Contacts of the strand formed by residues 223 - 237 (chain A) in PDB entry 1N9P
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 MSE 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A MSE 3.7 18.8 - - + -
217A ASN* 2.7 43.5 + - - +
218A LEU* 3.6 29.4 - - + -
221A SER 3.5 9.6 - - - +
222A HIS* 1.3 82.4 + - - +
224A VAL* 1.3 63.7 + - - +
225A SER 3.9 8.7 - - - +
264A LEU* 3.8 13.0 - - + +
299A LEU* 3.7 17.9 - - + -
301A GLY* 3.3 26.0 - - - -
302A ILE 3.2 22.9 - - - +
303A VAL* 4.0 2.9 - - - +
310A CYS* 3.6 19.1 - - - -
312A ALA* 6.0 0.2 - - - -
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Residues in contact with VAL 224 (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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53A CYS* 4.7 11.7 - - - -
222A HIS* 4.6 2.9 - - + +
223A MSE 1.3 77.5 - - - +
225A SER* 1.3 62.2 + - - +
263A PHE* 3.5 31.6 - - + -
264A LEU* 2.7 38.9 + - - +
302A ILE 3.6 4.2 + - - +
304A GLU* 3.9 31.4 - - + +
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Residues in contact with SER 225 (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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223A MSE 3.9 4.5 - - - +
224A VAL* 1.3 82.3 - - - +
226A ALA* 1.3 68.5 + - - +
262A LEU 3.6 8.7 + - - -
263A PHE* 6.0 0.2 - - - -
264A LEU* 4.9 0.2 - - - -
301A GLY* 3.4 0.5 - - - -
302A ILE* 2.9 52.2 + - - +
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Residues in contact with ALA 226 (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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225A SER* 1.3 81.4 + - - +
227A GLN* 1.3 57.8 + - - +
261A GLN* 3.5 6.4 - - - +
262A LEU* 2.7 42.1 + - + -
264A LEU* 4.1 14.8 - - + -
299A LEU* 3.7 23.3 - - + -
300A GLU 3.4 7.6 - - - +
301A GLY* 3.5 14.8 - - - -
302A ILE* 5.7 0.9 - - - -
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Residues in contact with GLN 227 (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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226A ALA* 1.3 76.2 - - - +
228A ILE* 1.3 68.4 + - - +
229A ARG* 3.4 29.6 + - - +
260A ASP* 3.2 21.0 - - - +
261A GLN* 2.6 37.7 + - - +
298A ILE 3.7 0.9 - - - +
299A LEU* 3.4 2.9 - - - +
300A GLU* 2.9 44.1 + - + +
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Residues in contact with ILE 228 (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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213A PHE* 3.7 21.1 - - + -
215A VAL* 3.9 15.9 - - + -
227A GLN* 1.3 78.7 - - - +
229A ARG* 1.3 68.4 + - - +
253A VAL* 3.7 16.3 - - + +
260A ASP* 2.9 43.7 + - - +
262A LEU* 3.9 26.7 - - + -
270A ILE* 3.9 12.1 - - + -
297A VAL* 3.6 28.3 - - + -
298A ILE 3.3 10.8 - - - +
299A LEU* 4.6 7.4 - - + -
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Residues in contact with ARG 229 (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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227A GLN* 3.4 25.7 + - - +
228A ILE* 1.3 76.7 - - - +
230A CYS* 1.3 61.9 + - - +
231A LYS* 4.0 23.4 - - - +
250A GLU* 4.8 7.9 - - - +
253A VAL* 3.9 7.2 - - - -
297A VAL* 3.6 5.5 - - - +
298A ILE* 2.9 68.5 + - + +
300A GLU* 3.2 43.4 + - - +
311A GLN* 4.3 2.8 - - - +
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Residues in contact with CYS 230 (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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211A LEU* 5.3 2.7 - - - -
213A PHE* 4.6 9.6 - - + -
229A ARG* 1.3 78.0 - - - +
231A LYS* 1.3 63.8 + - - +
250A GLU* 3.8 9.8 + - - +
251A LEU* 3.1 54.9 + - + +
253A VAL* 3.9 17.3 - - + +
295A VAL* 3.3 33.9 - - - -
296A VAL 3.3 7.2 - - - -
297A VAL* 4.4 9.0 - - + -
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Residues in contact with LYS 231 (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 ARG* 4.0 28.7 - - - +
230A CYS* 1.3 74.6 - - - +
232A LEU* 1.3 60.6 + - - +
233A LEU* 3.8 18.7 + - + -
248A GLN* 3.7 26.2 + - + +
249A LEU 3.5 6.1 - - - +
250A GLU* 2.7 33.3 + - - +
251A LEU* 4.1 4.1 - - - +
294A GLU 3.6 1.0 - - - +
295A VAL* 3.5 2.9 - - - -
296A VAL* 2.8 36.6 + - + +
298A ILE* 4.1 17.7 - - + -
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Residues in contact with LEU 232 (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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231A LYS* 1.3 72.8 - - - +
233A LEU* 1.3 60.2 + - - +
234A LYS* 4.0 15.4 + - + +
247A ASP 3.3 5.5 - - - +
248A GLN* 3.3 0.9 - - - -
249A LEU* 2.6 58.6 + - + +
251A LEU* 3.9 12.3 - - + +
279A PRO* 3.6 27.6 - - + +
280A PHE* 3.6 39.9 - - + -
293A PHE* 3.7 28.5 - - + -
294A GLU 3.7 1.3 - - - +
295A VAL* 4.0 7.6 - - + -
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Residues in contact with LEU 233 (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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231A LYS* 3.8 14.1 - - + +
232A LEU* 1.3 75.0 - - - +
234A LYS* 1.3 65.2 + - - +
246A LEU* 3.9 33.0 - - + -
247A ASP 3.3 2.5 - - - -
248A GLN* 3.6 32.8 - - + +
293A PHE* 3.4 2.4 - - - +
294A GLU* 2.8 53.4 + - + +
296A VAL* 3.8 29.8 - - + -
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Residues in contact with LYS 234 (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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232A LEU* 4.2 14.1 - - + +
233A LEU* 1.3 77.6 - - - +
235A SER* 1.3 74.4 + - - +
236A ARG* 4.5 13.8 - - + +
245A PRO 4.2 2.2 - - - -
246A LEU* 4.3 5.6 - - - +
247A ASP* 2.7 40.6 + - + +
249A LEU* 4.1 26.7 - - + -
291A GLU* 3.2 28.3 + - - -
292A GLN 3.8 19.5 - - - +
293A PHE* 4.1 6.1 - - + +
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Residues in contact with SER 235 (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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234A LYS* 1.3 86.3 - - - +
236A ARG* 1.3 65.9 + - - +
243A PHE* 3.6 25.0 - - - -
244A LEU 3.1 7.0 - - - -
245A PRO 2.5 19.8 + - - -
246A LEU* 5.8 0.2 - - - +
292A GLN 5.0 2.5 + - - +
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Residues in contact with ARG 236 (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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234A LYS* 4.5 13.9 - - - +
235A SER* 1.3 78.4 - - - +
237A GLN* 1.3 60.5 + - - +
238A THR* 4.0 24.9 - - - +
239A PRO* 5.0 4.9 - - - +
242A GLU 3.6 0.5 - - - +
243A PHE* 3.5 9.2 - - - -
244A LEU* 2.6 61.9 + - + +
247A ASP* 2.8 35.0 + - + -
249A LEU* 4.5 22.5 - - - +
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Residues in contact with GLN 237 (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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236A ARG* 1.3 79.2 + - - +
238A THR* 1.3 75.0 + - - +
239A PRO* 4.6 0.5 - - - +
241A GLY* 3.7 25.3 + - - +
242A GLU 3.1 13.5 - - - +
243A PHE* 4.2 13.4 - - + +
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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