRO* 3.8 18.8 - - + -
203B GLY* 3.7 14.4 - - - -
204B LEU* 3.8 15.3 - - - +
219B VAL* 4.1 11.9 - - + +
220B TYR* 1.3 72.7 - - - +
222B LYS* 1.3 70.7 + - - +
223B PRO 3.5 0.9 - - - -
225B TYR* 3.6 17.9 - - + +
226B ALA* 4.3 7.2 - - + +
242B GLU* 3.6 6.9 - - - +
243B LEU* 3.1 33.3 + - + +
245B TYR* 4.2 16.8 - - + -
----------------------------------------------------------
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