Contacts of the strand formed by residues 243 - 254 (chain A) in PDB entry 1PO3
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 LYS 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A THR* 5.9 1.8 - - + -
142A ASP* 2.8 32.5 + - - +
230A GLU 3.4 4.9 - - - +
231A GLY* 3.8 0.8 - - - -
232A GLN* 3.2 55.2 + - + +
242A PRO* 1.3 75.7 - - - +
244A GLU* 1.3 68.3 + - - +
245A THR* 4.6 4.7 - - + -
267A THR* 4.1 14.1 - - + -
268A ARG 3.8 2.9 - - - -
269A GLY* 3.8 23.6 + - - -
270A SER* 3.6 13.2 + - - +
271A ASP* 3.9 30.3 + - + +
276A SER 4.6 1.6 + - - -
278A THR* 4.2 5.0 + - - -
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Residues in contact with GLU 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A VAL* 4.2 9.6 - - + +
230A GLU 3.3 8.1 - - - +
231A GLY* 4.5 3.8 - - - -
242A PRO* 3.9 4.6 + - + -
243A LYS* 1.3 75.1 - - - +
245A THR* 1.3 72.9 + - - +
246A HIS* 2.4 47.5 + - - +
266A GLY 3.6 2.1 - - - +
267A THR* 3.5 1.2 - - - +
268A ARG* 2.7 53.9 + - + +
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Residues in contact with THR 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A THR* 3.0 37.2 + - + +
119A THR* 5.7 2.2 - - + -
229A VAL* 3.0 20.0 - - - +
230A GLU* 3.1 22.5 + - - +
232A GLN* 4.8 1.1 + - - +
243A LYS* 4.6 9.6 - - + -
244A GLU* 1.3 86.9 + - - +
246A HIS* 1.3 67.9 + - - +
266A GLY 3.5 4.7 - - - -
267A THR* 3.6 24.5 - - + +
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Residues in contact with HIS 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A GLY 3.1 13.9 - - - +
229A VAL* 4.3 6.5 - - + +
244A GLU* 2.4 45.8 + - - +
245A THR* 1.3 77.6 - - - +
247A ASN* 1.3 62.5 + - - +
248A LEU* 6.3 0.2 - - + -
264A TYR* 3.5 37.3 + + - -
265A SER* 3.3 5.4 + - - -
266A GLY 2.9 42.4 + - - -
268A ARG* 4.3 14.5 + - + -
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Residues in contact with ASN 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ARG* 3.8 22.4 - - - +
187A GLY* 3.6 32.1 + - - +
217A ARG* 4.1 13.9 - - - +
226A GLU* 5.5 0.6 - - - +
227A ALA* 3.2 8.3 - - - +
228A GLY* 2.9 51.7 + - - +
246A HIS* 1.3 78.0 - - - +
248A LEU* 1.3 61.6 + - - +
264A TYR* 3.0 12.8 - - - +
265A SER* 4.2 0.4 - - - +
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Residues in contact with LEU 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ARG* 5.3 2.7 - - - -
225A ILE* 4.7 6.5 - - + -
226A GLU 3.5 16.2 - - - +
227A ALA* 3.8 15.3 - - + -
246A HIS* 6.3 0.2 - - + -
247A ASN* 1.3 75.8 - - - +
249A MET* 1.3 60.8 + - - +
250A VAL* 4.6 19.5 - - + -
262A LEU* 3.6 9.7 - - + +
263A LEU* 3.9 1.7 - - - +
264A TYR* 2.7 58.3 + - + +
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Residues in contact with MET 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ARG* 4.6 11.4 - - - +
220A PRO* 6.4 0.9 - - - -
224A GLY 4.3 0.7 - - - -
225A ILE* 2.9 9.9 - - - +
226A GLU* 2.7 41.5 + - - +
248A LEU* 1.3 75.1 - - - +
250A VAL* 1.3 65.2 + - - +
262A LEU 3.7 4.3 - - - -
263A LEU* 4.8 8.3 - - - -
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Residues in contact with VAL 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A PRO* 5.5 0.9 - - - -
223A PHE* 4.6 10.8 - - + -
224A GLY 3.4 4.7 - - - +
225A ILE* 3.5 31.4 - - + -
248A LEU* 4.6 15.9 - - + -
249A MET* 1.3 79.7 - - - +
251A GLY* 1.3 60.1 + - - +
260A THR* 5.7 0.2 - - - +
261A ALA* 4.2 2.4 - - - +
262A LEU* 2.6 52.7 + - + +
263A LEU* 5.6 0.4 - - - +
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Residues in contact with GLY 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A PRO* 3.8 13.2 - - - +
223A PHE* 3.6 8.3 - - - -
224A GLY 3.1 31.1 + - - +
250A VAL* 1.3 81.1 - - - +
252A GLY* 1.3 58.8 + - - -
260A THR 2.8 14.6 - - - -
261A ALA* 3.7 3.8 - - - -
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Residues in contact with GLY 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ILE* 3.8 0.8 - - - +
220A PRO* 3.5 11.2 - - - +
222A ASP 2.8 15.7 - - - -
223A PHE* 4.2 4.5 - - - -
251A GLY* 1.3 75.3 - - - -
253A THR* 1.3 61.6 + - - -
259A GLY* 3.0 1.4 - - - -
260A THR 2.6 37.0 + - - +
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Residues in contact with THR 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ILE* 4.0 4.9 - - + +
220A PRO 2.7 12.3 + - - -
221A GLN* 2.3 36.5 + - - +
222A ASP* 2.8 19.6 + - - +
252A GLY* 1.3 71.6 - - - -
254A ALA* 1.3 69.0 + - - +
255A ASP 3.8 0.2 + - - -
257A GLY* 4.4 4.5 - - - +
258A PHE* 2.7 31.6 - - - +
259A GLY* 3.3 6.5 - - - +
288A LYS* 5.3 5.6 - - + +
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Residues in contact with ALA 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A ASP* 5.2 0.7 - - - -
252A GLY 4.4 0.4 - - - -
253A THR* 1.3 78.1 - - - +
255A ASP* 1.3 62.9 + - - +
256A ASN* 2.9 28.3 + - + +
257A GLY* 3.1 12.1 + - - -
258A PHE* 2.7 15.1 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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