Contacts of the strand formed by residues 210 - 219 (chain D) in PDB entry 2J2M
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 210 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202D LYS* 4.0 17.3 - - - +
203D TRP 3.1 9.7 + - - -
204D VAL* 3.7 17.0 - - + -
208D GLY 4.4 8.1 - - - +
209D ASN* 1.3 75.4 - - - +
211D VAL* 1.3 69.6 + - - +
266D ASP* 5.2 0.3 - - - +
267D PRO* 3.3 27.3 - - + +
401D ASP* 5.4 0.2 - - - +
403D GLN* 3.2 39.3 + - - +
404D PRO* 5.8 2.0 - - + -
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Residues in contact with VAL 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D TYR* 4.2 22.2 - - + +
202D LYS* 3.4 4.2 - - - -
203D TRP* 2.9 42.4 + - + +
209D ASN* 5.3 4.7 - - + +
210D THR* 1.3 82.6 + - - +
212D TYR* 1.3 63.0 + - - +
213D ILE* 3.6 21.0 + - + -
264D VAL* 3.6 27.4 - - + -
265D LEU 3.7 7.4 - - - +
266D ASP* 4.9 10.1 - - - +
267D PRO* 4.0 6.1 - - + -
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Residues in contact with TYR 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ARG* 4.9 4.7 + - - -
200D SER* 4.1 1.6 - - - -
201D PHE 3.3 10.8 - - - -
202D LYS* 3.5 29.2 + - + -
211D VAL* 1.3 73.2 - - - +
213D ILE* 1.3 62.7 + - - +
263D GLN 3.9 0.2 - - - +
264D VAL* 3.6 0.3 - - - -
265D LEU* 2.7 46.9 + - + +
267D PRO* 4.0 25.8 - - + +
270D VAL* 3.8 31.2 - - + -
278D LEU* 3.7 28.3 - - + +
284D TRP* 3.8 19.1 - - + -
327D SER* 3.7 12.6 - - - -
328D GLU* 2.8 32.8 + - - -
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Residues in contact with ILE 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D HIS 4.2 0.2 - - - +
200D SER* 2.9 7.1 - - - -
201D PHE* 2.7 54.1 + - + +
203D TRP* 3.6 55.2 - - + +
211D VAL* 3.6 24.0 - - + +
212D TYR* 1.3 81.6 - - - +
214D LYS* 1.3 64.8 + - - +
215D LEU* 3.9 28.0 - - + +
262D VAL* 3.9 8.7 - - + -
263D GLN 3.2 9.4 - - - +
264D VAL* 4.4 4.3 - - + -
284D TRP* 3.8 3.6 - - - -
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Residues in contact with LYS 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D PRO 5.1 2.0 + - - -
197D SER* 3.3 17.9 - - - +
198D VAL* 2.9 24.5 + - - +
199D HIS* 3.5 13.9 - - - +
200D SER* 3.6 12.5 - - - +
213D ILE* 1.3 73.2 - - - +
215D LEU* 1.3 66.7 - - - +
216D ARG* 4.9 6.5 - - - +
261D PHE 3.9 0.2 - - - +
262D VAL* 3.4 6.4 - - - +
263D GLN* 2.9 43.9 + - + +
277D PRO 4.2 7.5 + - - -
279D ASP 5.1 2.0 + - - -
282D LYS 3.3 21.2 + - - -
283D ASP* 5.1 1.3 - - - +
284D TRP* 3.4 60.8 - - + +
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Residues in contact with LEU 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D TRP* 3.7 35.7 - - + -
126D PHE* 3.9 16.4 - - + -
196D SER* 3.7 1.7 - - - -
197D SER* 2.8 46.5 + - - -
201D PHE* 5.9 3.1 - - + -
203D TRP* 4.1 13.0 - - + +
213D ILE* 3.9 17.7 - - + +
214D LYS* 1.3 82.8 - - - +
216D ARG* 1.3 70.1 + - - +
260D LEU* 3.9 20.6 - - + -
261D PHE 3.7 9.2 - - - +
262D VAL* 3.7 22.7 - - + -
294D VAL* 5.4 0.2 - - + -
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Residues in contact with ARG 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D PRO* 3.3 24.1 - - - +
194D ARG* 4.1 12.1 - - - +
195D GLY 3.7 4.7 + - - +
196D SER* 4.4 10.9 + - - +
214D LYS* 4.9 8.6 - - - +
215D LEU* 1.3 85.1 + - - +
217D TRP* 1.3 65.2 + - - +
218D VAL* 4.2 1.3 + - + -
259D ASP 3.4 1.2 - - - +
260D LEU* 3.4 7.3 - - - +
261D PHE* 2.7 56.1 + - + +
263D GLN* 2.6 39.7 + - + +
283D ASP* 3.1 31.5 + - - -
284D TRP* 3.2 11.9 + - - +
291D PHE* 3.2 34.8 - - + -
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Residues in contact with TRP 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D PHE* 3.9 21.8 - + - -
113D PHE* 3.4 29.3 - + + -
115D VAL* 4.2 9.6 - - + -
117D PHE* 3.9 23.3 - + - -
124D TRP* 6.0 0.4 - + - -
126D PHE* 3.3 46.8 - + - -
194D ARG* 3.3 11.6 - - - +
195D GLY* 2.9 41.0 + - - +
216D ARG* 1.3 73.8 - - - +
218D VAL* 1.3 63.0 + - - +
219D PRO 4.2 0.2 - - - -
258D TRP* 3.6 25.1 - - + -
259D ASP 3.3 5.4 - - - -
260D LEU* 3.8 32.8 - - + +
297D MET* 3.5 34.8 - - + -
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Residues in contact with VAL 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D ARG* 5.1 0.7 - - + -
216D ARG* 5.7 0.4 - - + -
217D TRP* 1.3 77.3 - - - +
219D PRO* 1.3 77.9 - - + +
220D LYS 3.6 0.3 + - - -
258D TRP* 3.1 5.2 - - - -
259D ASP* 2.8 43.9 + - + +
261D PHE* 3.7 32.3 - - + -
291D PHE* 4.7 16.2 - - + -
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Residues in contact with PRO 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D ARG 3.7 13.7 - - - +
193D MET 3.3 31.0 - - - +
194D ARG* 3.8 13.2 - - + -
218D VAL* 1.3 96.2 - - + +
220D LYS* 1.3 64.3 + - - +
221D GLU 4.1 0.2 - - - +
222D GLY* 3.1 42.7 + - - +
223D VAL* 3.8 8.3 - - + -
257D GLU 3.7 2.2 - - - +
258D TRP* 3.4 12.8 - - + +
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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