Contacts of the strand formed by residues 255 - 263 (chain A) in PDB entry 1S9C
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 THR 255 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A THR* 4.3 11.4 - - - -
178A ASP 3.3 19.3 - - - +
179A THR* 4.1 19.0 + - - +
253A GLY 4.4 1.2 + - - -
254A GLN* 1.3 74.1 + - - +
256A LEU* 1.3 68.9 + - - +
273A VAL* 3.3 6.4 - - - -
274A GLN* 3.0 48.2 + - + +
275A GLU* 2.7 25.0 + - - -
171E PRO* 4.4 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LEU 4.8 0.2 - - - -
177A THR* 3.3 9.0 - - - -
178A ASP* 2.8 39.5 + - + +
180A THR* 4.0 15.5 - - - +
214A LEU* 5.3 2.0 - - + -
219A THR* 3.7 32.1 - - + +
222A PHE* 3.6 44.0 - - + -
223A SER* 5.5 0.2 - - - +
250A VAL* 4.0 27.8 - - + -
254A GLN 5.5 0.2 - - - +
255A THR* 1.3 77.0 - - - +
257A GLN* 1.3 60.8 + - - +
258A THR* 4.1 4.5 - - - +
271A THR* 4.4 8.3 - - + -
272A LYS 3.4 9.9 - - - +
273A VAL* 4.5 2.0 - - + -
280A VAL* 4.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A VAL* 4.0 16.6 - - + -
176A LEU 3.9 2.7 - - - -
177A THR* 3.9 20.1 - - + +
256A LEU* 1.3 75.8 - - - +
258A THR* 1.3 61.5 + - - +
259A GLU* 3.6 9.8 + - + +
270A GLN 3.6 0.2 - - - +
271A THR* 3.3 4.4 - - - -
272A LYS* 2.8 59.4 + - + +
274A GLN* 2.9 43.9 - - - +
277A GLY* 5.7 1.4 - - - -
171E PRO* 5.1 1.6 - - - +
172E PRO* 6.0 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A VAL* 3.1 4.5 - - - -
176A LEU 3.0 35.5 + - - -
178A ASP* 5.0 2.6 + - - -
222A PHE* 5.6 1.0 - - - +
223A SER* 2.9 51.4 + - - +
226A ARG* 4.6 9.0 - - + +
227A VAL* 4.8 0.2 - - + -
256A LEU* 5.1 3.6 - - - +
257A GLN* 1.3 73.2 + - - +
259A GLU* 1.3 61.3 + - - +
260A MET* 3.9 25.3 - - + +
269A PHE* 4.1 14.6 - - + -
270A GLN 3.5 2.5 - - - -
271A THR* 4.0 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A PRO* 4.2 15.1 - - + +
174A ALA 3.8 4.0 - - - -
175A VAL* 4.0 15.2 - - + +
257A GLN* 4.2 12.9 - - + +
258A THR* 1.3 73.2 - - - +
260A MET* 1.3 60.0 + - - +
261A TRP* 3.4 19.8 - - + -
269A PHE* 3.0 8.1 - - - +
270A GLN* 2.7 68.0 + - + +
272A LYS* 3.0 36.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A PRO* 3.6 2.3 - - - +
173A ASP* 2.7 32.9 + - - -
174A ALA 2.7 21.8 + - - +
176A LEU* 3.4 42.4 - - + +
226A ARG* 4.3 9.4 - - + -
227A VAL* 3.8 27.4 - - + -
230A GLN* 4.2 7.4 - - + -
231A PHE* 3.5 31.6 - - + -
258A THR* 3.9 22.0 - - + +
259A GLU* 1.3 78.5 - - - +
261A TRP* 1.3 59.5 + - - +
262A LYS 4.3 0.2 - - - -
267A ILE* 4.1 2.5 - - + -
268A HIS 3.3 6.1 - - - +
269A PHE* 4.2 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 3.5 33.0 - - + -
168A PRO* 3.7 41.7 + - + -
170A ARG* 2.7 44.7 + - + +
171A PRO 3.8 0.2 - - - -
172A PRO* 3.3 34.4 - - + +
173A ASP* 3.4 4.9 - - - -
231A PHE* 5.3 0.2 - - - -
259A GLU* 3.4 42.6 - - + -
260A MET* 1.3 76.5 - - - +
262A LYS* 1.3 63.5 + - - +
263A GLU* 3.6 1.6 + - - -
267A ILE* 3.4 4.9 - - - -
268A HIS* 2.8 54.0 + - + +
269A PHE* 4.1 0.7 - - - -
270A GLN* 3.7 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ARG* 3.4 14.4 + - - -
173A ASP* 2.7 17.3 + - - +
231A PHE* 3.8 31.8 - - + -
260A MET 4.3 0.2 - - - -
261A TRP* 1.3 71.1 - - - +
263A GLU* 1.3 64.4 + - - +
264A GLY* 3.0 26.5 + - - +
265A ASN* 5.8 0.9 - - - +
267A ILE* 3.5 20.0 - - + -
39E LYS 5.7 3.0 + - - -
41E PRO* 6.1 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PRO* 3.9 13.8 - - + +
170A ARG* 2.7 37.5 + - - +
261A TRP 4.5 0.2 - - - +
262A LYS* 1.3 72.5 - - - +
264A GLY* 1.3 62.6 + - - +
265A ASN 3.3 0.3 + - - -
266A ARG* 2.9 28.9 + - + +
268A HIS* 3.5 31.4 - - + +
----------------------------------------------------------
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