Contacts of the strand formed by residues 171 - 175 (chain A) in PDB entry 1YBY
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 ILE 171 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLU* 3.9 28.5 - - + +
131A LEU 3.4 12.3 - - - +
132A GLU* 4.5 15.9 - - + +
169A GLY 4.2 7.4 - - - +
170A ASP* 1.3 76.0 - - - +
172A ILE* 1.3 58.4 + - - +
184A ARG* 3.5 7.3 - - - +
185A VAL* 2.7 44.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A VAL 3.6 0.5 - - - +
130A GLU* 3.4 3.0 - - - -
131A LEU 2.8 39.8 + - - +
133A VAL* 3.8 28.3 - - + -
154A VAL* 3.9 14.4 - - + -
160A ILE* 4.3 5.8 - - + -
162A VAL* 4.0 19.3 - - + -
166A VAL* 4.3 8.7 - - + -
170A ASP* 4.7 1.8 - - + -
171A ILE* 1.3 81.0 - - - +
173A ARG* 1.3 59.7 + - - +
174A ILE* 3.9 19.7 + - + +
181A TYR* 3.6 29.6 - - + -
183A GLU 3.5 6.3 - - - +
184A ARG* 4.1 11.7 - - + -
185A VAL* 4.0 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A PHE* 4.6 4.0 - - + -
129A VAL 3.3 11.7 - - - +
130A GLU* 3.3 21.0 + - + +
172A ILE* 1.3 72.2 - - - +
174A ILE* 1.3 63.7 - - - +
181A TYR* 3.7 1.9 - - - -
182A MSE 2.9 43.8 + - + -
183A GLU* 2.3 50.4 + - + +
185A VAL* 3.3 32.1 + - - +
1005A UNX 3.5 21.5 - - - -
149B THR* 4.6 9.7 + - - -
150B LYS* 5.1 1.0 - - - +
151B PRO* 3.7 33.2 - - - +
161B LYS* 5.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PHE* 4.0 24.7 - - + -
128A PHE* 3.2 12.0 - - - +
129A VAL* 2.9 37.6 + - + +
131A LEU* 3.9 29.4 - - + -
154A VAL* 4.2 8.7 - - + -
160A ILE* 3.6 24.9 - - + -
172A ILE* 4.1 22.9 - - + +
173A ARG* 1.3 79.5 - - - +
175A ASP* 1.3 76.7 + - - +
176A THR 3.6 1.8 + - - +
179A GLY* 4.1 10.1 - - - -
180A GLU 3.5 8.1 - - - +
182A MSE 4.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ASN 3.7 6.0 - - - +
128A PHE* 4.0 8.1 - - - -
174A ILE* 1.3 70.1 - - - +
176A THR* 1.3 55.1 + - - +
177A ARG* 2.9 24.1 + - - +
178A THR* 3.3 31.6 + - - +
179A GLY* 2.7 36.7 + - - -
180A GLU* 3.0 12.3 + - + +
182A MSE 4.1 9.8 - - + +
153B ILE* 4.6 6.0 - - - +
157B GLY 5.2 1.9 - - - +
158B ALA* 5.6 0.2 - - - -
159B SER* 2.7 38.9 + - - +
----------------------------------------------------------
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