Contacts of the strand formed by residues 220 - 238 (chain D) in PDB entry 5U07
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 HIS 220 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204D PHE* 3.7 7.8 - + - +
205D THR* 3.1 10.0 - - - -
206D ALA* 2.8 43.7 + - + -
218D SER* 3.5 2.6 + - - -
219D GLY* 1.3 81.0 + - - +
221D MET* 1.3 68.3 + - - +
222D ASN* 3.7 15.7 - - + +
63H ARG* 4.7 1.2 + - - +
116H LEU* 4.3 9.9 - - + -
13K U 4.6 4.0 - - - -
38M C 3.6 21.6 - - - -
39M A 3.0 81.5 + + - -
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Residues in contact with MET 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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446C SER* 5.5 6.1 - - - +
203D PHE* 3.9 24.2 - - + -
204D PHE 4.0 2.5 - - - -
205D THR* 4.1 12.8 - - + +
220D HIS* 1.3 83.5 - - - +
222D ASN* 1.3 66.6 + - - +
21H ASP* 6.3 0.7 - - + -
15K A 3.9 14.6 - - - +
37M T 3.1 59.6 - - + +
38M C 3.6 52.6 + - + +
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Residues in contact with ASN 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D PHE* 3.1 14.3 - - - -
204D PHE* 2.9 56.8 + - + +
220D HIS* 3.7 11.4 - - + +
221D MET* 1.3 75.9 - - - +
223D ALA* 1.3 74.8 + - - +
38M C 5.2 0.9 - - - -
39M A 3.4 26.7 + - - -
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Residues in contact with ALA 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C ASN* 3.2 42.0 + - - +
446C SER 6.0 0.4 - - - +
201D VAL* 3.8 6.1 - - + -
202D ASP 3.5 5.8 - - - -
203D PHE* 4.1 9.6 - - + -
204D PHE* 4.0 3.8 - - - -
222D ASN* 1.3 88.8 + - - +
224D GLY* 1.3 59.7 + - - +
225D GLN* 4.3 10.4 + - - +
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Residues in contact with GLY 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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23D GLY* 5.9 1.6 - - - -
201D VAL* 4.7 1.3 - - - -
202D ASP* 2.8 38.5 + - - +
204D PHE* 3.7 14.4 - - - -
223D ALA* 1.3 73.7 - - - +
225D GLN* 1.3 67.0 + - - -
226D PHE* 4.6 9.1 - - - -
271D LYS* 6.0 1.6 - - - -
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Residues in contact with GLN 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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441C TRP* 3.5 38.6 - - + +
445C ASN* 4.3 9.7 - - - +
463C GLY* 6.1 0.2 - - - -
464C PRO* 4.9 4.6 - - - +
16D ASN* 2.6 34.0 + - - +
22D LEU* 6.4 0.2 - - - -
23D GLY* 3.4 11.6 + - - -
24D SER* 3.3 33.2 + - - -
25D PRO* 4.5 1.1 - - - -
199D VAL* 3.4 26.5 - - + -
200D GLU 3.9 3.8 - - - -
201D VAL* 4.1 6.1 - - + +
223D ALA 4.3 5.7 + - - +
224D GLY* 1.3 75.9 - - - -
226D PHE* 1.3 64.0 + - - +
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Residues in contact with PHE 226 (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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14D TYR* 3.2 43.3 - + + -
15D SER 3.8 10.3 - - - +
16D ASN* 3.3 21.1 - - + -
25D PRO* 4.8 1.1 - - - -
199D VAL* 3.8 4.1 - - - +
200D GLU* 2.8 34.4 + - - +
202D ASP* 4.3 17.5 - - + -
224D GLY* 3.9 9.8 + - - -
225D GLN* 1.3 95.0 - - - +
227D SER* 1.3 64.2 + - - +
271D LYS* 3.0 37.9 - - + -
274D ALA* 5.3 2.7 - - + -
275D THR* 4.0 11.7 - - + -
41H GLN* 5.7 1.3 - - - -
190H HIS* 3.8 20.9 - + - -
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Residues in contact with SER 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D TYR* 4.4 5.6 - - - -
15D SER* 2.6 40.5 + - - +
16D ASN* 5.6 0.2 - - - -
25D PRO* 3.5 17.9 - - - +
36D THR* 3.4 33.0 + - - +
197D THR* 4.1 11.4 - - - -
198D THR 4.8 1.1 - - - -
199D VAL* 4.7 7.9 - - - -
200D GLU* 4.8 4.0 - - - +
226D PHE* 1.3 76.6 - - - +
228D ALA* 1.3 60.8 - - - +
231D PHE* 5.8 2.8 - - - -
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Residues in contact with ALA 228 (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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12D LEU* 3.4 9.2 - - - +
13D PRO 3.4 0.7 - - - -
14D TYR* 3.3 32.7 - - + +
15D SER* 5.2 0.2 - - - -
36D THR* 6.5 0.9 - - - -
193D THR* 5.1 1.6 - - - -
195D HIS* 3.9 6.8 + - - -
197D THR* 3.9 14.8 + - - -
227D SER* 1.3 73.7 - - - +
229D GLY* 1.3 60.5 + - - +
231D PHE* 5.3 3.1 - - - -
28H VAL* 4.6 10.3 - - + +
29H VAL 4.9 8.5 + - - +
30H TYR* 4.0 19.0 - - + -
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Residues in contact with GLY 229 (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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11D THR* 3.5 2.6 - - - -
12D LEU* 2.8 35.1 + - - +
193D THR* 3.9 11.2 - - - +
195D HIS* 3.5 16.2 - - - -
228D ALA* 1.3 74.9 - - - +
230D THR* 1.3 67.1 + - - -
231D PHE* 3.6 8.5 + - - -
30H TYR* 5.1 4.6 - - - -
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Residues in contact with THR 230 (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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9D ILE* 4.6 14.4 - - - -
11D THR* 3.6 28.7 - - - +
193D THR* 4.0 0.4 - - - +
194D VAL* 3.1 40.3 + - - +
195D HIS* 3.5 14.3 + - + -
229D GLY* 1.3 69.6 - - - -
231D PHE* 1.3 66.8 + - - +
282D ASP* 6.0 0.2 - - - -
310D TYR* 4.2 23.4 - - + +
311D THR* 4.9 7.0 - - + +
314D ALA* 5.3 0.5 - - - +
30H TYR* 6.3 0.2 - - + -
301H GLU* 4.3 14.8 - - + +
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Residues in contact with PHE 231 (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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9D ILE* 3.5 2.6 - - - -
10D GLN 2.8 39.9 + - - +
12D LEU* 3.3 35.2 - - + -
15D SER* 5.9 1.1 - - - -
17D ILE* 5.4 0.4 - - + -
36D THR* 4.1 27.1 - - + -
37D ARG 5.0 0.2 - - - -
38D VAL* 3.6 37.0 - - + -
191D ALA* 4.2 7.2 - - + -
192D PHE* 3.6 4.7 - - - +
193D THR* 3.3 35.7 - - + -
194D VAL* 4.9 0.7 - - - -
227D SER* 5.8 3.4 - - - -
228D ALA* 5.3 1.3 - - - -
229D GLY* 3.6 13.4 + - - -
230D THR* 1.3 71.9 - - - +
232D TYR* 1.3 60.1 + - - +
233D ARG* 3.6 17.9 + - + +
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Residues in contact with TYR 232 (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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7D HIS* 3.0 29.0 - + + -
8D ALA 3.5 10.8 - - - -
9D ILE* 4.0 10.1 - - + +
190D HIS 4.7 0.9 - - - +
191D ALA* 3.8 2.8 - - - -
192D PHE* 3.0 51.4 + + + +
194D VAL* 4.2 8.5 - - + -
230D THR 3.5 1.6 + - - -
231D PHE* 1.3 69.4 - - - +
233D ARG* 1.3 64.8 + - - +
234D TYR* 4.2 15.6 + - + +
295D SER* 4.0 1.0 - - - -
296D PHE* 2.9 30.9 + - - +
297D ALA* 3.6 22.9 - - + -
300D PHE* 3.5 27.6 - + + -
318D LEU* 3.6 22.0 - - + -
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Residues in contact with ARG 233 (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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7D HIS* 3.5 2.4 - - - -
8D ALA* 2.9 48.0 + - + +
10D GLN* 2.6 50.5 + - - +
12D LEU* 6.2 0.7 - - - -
38D VAL* 5.6 1.9 - - - +
43D TRP* 2.7 55.9 - - - +
189D ALA 6.0 0.2 - - - +
191D ALA* 3.4 29.9 - - + +
231D PHE* 4.0 16.2 - - + +
232D TYR* 1.3 76.9 - - - +
234D TYR* 1.3 65.3 + - - +
263D PHE* 3.3 18.4 + - + -
266D THR 4.5 0.6 + - - -
281D PRO* 4.1 4.9 - - - +
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Residues in contact with TYR 234 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5D ASP* 3.6 10.5 + - + -
6D ILE 3.2 20.0 - - - -
7D HIS* 3.5 37.0 - + - -
187D GLN 4.8 0.2 - - - -
188D PHE* 3.9 1.0 - - - +
189D ALA* 2.9 52.9 + - + +
190D HIS 6.0 0.2 - - - -
232D TYR* 4.2 15.0 + - + +
233D ARG* 1.3 78.0 - - - +
235D ALA* 1.3 82.8 + - - +
236D ASN* 3.5 25.3 + - - +
263D PHE* 4.5 5.7 - - - -
293D PRO* 3.7 7.8 - - - +
294D ILE 3.7 11.1 + - - -
295D SER* 3.8 22.2 + - - -
144N VAL* 4.0 18.6 - - + -
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Residues in contact with ALA 235 (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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5D ASP* 3.3 4.7 - - - +
6D ILE* 2.9 36.6 + - + +
187D GLN 3.3 6.1 - - - -
188D PHE* 3.5 31.2 - - + -
234D TYR* 1.3 84.2 - - - +
236D ASN* 1.3 62.5 + - - +
259D PHE* 5.1 2.9 - - + -
263D PHE* 3.5 22.2 - - + -
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Residues in contact with ASN 236 (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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3D PHE* 5.4 3.1 - - + -
4D VAL 3.7 5.6 - - - +
5D ASP* 3.6 17.0 - - + -
6D ILE* 5.2 1.3 - - - -
186D VAL* 3.4 5.5 - - - +
187D GLN* 2.8 67.6 + - - +
234D TYR* 3.5 9.8 + - - +
235D ALA* 1.3 76.5 - - - +
237D VAL* 1.3 61.9 + - - +
259D PHE* 6.0 1.1 - - - -
293D PRO* 3.2 32.5 - - + +
135N GLN* 3.6 13.7 - - - +
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Residues in contact with VAL 237 (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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3D PHE* 3.5 2.8 - - - -
4D VAL* 2.9 61.9 + - + +
6D ILE* 5.1 3.6 - - + -
169D LEU* 4.0 15.0 - - + -
185D ALA 3.6 11.9 - - - +
186D VAL* 3.7 17.0 - - + -
236D ASN* 1.3 75.4 - - - +
238D ASN* 1.3 65.3 + - - +
239D LEU* 3.3 13.2 + - + +
242D LEU* 4.5 10.1 - - + -
256D VAL* 4.7 9.9 - - + -
259D PHE* 4.7 15.9 - - + -
260D LEU* 5.6 0.7 - - + -
135N GLN* 4.6 0.9 - - - -
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Residues in contact with ASN 238 (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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3D PHE* 2.9 33.1 - - - -
185D ALA* 3.1 24.1 + - + +
237D VAL* 1.3 68.8 - - - +
239D LEU* 1.3 63.1 + - - +
240D ASP* 3.3 15.2 + - - +
241D ARG* 3.2 26.3 + - - +
242D LEU* 3.3 17.7 + - - +
133N TYR 3.4 18.4 + - - -
134N TRP* 4.2 6.5 - - - +
135N GLN* 2.9 27.2 - - - +
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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