Contacts of the strand formed by residues 255 - 260 (chain A) in PDB entry 1I9R
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 SER 255 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A HIS* 3.2 35.7 + - - -
126A VAL 3.6 9.0 - - - -
127A ILE* 5.2 1.6 - - - -
140A TRP* 3.4 6.8 - - - -
172A TYR* 5.3 1.3 - - - -
173A ALA* 3.4 1.4 - - - -
174A GLN* 2.8 47.1 + - - +
252A GLY 4.8 4.3 + - - -
253A PHE 4.5 1.9 + - - -
254A THR* 1.3 75.8 - - - +
256A PHE* 1.3 63.9 + - - +
205B LEU 6.1 0.2 - - - -
206B LEU* 4.6 9.7 - - - +
226B GLY 5.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A HIS* 3.6 2.6 + - - -
126A VAL* 3.0 34.7 + - + +
140A TRP* 3.4 51.8 - + + -
159A LYS 4.5 1.1 - - - -
160A GLN* 4.6 0.7 - - - -
161A LEU* 3.3 37.0 - - + -
171A ILE* 4.6 5.2 - - + -
172A TYR* 3.3 21.1 - - - -
173A ALA* 4.0 2.0 - - + +
193A LEU* 4.3 11.9 - - + -
237A VAL* 3.4 41.1 - - + -
238A PHE* 4.1 6.3 - - - -
239A VAL* 3.4 19.7 - - + -
255A SER* 1.3 80.0 - - - +
257A GLY* 1.3 67.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ALA 2.8 14.6 - - - -
161A LEU* 3.9 10.1 - - - -
171A ILE* 3.8 2.1 - - - +
172A TYR* 2.8 54.8 + - - +
256A PHE* 1.3 79.7 - - - +
258A LEU* 1.3 63.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ILE* 4.6 4.0 - - + -
123A ALA* 3.1 3.5 - - - +
124A ALA* 2.8 34.1 + - + +
153A VAL* 3.6 25.8 - - + -
161A LEU* 3.9 31.0 - - + +
163A VAL* 4.2 13.5 - - + -
169A TYR* 3.6 25.8 - - + -
170A TYR 3.2 12.3 - - - +
171A ILE* 3.7 19.1 - - + -
172A TYR* 3.8 3.5 - - - -
231A LEU* 5.1 2.2 - - + -
237A VAL* 3.9 18.2 - - + -
257A GLY* 1.3 73.9 - - - +
259A LEU* 1.3 62.8 + - - +
228B VAL* 5.2 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ILE 3.4 6.1 - - - +
123A ALA* 4.0 8.7 - - + +
169A TYR* 3.2 4.9 - - - -
170A TYR* 2.7 67.0 + - + +
172A TYR* 4.9 1.6 - - + -
258A LEU* 1.3 74.5 - - - +
260A LYS* 1.3 64.0 + - - +
261A LEU* 3.4 21.8 - - + -
170B TYR* 4.2 15.0 - - + -
228B VAL* 3.3 33.4 - - + -
259B LEU* 6.3 0.9 - - + -
261B LEU* 4.2 21.1 - - + -
259C LEU* 6.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLN* 5.7 1.6 - - - +
122A ILE* 2.9 44.6 + - + +
165A ARG* 4.5 10.3 - - + +
166A GLN 3.6 23.3 - - - -
167A GLY* 4.4 5.2 - - - -
168A LEU 3.6 9.2 - - - +
169A TYR* 3.4 38.8 - - + +
259A LEU* 1.3 77.6 - - - +
261A LEU* 1.3 80.1 + - - +
261B LEU* 5.6 5.9 - - - +
121C GLN* 5.2 2.2 - - - +
----------------------------------------------------------
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