Contacts of the strand formed by residues 213 - 225 (chain D) in PDB entry 6CET
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 213 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105D LYS* 5.9 0.6 + - - -
106D ASP* 3.1 16.4 + - - -
167D THR 2.8 6.3 + - - +
168D SER* 3.0 42.7 + - - -
169D ALA 3.0 4.0 + - - -
212D CYS* 1.3 78.8 - - - +
214D HIS* 1.3 64.8 + - - +
263D ARG* 5.9 1.6 - - - -
328D ARG* 3.5 18.2 + - - -
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Residues in contact with HIS 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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167D THR* 4.4 6.5 - - - -
169D ALA* 2.9 50.7 + - + +
170D MET 4.1 0.4 + - - -
171D VAL* 3.8 21.7 - - + +
207D TRP* 3.5 39.5 + + + -
212D CYS* 3.5 32.1 - - - +
213D SER* 1.3 76.0 + - - +
215D GLU* 1.3 63.0 + - - +
216D VAL* 3.8 3.3 + - + +
262D GLU 4.2 0.5 - - - +
263D ARG* 3.6 23.8 - - - +
267D TRP* 4.7 7.5 - - + +
328D ARG* 4.5 5.1 - - - +
332D MET* 5.7 0.7 - - - -
747D LEU 5.6 0.2 + - - -
748D THR 4.7 2.8 + - - -
750D PRO* 4.2 21.8 - - + +
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Residues in contact with GLU 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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169D ALA 2.9 8.3 + - - -
170D MET* 3.5 28.6 - - + +
171D VAL* 2.9 27.8 + - - +
172D TYR* 4.5 4.3 - - + -
214D HIS* 1.3 72.5 - - - +
216D VAL* 1.3 62.1 + - - +
261D ASN* 3.5 27.8 + - - +
262D GLU 4.7 3.6 - - - -
263D ARG* 2.4 43.4 + - + +
325D ASN* 3.1 29.4 + - - +
328D ARG* 4.2 6.7 - - + +
1552D THR 5.6 0.9 - - - +
1553D MET* 5.8 0.2 - - - +
1555D THR* 4.8 2.4 - - - +
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Residues in contact with VAL 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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171D VAL* 3.1 21.5 - - + +
173D ILE* 4.4 8.5 - - + -
204D PHE* 6.0 6.3 - - + -
207D TRP* 5.5 7.4 - - + -
214D HIS* 3.8 3.6 + - + +
215D GLU* 1.3 75.4 - - - +
217D THR* 1.3 67.1 + - - +
218D VAL* 3.8 24.0 - - + -
259D VAL* 3.6 13.3 - - + +
260D GLN 3.0 14.9 - - - +
261D ASN* 3.7 7.4 - - - -
262D GLU 3.9 5.9 + - - +
267D TRP* 3.6 38.6 - - + -
270D LEU* 5.0 4.3 - - + -
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Residues in contact with THR 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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171D VAL 3.0 5.1 + - - -
172D TYR* 3.3 45.7 - - + +
173D ILE* 2.9 23.2 + - - +
174D PHE* 4.5 8.1 - - - -
216D VAL* 1.3 74.4 - - - +
218D VAL* 1.3 65.4 + - - +
219D VAL* 4.6 7.6 - - - +
257D VAL* 6.5 0.7 - - - -
258D VAL 4.5 0.2 - - - -
259D VAL 4.0 1.8 - - - -
260D GLN* 3.2 22.9 - - - +
261D ASN* 4.9 6.7 - - - +
1435D LEU* 4.3 18.2 - - + -
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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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173D ILE* 3.3 31.4 - - + -
175D ILE* 4.4 7.6 - - + -
204D PHE* 6.2 2.0 - - + -
216D VAL* 3.8 15.0 - - + -
217D THR* 1.3 77.9 - - - +
219D VAL* 1.3 63.1 + - - +
220D LEU* 4.0 2.0 + - + -
257D VAL* 3.6 1.9 - - - +
258D VAL* 2.9 62.1 + - + +
259D VAL 5.2 0.2 - - - +
270D LEU* 4.4 19.7 - - + -
274D ILE* 4.1 18.8 - - + -
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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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173D ILE 3.1 8.3 + - - -
174D PHE* 3.5 32.4 - - + -
175D ILE 2.9 25.1 + - - +
217D THR* 4.6 9.9 - - - +
218D VAL* 1.3 77.7 - - - +
220D LEU* 1.3 75.7 + - - +
221D PHE* 3.9 6.1 - - + -
255D TYR* 4.4 25.6 - - + -
256D LYS 3.7 7.0 - - - +
257D VAL* 3.9 20.6 - - + -
312D LEU* 6.3 1.6 - - + -
1435D LEU* 6.4 2.5 - - + -
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Residues in contact with LEU 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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175D ILE* 3.7 40.6 - - + -
177D MET* 3.7 22.0 - - + -
218D VAL* 5.0 1.3 - - + -
219D VAL* 1.3 73.9 - - - +
221D PHE* 1.3 64.7 + - - +
255D TYR* 3.5 1.0 - - - -
256D LYS* 2.9 47.0 + - + +
258D VAL* 4.9 9.9 - - + -
274D ILE* 4.7 24.0 - - + +
277D LEU* 4.0 36.6 - - + -
281D TYR* 5.4 7.1 - - + -
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Residues in contact with PHE 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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174D PHE* 3.6 25.1 - + + -
175D ILE 3.1 38.0 + - - +
176D GLN* 3.5 26.9 - - + -
177D MET* 3.0 31.6 + - - +
219D VAL* 3.9 12.1 - - + -
220D LEU* 1.3 76.3 - - - +
222D SER* 1.3 63.3 + - - +
254D PHE 3.2 13.2 - - - +
255D TYR* 3.5 20.6 - + + -
281D TYR* 4.2 4.3 - - - -
305D ASN* 3.4 44.0 - - - -
306D TYR* 4.9 5.6 - + - -
309D ALA* 4.5 12.3 - - + -
335D VAL* 4.9 8.7 - - + -
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Residues in contact with SER 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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176D GLN* 5.2 2.0 - - - -
177D MET* 3.3 23.3 - - - +
221D PHE* 1.3 78.4 - - - +
223D ARG* 1.3 66.1 + - - +
253D ASP* 3.2 0.5 - - - +
254D PHE* 2.9 33.0 + - - +
281D TYR* 2.6 27.4 + - - -
285D VAL* 4.6 5.7 - - - +
297D ASP* 4.9 8.0 + - - +
298D ASN* 5.3 0.2 - - - -
305D ASN* 3.1 22.8 + - - +
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Residues in contact with ARG 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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222D SER* 1.3 74.3 + - - +
224D THR* 1.3 69.0 + - - +
225D PHE* 5.0 2.5 - - + -
251D TYR* 3.3 42.9 + - - -
252D GLU 3.1 15.3 - - - +
253D ASP* 3.7 6.4 - - + +
254D PHE* 4.6 0.9 - - - +
296D GLY 3.7 0.3 - - - -
297D ASP* 2.9 27.0 + - - -
298D ASN* 3.6 32.2 + - - +
303D GLN* 3.7 12.2 - - - +
304D GLY 3.0 43.0 + - - +
305D ASN* 3.3 33.8 - - - +
308D GLU* 3.5 25.9 + - - -
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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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222D SER* 5.4 0.7 - - - +
223D ARG* 1.3 79.1 - - - +
225D PHE* 1.3 66.3 + - - +
227D ASP* 2.3 34.1 + - - +
251D TYR* 3.2 8.7 - - - +
252D GLU* 2.8 35.7 + - - +
254D PHE* 3.9 19.0 - - + -
285D VAL* 3.6 31.0 - - + +
289D GLN* 3.9 5.1 + - - +
295D GLN 3.6 9.4 - - - -
296D GLY* 3.9 7.2 - - - -
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Residues in contact with PHE 225 (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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223D ARG* 5.0 3.8 - - + -
224D THR* 1.3 78.0 - - - +
226D TYR* 1.3 70.5 + - - +
227D ASP* 4.0 2.4 - - - +
240D ALA* 5.1 3.6 - - + -
249D ARG* 3.6 41.3 - - + +
250D PHE 3.7 7.9 - - - -
251D TYR* 3.6 29.6 - + + +
294D PRO* 3.8 1.0 - - - +
295D GLN* 2.8 60.2 + - + +
298D ASN* 3.5 31.0 - - + -
303D GLN* 3.2 38.4 - - + -
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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