Contacts of the helix formed by residues 276 - 291 (chain D) in PDB entry 1FTA
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 ARG 276 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97D GLU* 2.8 41.1 + - - +
118D ASP* 5.0 0.2 + - - -
274D LYS 3.7 11.0 + - - -
275D LEU* 1.3 80.6 - - - +
277D LEU* 1.3 57.5 + - - +
278D LEU 4.8 1.3 - - - +
279D TYR* 3.4 36.9 + - + +
280D GLU* 2.9 42.9 + - - +
281D CYS* 2.8 32.4 + - - -
310D ILE 5.6 0.4 - - - +
311D HIS* 4.0 21.2 + - + +
312D GLN 3.5 5.8 - - - +
313D ARG* 4.5 17.1 - - + +
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Residues in contact with LEU 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D LEU 4.2 0.6 + - - -
276D ARG* 1.3 72.6 - - - +
278D LEU* 1.3 63.4 + - + +
279D TYR 3.3 0.2 + - - -
281D CYS* 3.9 4.7 - - + -
282D ASN* 3.0 53.0 + - - +
302D VAL* 4.1 9.6 - - + -
305D VAL* 3.5 44.4 - - + +
307D PRO* 3.8 29.2 - - + -
312D GLN* 2.9 35.8 + - + +
313D ARG* 4.4 0.8 - - - +
314D ALA* 3.9 19.3 - - + -
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Residues in contact with LEU 278 (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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95D VAL* 4.5 2.7 - - + -
116D CYS* 3.4 26.1 - - + +
137D GLY* 5.4 0.7 + - - -
139D TYR* 4.5 8.2 - - - +
152D ALA* 3.5 34.5 - - + +
153D LEU* 4.5 2.7 - - + -
154D GLN 4.2 6.3 - - - +
276D ARG* 3.7 1.0 - - - +
277D LEU* 1.3 80.8 - - + +
279D TYR* 1.3 65.3 + - + +
282D ASN* 4.4 9.0 - - - +
283D PRO* 3.8 12.3 - - - +
307D PRO* 3.7 30.7 - - + -
309D ASP 4.8 1.6 - - - +
310D ILE* 3.6 50.4 + - + +
312D GLN 4.7 1.0 + - - +
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Residues in contact with TYR 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D VAL* 4.2 15.3 - - + -
97D GLU* 3.5 47.6 + - + +
116D CYS* 4.0 1.3 - - + -
117D PHE* 3.8 29.4 - - - +
118D ASP* 3.7 9.4 - - + +
135D ILE* 3.5 16.2 - - - +
276D ARG* 3.4 41.3 + - + +
277D LEU 3.3 0.2 - - - -
278D LEU* 1.3 87.2 - - + +
280D GLU* 1.3 72.1 + - + +
283D PRO* 4.2 10.1 - - - -
310D ILE 3.7 17.5 - - - -
311D HIS* 2.6 31.8 + + - -
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Residues in contact with GLU 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D ASP* 3.3 9.5 - - - +
121D ASP* 2.9 23.8 - - - +
135D ILE* 4.4 6.5 - - + -
248D MET* 3.4 19.5 - - + +
275D LEU* 3.5 20.1 - - + +
276D ARG* 2.9 63.8 + - - +
278D LEU 3.8 0.4 - - - -
279D TYR* 1.3 94.7 - - + +
281D CYS* 1.3 65.4 + - - +
282D ASN 3.7 0.2 - - - -
283D PRO* 4.0 2.6 - - - +
284D MET* 3.3 29.1 + - - +
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Residues in contact with CYS 281 (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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248D MET* 4.4 4.7 - - - -
275D LEU* 3.9 22.2 - - - -
276D ARG 2.8 26.6 + - - +
277D LEU* 3.8 11.0 - - + +
280D GLU* 1.3 75.3 - - - +
282D ASN* 1.3 61.9 + - - +
284D MET* 3.2 4.2 + - - +
285D ALA* 2.8 28.4 + - - +
302D VAL* 3.9 18.3 - - + +
314D ALA* 4.1 14.1 - - - -
316D ILE* 3.9 26.8 - - + +
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Residues in contact with ASN 282 (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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139D TYR* 3.6 11.1 + - - +
154D GLN 4.4 0.7 - - - +
155D PRO* 4.7 1.2 - - - +
156D GLY* 3.4 30.6 + - - +
159D LEU* 4.4 5.2 - - + -
277D LEU* 3.0 35.4 + - - +
278D LEU* 4.4 8.2 - - - +
281D CYS* 1.3 76.0 - - - +
283D PRO* 1.3 69.4 - - + +
285D ALA* 3.0 4.3 + - - +
286D TYR* 2.8 25.1 + - - +
302D VAL* 3.3 33.5 + - - +
303D LEU* 3.5 12.1 - - - +
305D VAL 5.3 0.7 + - - +
307D PRO* 4.9 0.5 - - - +
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Residues in contact with PRO 283 (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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135D ILE* 3.6 23.3 - - + -
136D PHE 3.5 33.7 - - - +
137D GLY* 3.9 9.2 - - - +
159D LEU* 4.5 1.8 - - + -
162D ALA* 3.9 12.5 - - + +
163D GLY 4.3 3.4 - - - +
278D LEU 3.8 16.8 - - - +
279D TYR* 4.4 2.7 - - - -
280D GLU 4.0 8.3 - - - +
281D CYS 3.8 2.2 - - - -
282D ASN* 1.3 93.9 - - + +
284D MET* 1.3 59.2 + - - +
286D TYR* 3.4 1.9 + - - +
287D VAL* 3.0 32.7 + - - +
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Residues in contact with MET 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D ILE* 3.9 29.2 - - + -
163D GLY 5.2 0.4 - - - +
164D TYR* 3.7 43.3 - - + -
248D MET* 3.7 15.9 - - + +
249D VAL* 4.0 20.0 - - - +
252D VAL* 4.0 21.8 - - + -
280D GLU 3.3 19.0 + - - +
281D CYS 3.2 3.7 + - - +
283D PRO* 1.3 76.7 - - - +
285D ALA* 1.3 59.7 + - - +
287D VAL* 3.9 4.3 - - - +
288D MET* 2.9 33.4 + - - +
318D LEU* 3.8 20.4 - - + -
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Residues in contact with ALA 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D CYS 2.8 18.6 + - - +
282D ASN 3.4 4.7 - - - +
284D MET* 1.3 74.9 - - - +
286D TYR* 1.3 64.6 + - - +
288D MET* 3.5 1.6 + - - +
289D GLU* 3.0 30.2 + - - +
295D ALA* 3.6 29.2 - - + +
302D VAL* 3.7 16.6 - - + -
303D LEU* 3.6 18.4 - - + -
316D ILE* 4.9 0.7 - - + -
318D LEU* 4.5 1.1 - - - +
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Residues in contact with TYR 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D GLY 4.0 8.7 - - - -
157D ARG* 5.3 3.1 - - - -
159D LEU* 3.8 42.3 + - + -
160D VAL 3.5 16.6 + - - -
161D ALA* 4.5 0.7 - - - -
162D ALA* 3.7 19.3 - - + -
176D ALA* 3.5 32.3 - - + -
177D MET 3.8 0.3 - - - -
178D ASP* 3.7 18.4 + - - +
282D ASN 2.8 15.4 + - - +
283D PRO 3.5 4.3 - - - +
285D ALA* 1.3 73.7 - - - +
287D VAL* 1.3 65.8 + - - +
289D GLU* 3.2 4.9 + - + +
290D LYS* 3.1 47.6 + - + +
303D LEU* 3.7 17.2 - - + +
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Residues in contact with VAL 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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162D ALA 4.2 9.4 - - - +
163D GLY* 4.3 12.6 - - - -
164D TYR* 4.5 16.6 - - + -
174D VAL* 4.3 6.7 - - + -
176D ALA* 3.6 26.0 - - + -
181D VAL* 3.7 21.1 - - + +
252D VAL* 6.0 0.2 - - + -
256D LEU* 4.2 18.6 - - + -
283D PRO 3.0 21.1 + - - +
284D MET* 3.9 6.3 - - - +
286D TYR* 1.3 74.4 - - - +
288D MET* 1.3 72.2 + - + +
290D LYS 3.2 1.2 + - - -
291D ALA* 2.9 20.8 + - - +
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Residues in contact with MET 288 (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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164D TYR* 6.0 0.2 - - - +
202D ILE* 3.3 28.5 - - + -
252D VAL* 3.7 30.3 - - + +
255D THR* 5.0 1.1 - - - -
256D LEU* 4.0 29.8 - - + +
284D MET 2.9 22.8 + - - +
285D ALA* 3.6 7.4 - - - +
286D TYR 3.2 0.2 - - - -
287D VAL* 1.3 76.5 - - + +
289D GLU* 1.3 61.6 + - - +
291D ALA* 3.0 11.1 + - - +
292D GLY 3.2 0.2 + - - -
293D GLY* 2.7 24.7 + - - -
294D MET 4.2 15.0 - - - +
318D LEU* 4.2 25.6 - - + -
319D GLY* 4.3 12.1 - - - +
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Residues in contact with GLU 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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157D ARG* 2.9 36.4 + - - -
285D ALA 3.0 14.2 + - - +
286D TYR* 3.2 4.0 + - + +
288D MET* 1.3 75.4 - - - +
290D LYS* 1.3 62.0 + - + +
292D GLY* 3.0 17.3 + - - -
293D GLY 3.3 17.2 + - - +
294D MET* 4.9 6.1 - - - -
295D ALA* 5.0 8.7 + - - +
301D ALA* 4.5 9.9 - - - +
303D LEU* 3.7 19.2 - - + +
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Residues in contact with LYS 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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176D ALA* 4.6 2.0 - - + -
177D MET 3.9 14.4 - - - +
178D ASP* 3.8 30.9 + - - +
179D CYS 5.5 0.2 - - - -
180D GLY* 4.6 8.7 - - - +
181D VAL* 3.7 24.9 + - + +
200D VAL 4.4 1.0 - - - +
201D LYS* 3.8 13.7 - - - -
286D TYR* 3.1 57.6 + - + +
287D VAL* 4.5 1.6 - - - -
289D GLU* 1.3 78.6 - - + +
291D ALA* 1.3 57.5 + - - +
292D GLY 3.2 1.5 + - - -
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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
----------------------------------------------------------
181D VAL* 4.0 6.5 - - + -
200D VAL 3.5 17.7 - - - +
201D LYS* 3.4 10.9 - - - +
202D ILE* 2.9 28.7 + - + +
256D LEU* 3.5 31.6 - - + -
287D VAL 2.9 15.4 + - - +
288D MET* 3.0 6.2 + - - +
290D LYS* 1.3 75.6 - - - +
292D GLY* 1.3 58.6 + - - +
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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