Contacts of the helix formed by residues 283 - 298 (chain D) in PDB entry 4GQS
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 283 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267D PHE* 3.0 17.2 - - - -
271D MET* 3.5 6.7 - - - -
280D SER* 3.9 18.6 - - - +
281D GLU 3.3 2.6 + - - -
282D PHE* 1.3 76.6 - - - +
284D ILE* 1.3 65.9 + - - +
285D GLU* 3.0 22.7 + - - +
286D ASN* 2.8 31.0 + - - +
287D LEU 3.2 7.6 + - - -
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Residues in contact with ILE 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D LEU* 3.3 29.6 - - + -
248D VAL* 4.5 16.8 - - + -
249D LYS* 3.1 34.5 - - + +
252D GLN* 5.3 4.0 - - - +
271D MET* 3.3 21.2 - - + +
283D THR* 1.3 73.3 - - - +
285D GLU* 1.3 74.4 + - + +
287D LEU* 3.5 3.6 - - + +
288D VAL* 3.2 23.2 + - + +
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Residues in contact with GLU 285 (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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110D PHE* 3.7 31.2 - - + -
283D THR* 3.0 16.5 + - - +
284D ILE* 1.3 87.6 - - + +
286D ASN* 1.3 66.6 + - - +
287D LEU 3.2 0.9 + - - -
288D VAL* 3.4 1.7 + - - +
289D ILE* 3.1 32.9 + - + +
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Residues in contact with ASN 286 (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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110D PHE* 3.1 15.3 - - - +
111D GLY 4.3 3.5 + - - +
119D ARG* 2.6 39.5 + - - +
123D ILE* 4.2 12.1 - - + +
267D PHE* 4.2 5.4 - - + -
281D GLU* 2.7 35.9 + - - +
283D THR* 2.8 28.0 + - - +
285D GLU* 1.3 79.8 - - - +
287D LEU* 1.3 50.6 + - - +
289D ILE* 4.0 2.5 - - - +
290D THR* 2.5 42.9 + - - +
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Residues in contact with LEU 287 (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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244D ILE* 6.1 0.4 - - + -
248D VAL* 3.5 40.4 - - + -
263D PHE* 5.2 9.4 - - + -
264D ILE* 4.2 22.2 - - + -
267D PHE* 3.3 55.1 - - + -
268D LEU* 4.3 4.3 - - + -
271D MET* 4.3 8.7 - - + -
283D THR 3.2 5.1 + - - +
284D ILE* 3.5 10.1 - - - +
285D GLU 3.1 0.4 - - - -
286D ASN* 1.3 74.8 - - - +
288D VAL* 1.3 66.1 + - - +
290D THR* 3.1 6.6 + - - -
291D ALA* 3.0 25.7 + - + +
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Residues in contact with VAL 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241D GLU* 3.6 42.0 - - + +
244D ILE* 3.6 19.5 - - + +
245D LEU* 3.8 36.6 - - + -
248D VAL* 4.6 5.8 - - + -
284D ILE* 3.2 18.2 + - + +
285D GLU* 4.0 4.0 - - - +
287D LEU* 1.3 79.7 - - - +
289D ILE* 1.3 67.0 + - + +
291D ALA* 3.5 2.9 + - - +
292D ALA* 3.2 18.4 + - - +
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Residues in contact with ILE 289 (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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107D ASN* 3.3 28.5 - - - +
108D ARG* 4.4 8.7 - - - +
110D PHE* 3.3 23.1 - - + -
111D GLY* 3.1 31.4 - - - +
241D GLU* 3.3 27.6 - - - +
285D GLU* 3.1 22.8 + - + +
286D ASN 4.0 1.6 - - - +
287D LEU 3.2 0.6 - - - -
288D VAL* 1.3 80.7 - - + +
290D THR* 1.3 66.2 + - - +
292D ALA* 3.3 7.3 + - - +
293D ASP* 3.0 21.7 + - - +
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Residues in contact with THR 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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111D GLY* 3.9 13.7 - - - -
112D ILE* 4.6 5.4 - - + +
123D ILE* 3.5 34.5 - - + +
126D PHE* 6.4 0.4 - - + -
127D SER* 4.5 7.6 - - - +
263D PHE* 4.4 23.1 - - + -
267D PHE* 5.0 4.7 - - + -
286D ASN* 2.5 31.5 + - - -
287D LEU* 3.5 7.4 - - - -
289D ILE* 1.3 73.4 - - - +
291D ALA* 1.3 63.9 + - - +
293D ASP* 3.2 5.2 + - - +
294D LEU* 3.0 28.4 + - + +
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Residues in contact with ALA 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D ILE* 4.4 23.0 - - + +
183D PHE* 5.9 0.9 - - + -
244D ILE* 3.8 22.9 - - + -
263D PHE* 6.1 4.3 - - + -
264D ILE* 6.2 2.2 - - + -
287D LEU* 3.0 15.4 + - + +
288D VAL 3.6 9.6 - - - +
289D ILE 3.2 0.2 - - - -
290D THR* 1.3 74.4 - - - +
292D ALA* 1.3 57.5 + - - +
293D ASP 2.9 0.5 + - - -
294D LEU* 3.0 6.5 + - - +
295D LEU* 2.7 39.1 + - + +
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Residues in contact with ALA 292 (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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107D ASN* 6.3 0.4 - - - +
237D LEU* 5.4 12.1 - - + +
240D MET* 5.0 16.1 - - - +
241D GLU* 4.5 13.9 - - + -
244D ILE* 3.6 16.5 - - + +
288D VAL 3.2 11.7 + - - +
289D ILE* 3.3 10.7 + - - +
291D ALA* 1.3 79.6 - - - +
293D ASP* 1.3 62.5 + - - +
295D LEU* 3.9 5.4 - - - +
296D GLY* 3.2 18.4 + - - -
502D 0XV 4.9 1.9 - - - +
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Residues in contact with ASP 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D ASN* 3.0 33.5 + - - +
110D PHE 3.9 0.3 - - - +
111D GLY* 3.2 22.2 - - - -
112D ILE* 3.2 10.5 + - + -
113D VAL* 3.7 24.5 + - + +
114D PHE* 4.8 0.3 - - - -
289D ILE 3.0 8.5 + - - +
290D THR 3.3 10.1 - - - +
291D ALA 2.9 1.4 + - - -
292D ALA* 1.3 76.2 - - - +
294D LEU* 1.3 55.1 + - - +
296D GLY 3.0 1.9 + - - -
297D ALA* 2.6 40.5 + - - +
502D 0XV 3.4 20.5 - - - +
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Residues in contact with LEU 294 (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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112D ILE* 4.6 9.2 - - + +
127D SER* 4.6 9.2 - - - +
131D LEU* 4.9 11.9 - - + -
178D ILE* 3.7 15.3 - - + +
182D ILE* 5.2 7.6 - - + -
263D PHE* 4.3 30.7 - - + -
290D THR* 3.0 20.0 + - + +
291D ALA* 3.9 4.0 - - - +
293D ASP* 1.3 78.6 - - - +
295D LEU* 1.3 60.8 + - - +
296D GLY 3.2 1.2 + - - -
297D ALA* 4.4 3.4 - - - +
298D GLY* 3.2 18.9 + - - -
436D VAL* 5.2 5.2 - - + -
501D HEM 3.6 56.8 - - + +
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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
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175D CYS* 4.4 1.6 - - - +
178D ILE* 3.4 28.7 - - + +
179D CYS* 3.8 18.4 - - - -
182D ILE* 3.6 16.5 - - + +
183D PHE* 4.6 13.0 - - + -
197D LEU* 4.1 32.1 - - + -
201D LEU* 3.6 9.4 - - + +
240D MET* 5.1 9.0 - - + -
244D ILE* 4.8 16.2 - - + -
291D ALA 2.7 22.6 + - - +
292D ALA* 4.0 4.7 - - - +
294D LEU* 1.3 71.2 - - - +
296D GLY* 1.3 57.1 + - - +
298D GLY 4.5 0.4 - - - -
299D THR* 3.1 26.5 + - - +
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Residues in contact with GLY 296 (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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201D LEU* 3.7 18.9 - - - +
205D ILE* 5.4 3.5 - - - +
292D ALA 3.2 9.9 + - - -
293D ASP 3.0 5.6 + - - -
295D LEU* 1.3 79.1 - - - +
297D ALA* 1.3 60.0 + - - +
298D GLY 3.1 5.4 + - - -
299D THR* 3.9 5.9 + - - -
300D GLU* 4.2 13.3 + - - +
301D THR 5.1 0.3 + - - -
502D 0XV 4.6 15.2 - - - +
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Residues in contact with ALA 297 (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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113D VAL* 4.3 3.8 - - + -
293D ASP 2.6 24.1 + - - +
294D LEU* 4.4 1.3 - - - +
296D GLY* 1.3 70.4 - - - +
298D GLY* 1.3 56.7 + - - +
301D THR* 2.8 23.2 + - - +
501D HEM 3.2 42.0 + - + -
502D 0XV 3.1 33.5 - - + +
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Residues in contact with GLY 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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174D PRO* 5.3 0.2 - - - -
178D ILE* 4.3 8.7 - - - -
294D LEU 3.2 12.5 + - - -
296D GLY 3.1 0.8 - - - -
297D ALA* 1.3 78.9 - - - +
299D THR* 1.3 57.1 + - - +
301D THR* 2.8 13.1 + - - -
302D THR* 2.4 31.1 + - - -
501D HEM 3.5 25.5 - - - +
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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
------------------------------------------------------------
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