Contacts of the strand formed by residues 171 - 176 (chain C) in PDB entry 1Y8Q
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 171 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C LEU 3.2 2.9 + - - +
170C GLY* 1.3 70.7 - - - -
172C HIS* 1.3 61.6 + - - +
173C GLU* 3.8 5.7 + - - +
210C LYS* 3.5 31.5 + - + +
211C VAL 3.5 5.6 - - - -
212C VAL* 3.6 30.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 172 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C LYS* 3.7 16.7 + - - -
169C LEU* 3.6 33.8 + - + +
170C GLY 3.4 0.6 + - - -
171C GLU* 1.3 71.9 - - - +
173C GLU* 1.3 73.7 + - - +
174C PHE* 3.7 25.5 - + - +
210C LYS* 3.3 2.2 - - - -
211C VAL* 2.6 43.4 + - + +
213C PHE* 4.1 8.1 - - + -
316C LYS 4.4 0.8 + - - -
317C ALA* 3.2 35.3 + - - -
320C GLN* 4.3 6.8 - - + -
324C PRO* 3.7 27.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 173 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C GLU 3.8 6.3 + - - +
172C HIS* 1.3 81.6 + - - +
174C PHE* 1.3 63.4 - - - +
208C LYS* 3.3 35.4 + - - -
209C LYS 3.3 10.1 - - - +
210C LYS* 3.8 33.6 + - + +
320C GLN* 3.6 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 174 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C HIS* 3.7 22.9 - + - +
173C GLU* 1.3 77.7 - - - +
175C VAL* 1.3 66.6 + - - +
176C GLU* 4.4 6.1 - - + -
208C LYS* 3.5 6.7 - - - +
209C LYS* 2.8 69.6 + - + -
211C VAL* 3.4 32.3 - - + -
320C GLN* 3.4 23.8 - - - +
322C ASP 3.5 19.1 - - - +
323C PRO* 3.5 38.4 - - + -
324C PRO* 4.2 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 175 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ARG* 5.2 11.9 - - - +
174C PHE* 1.3 77.6 - - - +
176C GLU* 1.3 61.7 + - - +
177C GLU* 4.1 7.2 - - - +
206C MET* 3.7 29.6 - - + -
207C VAL 3.1 22.2 - - - +
208C LYS* 4.5 3.8 - - + +
320C GLN 3.1 13.8 + - - +
321C ARG* 3.7 16.9 - - + +
322C ASP 3.0 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 176 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C PHE* 4.4 11.1 - - + -
175C VAL* 1.3 76.9 - - - +
177C GLU* 1.3 78.8 + - - +
205C THR* 4.2 1.0 - - - +
206C MET 3.7 0.2 + - - -
207C VAL* 2.8 38.1 + - - +
209C LYS* 3.3 30.5 + - + +
322C ASP* 4.6 10.0 - - - +
323C PRO* 3.2 35.0 - - + +
420D LYS* 5.2 2.6 + - - +
421D GLN* 3.8 11.8 + - - -
----------------------------------------------------------
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