Contacts of the strand formed by residues 244 - 255 (chain P) in PDB entry 2IMW
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 244 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242P ARG* 3.7 6.5 - - - +
243P LYS* 1.3 80.1 - - - +
245P ILE* 1.3 69.8 + - - +
336P ARG* 3.0 31.7 + - - -
337P PHE 3.1 13.2 - - - -
338P SER* 4.1 6.5 - - - -
340P PHE* 3.9 2.2 - - - -
348P LYS* 5.3 3.1 - - - -
504P EDO 4.2 4.0 - - - -
1803S G 3.6 19.9 - - - +
1804S G 2.7 21.2 + - - -
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Residues in contact with ILE 245 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242P ARG* 3.6 22.2 - - + +
244P SER* 1.3 79.2 - - - +
246P GLY* 1.3 61.6 + - - +
272P SER* 3.9 11.9 - - - +
275P LYS* 3.6 38.4 - - + +
276P LEU* 4.0 20.0 - - + +
279P ARG* 3.2 43.7 - - - +
336P ARG* 4.1 2.2 - - - -
337P PHE* 2.8 37.6 + - - +
340P PHE* 4.0 4.9 - - + -
1803S G 3.5 9.0 - - - +
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Residues in contact with GLY 246 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245P ILE* 1.3 76.8 - - - +
247P ARG* 1.3 58.0 + - - -
272P SER* 3.6 9.4 - - - -
275P LYS* 2.8 30.3 + - - -
335P VAL 3.1 15.5 - - - -
336P ARG* 3.3 14.0 + - - +
1802S G 4.0 2.7 - - - +
1803S G 2.8 14.1 + - - -
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Residues in contact with ARG 247 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32P VAL* 6.3 0.4 - - - +
246P GLY* 1.3 74.7 - - - +
248P ILE* 1.3 69.5 + - - +
249P VAL* 3.8 19.4 - - + +
268P ALA* 3.6 13.4 - - - +
271P GLU* 3.2 40.4 + - + +
272P SER* 3.4 12.9 + - - +
275P LYS* 4.5 11.7 - - - +
334P GLY* 3.1 2.9 - - - -
335P VAL 2.9 28.5 + - - -
336P ARG* 4.4 1.6 - - - +
502P EDO 3.4 23.6 + - - -
506P EDO 4.0 15.0 + - - -
1801S G 3.9 15.1 + - - -
1802S G 3.2 24.6 + - - -
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Residues in contact with ILE 248 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247P ARG* 1.3 83.1 + - - +
249P VAL* 1.3 64.0 + - - +
250P THR* 4.2 0.9 + - - -
287P VAL* 3.8 31.2 - - + +
289P VAL* 4.3 13.2 - - + -
295P ILE* 6.5 0.9 - - + -
332P ARG* 3.7 30.9 - - + -
333P ILE 3.7 12.3 - - - +
334P GLY* 4.1 8.5 - - - +
335P VAL 4.7 0.9 - - - +
336P ARG* 4.9 14.6 - - - +
1801S G 4.3 9.8 - - - +
1802S G 2.8 35.6 + - + +
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Residues in contact with VAL 249 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247P ARG* 3.8 30.5 - - + +
248P ILE* 1.3 76.1 - - - +
250P THR* 1.3 62.3 + - - +
251P MET 3.7 0.9 + - - -
264P TYR* 3.5 48.5 - - + +
268P ALA* 4.3 10.5 - - + -
271P GLU* 4.1 3.4 - - - +
332P ARG* 3.3 3.5 - - - -
333P ILE* 2.8 40.7 + - - +
506P EDO 3.8 25.6 - - - +
1801S G 6.0 0.2 - - - -
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Residues in contact with THR 250 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34P SER* 4.5 27.2 - - - +
36P ARG* 3.9 27.6 - - + +
248P ILE 4.2 1.3 + - - -
249P VAL* 1.3 73.7 - - - +
251P MET* 1.3 76.0 + - - +
264P TYR* 4.0 11.0 - - - -
331P ARG* 4.4 8.7 - - - +
332P ARG* 3.5 31.4 + - + +
506P EDO 5.5 0.7 + - - -
1801S G 4.9 9.9 + - - -
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Residues in contact with MET 251 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36P ARG* 3.5 12.3 + - - +
249P VAL 4.3 1.1 - - - +
250P THR* 1.3 87.9 - - - +
252P LYS* 1.3 65.3 + - - +
253P ARG 3.3 17.4 + - - +
255P SER* 4.3 6.1 - - - +
260P GLU* 4.9 1.1 - - - +
261P ILE* 3.9 27.4 - - + -
264P TYR* 3.6 44.0 - - + -
330P ILE* 3.0 48.9 - - + +
331P ARG 3.1 14.7 + - - +
332P ARG 5.0 0.2 - - - -
333P ILE* 4.1 16.6 - - + -
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Residues in contact with LYS 252 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35P GLY 3.3 17.0 + - - +
36P ARG* 2.8 45.7 + - - +
251P MET* 1.3 75.9 - - - +
253P ARG* 1.3 64.2 + - + +
264P TYR* 3.2 21.1 + - - +
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Residues in contact with ARG 253 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36P ARG* 3.9 7.2 - - - +
251P MET* 3.7 18.9 - - - +
252P LYS* 1.3 84.6 - - + +
254P ASN* 1.3 75.5 + - - +
255P SER* 3.6 3.8 + - - -
260P GLU* 3.4 34.8 + - - +
331P ARG 5.4 0.4 - - - -
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Residues in contact with ASN 254 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36P ARG* 3.0 22.2 + - - +
253P ARG* 1.3 88.0 + - - +
255P SER* 1.3 60.8 + - - +
291P GLU* 3.6 31.2 + - - +
329P LYS* 4.0 31.7 + - + +
330P ILE 3.3 7.9 - - - +
331P ARG* 3.3 20.3 - - - +
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Residues in contact with SER 255 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251P MET* 4.3 3.6 - - - -
253P ARG 4.0 5.8 - - - -
254P ASN* 1.3 77.3 - - - +
256P ARG* 1.3 65.6 + - - +
257P ASN* 3.0 18.6 + - - +
260P GLU* 2.7 33.7 + - - +
261P ILE* 3.5 16.1 - - - +
329P LYS* 4.3 6.4 - - - +
330P ILE* 3.0 37.1 + - - +
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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