Contacts of the helix formed by residues 289 - 310 (chain D) in PDB entry 3U8Z
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 LYS 289 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D ASP* 5.8 5.5 - - - +
71D THR* 4.9 11.7 + - - +
287D SER* 3.5 2.5 + - - -
288D SER* 1.4 87.2 + - - +
290D LEU* 1.3 62.9 + - - +
291D ARG* 3.5 2.7 - - + +
292D VAL* 3.4 30.1 + - + +
293D ASN* 3.1 28.5 + - - +
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Residues in contact with LEU 290 (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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266D TYR* 5.1 1.3 - - - +
269D LYS* 6.0 1.3 - - - +
288D SER 3.9 3.2 + - - +
289D LYS* 1.3 69.8 - - + +
291D ARG* 1.4 93.0 + - + +
293D ASN* 3.3 15.6 + - - +
294D LYS* 3.2 46.0 + - - +
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Residues in contact with ARG 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D ILE* 3.5 39.5 + - + +
69D LYS* 3.4 41.4 - - - +
71D THR* 4.1 26.6 + - + +
72D VAL 5.3 1.3 - - - +
289D LYS* 3.5 2.8 - - + +
290D LEU* 1.4 91.9 - - + +
292D VAL* 1.3 65.7 - - + +
294D LYS* 3.5 12.0 + - + +
295D LEU* 3.2 22.2 + - - +
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Residues in contact with VAL 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D THR* 4.0 21.3 - - + +
222D PHE* 3.6 31.4 - - + -
223D ALA 5.7 1.3 - - - +
287D SER* 3.9 10.1 - - - +
289D LYS* 3.5 35.2 - - + +
290D LEU 3.3 0.2 - - - -
291D ARG* 1.3 74.3 - - + +
293D ASN* 1.4 52.8 + - - +
295D LEU* 3.1 8.9 + - + +
296D ILE* 2.8 49.4 + - + +
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Residues in contact with ASN 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266D TYR* 2.8 41.7 + - + +
269D LYS* 4.5 3.6 - - - +
271D PHE* 3.3 18.1 - - + -
287D SER* 3.1 45.7 + - - -
289D LYS 3.1 15.2 + - - -
290D LEU* 3.3 16.1 + - - +
292D VAL* 1.4 74.5 - - - +
294D LYS* 1.4 60.8 + - + +
296D ILE* 3.4 3.0 + - - +
297D LEU* 3.1 31.6 + - - +
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Residues in contact with LYS 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ARG* 5.4 1.4 + - - -
290D LEU* 3.2 32.8 + - - +
291D ARG* 3.7 13.2 - - + +
293D ASN* 1.4 74.6 - - + +
295D LEU* 1.4 61.1 + - - +
297D LEU* 3.5 9.5 + - + +
298D GLN* 3.1 35.7 + - - +
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Residues in contact with LEU 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D THR* 5.0 5.8 - - + -
72D VAL* 3.7 39.5 - - + +
74D TRP* 3.5 34.1 - - + +
99D LYS* 4.7 0.2 - - - -
222D PHE* 4.2 17.7 - - + -
291D ARG 3.2 13.5 + - - +
292D VAL* 3.1 10.0 + - + +
294D LYS* 1.4 73.1 - - - +
296D ILE* 1.4 64.5 + - - +
298D GLN* 3.2 15.6 + - - +
299D LEU* 3.0 47.1 + - + +
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Residues in contact with ILE 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D PHE* 3.7 41.5 - - + -
224D ILE* 5.2 1.8 - - + -
234D LEU* 3.8 23.6 - - + -
236D VAL* 4.5 2.4 - - + +
271D PHE* 3.7 34.3 - - + -
285D PHE* 5.3 0.7 - - + -
287D SER* 4.3 9.9 - - - +
292D VAL* 2.8 42.7 + - + +
293D ASN* 3.4 5.6 + - - +
295D LEU* 1.4 69.8 - - - +
297D LEU* 1.3 58.0 + - - +
299D LEU* 3.2 5.9 + - - +
300D CYS* 2.9 43.7 + - - -
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Residues in contact with LEU 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B GLN 5.4 3.1 - - - +
179B MET* 3.7 41.1 - - + -
187B ARG* 4.5 7.9 - - - +
264D ILE* 4.3 14.1 - - + -
266D TYR* 4.0 32.5 - - + -
271D PHE* 3.7 24.0 - - + -
293D ASN 3.1 22.4 + - - +
294D LYS* 3.9 7.9 - - + +
295D LEU 3.3 0.2 - - - -
296D ILE* 1.3 75.6 - - + +
298D GLN* 1.4 61.2 + - - +
300D CYS* 3.2 9.1 + - + +
301D ILE* 3.0 31.2 + - - +
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Residues in contact with GLN 298 (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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187B ARG* 5.0 8.2 - - - +
191B TRP* 5.2 1.7 + - - -
74D TRP* 4.1 16.8 + - - +
76D LYS* 4.4 23.9 - - - +
99D LYS* 3.2 31.4 + - - +
100D PHE* 4.0 9.0 - - - -
294D LYS* 3.1 25.7 + - - +
295D LEU* 3.4 21.0 - - - +
297D LEU* 1.4 75.1 - - - +
299D LEU* 1.3 59.9 + - - +
301D ILE* 3.5 8.2 + - - +
302D GLY 3.2 18.7 + - - -
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Residues in contact with LEU 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D TRP* 5.2 1.1 - - - +
99D LYS* 3.8 43.5 - - + +
100D PHE* 4.0 8.5 - - + -
220D ASN* 3.7 25.6 - - + +
222D PHE* 3.6 32.5 - - + -
236D VAL* 3.9 13.9 - - + -
295D LEU* 3.0 30.7 + - + +
296D ILE 3.6 5.8 - - - +
298D GLN* 1.3 72.2 - - - +
300D CYS* 1.3 64.2 + - - +
303D ASN* 2.7 33.8 + - - +
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Residues in contact with CYS 300 (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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184B TRP* 5.5 5.2 - - + +
234D LEU* 5.7 0.2 - - - -
236D VAL* 4.2 3.6 - - - -
241D LEU* 3.8 32.1 - - - -
258D TRP* 3.4 18.6 - - + -
264D ILE* 4.6 16.4 - - + -
296D ILE* 2.9 38.6 + - - -
297D LEU* 3.5 13.9 - - + +
299D LEU* 1.3 76.1 - - - +
301D ILE* 1.3 57.0 + - + +
304D HIS* 3.0 33.1 + - - +
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Residues in contact with ILE 301 (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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179B MET* 3.7 14.1 - - + -
184B TRP* 4.7 15.0 - - + +
187B ARG* 3.2 71.3 - - + +
188B ILE* 4.4 7.4 - - + +
191B TRP* 3.7 22.4 - - + -
297D LEU 3.0 22.6 + - - +
298D GLN* 3.9 7.0 - - - +
299D LEU 3.4 0.2 - - - -
300D CYS* 1.3 76.7 - - + +
302D GLY* 1.3 62.9 + - - +
304D HIS* 3.5 3.3 - - - +
305D ASP* 3.1 25.6 + - - +
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Residues in contact with GLY 302 (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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191B TRP* 3.6 26.5 - - - +
100D PHE* 3.6 22.0 - - - -
298D GLN 3.2 8.3 + - - -
301D ILE* 1.3 77.8 - - - +
303D ASN* 1.3 56.2 + - - +
305D ASP* 3.3 2.1 + - - +
306D LEU* 3.0 34.5 + - - +
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Residues in contact with ASN 303 (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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99D LYS 5.4 0.4 + - - -
100D PHE* 3.7 27.6 - - - +
101D TYR 4.9 4.2 + - - +
220D ASN* 4.6 7.3 - - - +
236D VAL* 3.9 12.1 - - - +
237D ASP* 3.4 34.5 + - - +
238D ALA* 3.8 10.2 + - - +
258D TRP* 3.6 11.2 + - + +
299D LEU* 2.7 33.1 + - - +
302D GLY* 1.3 70.7 - - - +
304D HIS* 1.3 66.0 + - - +
306D LEU* 4.1 5.7 - - - +
307D PHE* 3.0 25.8 + - - +
310D ARG* 4.9 1.6 + - - -
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Residues in contact with HIS 304 (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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184B TRP* 3.9 27.6 - + + +
188B ILE* 3.6 30.5 - - + +
192B TYR* 4.6 0.2 - - - -
258D TRP* 3.7 47.9 + + + -
261D ILE* 5.3 1.0 + - + -
300D CYS 3.0 21.0 + - - +
301D ILE* 3.5 5.4 - - - +
303D ASN* 1.3 76.4 - - - +
305D ASP* 1.3 77.3 + - - +
307D PHE* 3.3 4.7 - - - +
308D MET* 3.1 50.8 + - + +
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Residues in contact with ASP 305 (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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188B ILE* 2.6 40.3 - - - +
191B TRP* 3.1 38.3 - - + +
192B TYR* 3.4 30.5 + - + -
301D ILE 3.1 15.7 + - - +
302D GLY 3.8 0.7 - - - +
303D ASN 3.3 0.2 - - - -
304D HIS* 1.3 94.0 + - - +
306D LEU* 1.3 64.6 + - - +
308D MET* 3.4 1.2 + - - +
309D ARG* 3.1 21.3 + - - +
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Residues in contact with LEU 306 (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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191B TRP* 3.6 26.2 - - + -
60D TRP* 3.6 29.8 - - + +
61D PHE* 4.8 1.3 - - + -
100D PHE* 3.7 35.2 - - + -
101D TYR 5.3 0.4 - - - +
302D GLY 3.0 21.6 + - - +
303D ASN* 4.2 5.4 - - - +
305D ASP* 1.3 73.1 - - - +
307D PHE* 1.3 63.8 + - - +
309D ARG* 3.5 19.0 + - + +
310D ARG* 3.2 54.9 + - - +
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Residues in contact with PHE 307 (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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103D GLU* 3.9 16.2 - - - -
238D ALA 3.3 19.5 - - - +
239D LEU* 3.7 19.7 - - + -
257D PRO* 5.2 1.1 - - + -
258D TRP* 3.6 21.8 - + + -
259D ASN* 3.3 44.2 - - + -
303D ASN 3.0 19.5 + - - +
304D HIS 3.3 4.7 - - - +
306D LEU* 1.3 76.4 - - - +
308D MET* 1.3 73.3 + - - +
310D ARG* 3.4 20.8 + - - +
311D ARG* 3.3 47.0 + - - -
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Residues in contact with MET 308 (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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192B TYR* 3.2 26.2 - - - +
259D ASN* 4.9 12.1 - - + -
304D HIS* 3.1 36.1 + - + +
305D ASP 3.8 1.8 - - - +
306D LEU 3.3 0.4 - - - -
307D PHE* 1.3 95.5 - - - +
309D ARG* 1.4 62.5 + - - +
311D ARG* 3.1 23.8 + - + +
312D LYS 3.4 13.4 + - - +
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Residues in contact with ARG 309 (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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191B TRP* 4.0 13.5 - - - -
192B TYR* 2.6 59.2 + - + +
195B HIS 2.8 23.0 + - - -
196B ARG* 3.3 25.0 - - - +
60D TRP* 4.7 9.5 - - - -
305D ASP 3.1 20.1 + - - +
306D LEU* 3.8 21.0 - - + +
307D PHE 3.4 0.2 - - - -
308D MET* 1.4 75.2 - - - +
310D ARG* 1.3 56.7 + - + +
312D LYS* 3.1 25.3 + - - +
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Residues in contact with ARG 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D PHE* 4.1 7.7 - - - -
101D TYR 3.2 21.6 + - - -
102D PRO* 3.7 0.8 - - - +
103D GLU* 3.0 41.0 + - - +
108D GLU* 3.0 43.6 + - + +
238D ALA* 3.9 15.8 + - - +
303D ASN* 4.9 0.6 + - - -
306D LEU* 3.2 45.1 + - - +
307D PHE* 3.6 12.1 - - - +
308D MET 3.3 0.2 - - - -
309D ARG* 1.3 76.1 - - + +
311D ARG* 1.3 60.2 + - + +
312D LYS* 3.3 7.6 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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