Contacts of the strand formed by residues 210 - 224 (chain D) in PDB entry 6BAA
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 ILE 210 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299C GLN* 5.0 2.4 + - - -
177D ARG* 4.0 16.2 - - + +
181D LEU* 3.4 44.2 - - + -
204D ASP* 3.4 13.6 + - - +
209D MET* 1.3 84.6 - - - +
211D ILE* 1.3 63.2 + - - +
212D SER 3.8 0.2 + - - -
213D ALA* 3.7 24.0 + - + +
287D LEU* 5.3 4.5 - - + -
288D GLU 4.4 2.5 - - - +
289D GLY* 3.7 31.2 - - - -
290D VAL 3.3 11.7 - - - +
291D VAL* 5.2 4.5 - - + -
298D THR* 5.2 8.1 - - - +
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Residues in contact with ILE 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C GLU* 3.1 22.9 - - + +
297C THR* 3.2 46.7 - - + +
298C THR* 3.4 20.2 - - - +
299C GLN* 3.5 27.6 - - + +
301C ARG* 5.7 0.7 - - - +
209D MET* 5.0 1.1 - - + +
210D ILE* 1.3 68.8 - - - +
212D SER* 1.3 75.7 + - - +
213D ALA 3.1 3.4 + - - -
290D VAL* 2.8 41.6 + - + +
292D GLU* 4.1 25.6 - - + -
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Residues in contact with SER 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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216C HIS* 5.8 0.2 - - - -
288C GLU* 2.6 44.0 + - - +
297C THR* 4.6 5.4 - - - +
210D ILE 3.8 0.4 + - - -
211D ILE* 1.3 79.7 - - - +
213D ALA* 1.3 66.6 + - - +
214D THR* 3.0 16.1 + - - -
248D SER* 5.3 6.1 - - - -
289D GLY* 3.9 7.7 - - - -
290D VAL* 5.0 3.1 - - - -
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Residues in contact with ALA 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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210D ILE* 3.7 22.9 + - + +
211D ILE 3.1 3.5 - - - -
212D SER* 1.3 72.9 - - - +
214D THR* 1.3 60.3 + - - +
248D SER* 3.2 5.0 - - - -
249D ILE* 2.9 56.3 + - + +
251D LEU* 5.3 5.6 - - + +
287D LEU* 4.5 8.3 - - + -
288D GLU 3.4 11.7 - - - +
289D GLY* 4.3 1.3 - - - -
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Residues in contact with THR 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212D SER* 3.0 15.0 + - - -
213D ALA* 1.3 74.0 + - - +
215D ILE* 1.3 65.3 + - - +
216D HIS* 3.7 24.4 + - + +
247D ASN* 3.3 32.0 + - + +
248D SER* 4.5 5.9 - - - +
286D ILE 3.7 0.9 - - - +
287D LEU* 3.5 2.4 - - - -
288D GLU* 2.8 47.7 + - - +
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Residues in contact with ILE 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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183D PHE* 6.1 1.6 - - + -
202D VAL* 4.5 10.1 - - + -
214D THR* 1.3 72.1 - - - +
216D HIS* 1.3 71.1 + - - +
217D MET* 5.4 1.1 - - + -
240D MET* 3.6 39.6 - - + +
247D ASN* 2.9 27.0 + - - +
249D ILE* 4.0 18.8 - - + -
251D LEU* 5.7 0.4 - - + -
257D ILE* 3.5 41.1 - - + -
285D VAL* 4.7 13.5 - - + -
286D ILE 3.4 7.4 - - - +
287D LEU* 3.5 26.5 - - + -
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Residues in contact with HIS 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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244A VAL* 6.3 1.0 - - - +
248A SER* 3.3 34.7 + - - -
214D THR* 3.7 23.9 - - + +
215D ILE* 1.3 80.1 + - - +
217D MET* 1.3 63.0 + - - +
218D GLN* 5.4 8.3 - - + +
238D ILE 5.6 0.2 - - - -
240D MET* 5.4 0.2 - - - -
247D ASN* 4.4 17.2 + - - -
285D VAL* 3.8 1.2 - - - -
286D ILE* 2.8 47.0 + - + +
288D GLU* 3.5 35.2 + - + -
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Residues in contact with MET 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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198D PHE* 4.1 35.7 - - + -
200D LEU* 4.5 8.1 - - + -
215D ILE* 5.4 0.4 - - + -
216D HIS* 1.3 75.9 - - - +
218D GLN* 1.3 65.7 + - - +
236D VAL 3.7 0.2 - - - +
237D ASP* 3.9 0.3 - - - -
238D ILE* 2.8 56.3 + - + +
240D MET* 3.5 33.0 - - + +
257D ILE* 4.5 16.6 - - + +
258D TYR 5.7 0.4 - - - +
259D HIS* 4.6 3.4 - - + -
283D ILE* 4.0 14.1 - - + -
284D ILE 3.4 9.6 - - - +
285D VAL* 4.2 20.0 - - + -
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Residues in contact with GLN 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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248A SER 5.1 0.5 - - - +
249A ILE* 4.1 8.4 - - - +
250A PHE* 3.1 41.8 + - - +
216D HIS* 5.4 7.7 - - + +
217D MET* 1.3 81.6 - - - +
219D VAL* 1.3 62.8 + - - +
220D VAL* 4.0 0.4 - - + -
235D GLN* 2.8 44.7 + - + +
236D VAL 3.1 11.4 - - - +
237D ASP* 4.5 13.6 - - - +
238D ILE* 4.5 0.2 - - - -
283D ILE* 3.6 3.3 - - - +
284D ILE* 2.7 51.7 + - + +
286D ILE* 5.8 2.5 - - + -
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Residues in contact with VAL 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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218D GLN* 1.3 71.7 - - - +
220D VAL* 1.3 71.0 + - - +
221D ARG* 3.6 17.8 + - + +
234D HIS 2.9 14.7 - - - +
235D GLN* 3.4 1.4 - - - -
236D VAL* 2.9 33.5 + - + +
238D ILE* 3.5 32.5 - - + -
266D PRO* 4.0 14.1 - - + -
267D LEU* 4.6 11.9 - - + -
281D LEU* 5.2 4.9 - - + -
282D GLU 3.7 2.9 - - - +
283D ILE* 3.7 27.6 - - + -
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Residues in contact with VAL 220 (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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326A TYR* 5.9 0.7 - - - +
35D PHE* 4.2 19.7 - - + -
218D GLN* 5.3 1.3 - - + -
219D VAL* 1.3 73.1 - - - +
221D ARG* 1.3 63.5 + - - +
222D LYS 5.6 0.2 - - - +
233D LEU* 3.6 40.2 - - + -
234D HIS 3.4 4.0 - - - +
235D GLN* 4.8 13.5 - - + +
280D ASP 5.0 0.3 - - - +
281D LEU* 3.9 6.2 - - - +
282D GLU* 2.8 41.5 + - + +
284D ILE* 3.4 34.1 - - + -
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Residues in contact with ARG 221 (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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219D VAL* 4.5 10.7 - - + +
220D VAL* 1.3 77.6 - - - +
222D LYS* 1.3 72.3 + - - +
223D THR* 2.7 34.5 + - - +
232D PRO 4.4 1.3 - - - -
234D HIS* 3.0 29.2 + - + +
236D VAL* 5.7 5.9 - - + +
266D PRO* 3.3 39.3 + - - +
267D LEU* 4.5 6.9 - - - +
270D LEU* 5.2 2.4 - - - +
279D GLN* 5.1 4.2 + - - -
280D ASP 5.8 0.9 - - - -
281D LEU* 3.3 49.2 - - + +
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Residues in contact with LYS 222 (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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221D ARG* 1.3 79.2 - - - +
223D THR* 1.3 58.8 + - - +
224D THR* 5.4 5.5 - - + +
230D VAL* 3.7 26.9 - - + +
231D VAL 3.2 16.8 - - - +
232D PRO* 3.5 24.8 + - + +
280D ASP 5.9 0.8 + - - -
281D LEU* 5.0 1.4 - - - +
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Residues in contact with THR 223 (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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193A HIS* 5.8 6.1 - - + -
221D ARG* 2.7 42.7 + - - +
222D LYS* 1.3 71.5 - - - +
224D THR* 1.3 88.5 + - - +
225D SER* 5.5 0.4 - - - -
229D GLU 3.9 0.2 - - - +
230D VAL* 3.7 1.6 - - - +
231D VAL* 2.9 34.3 + - - +
234D HIS* 4.2 20.4 + - + +
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Residues in contact with THR 224 (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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193A HIS* 5.1 1.7 - - - -
222D LYS* 5.4 6.1 - - + +
223D THR* 1.3 93.2 - - - +
225D SER* 1.3 66.6 + - - +
226D PRO* 4.8 0.3 - - - +
228D GLY 5.6 2.0 - - - -
229D GLU 3.2 8.7 - - - -
230D VAL* 4.3 21.5 - - + -
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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