Contacts of the helix formed by residues 276 - 291 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B GLU* 2.8 47.0 + - - +
118B ASP* 4.0 1.2 + - - -
274B LYS 3.8 12.3 - - - -
275B LEU* 1.3 73.4 - - - +
277B LEU* 1.3 61.1 + - - +
278B LEU 4.6 1.6 - - - +
279B TYR* 3.4 40.1 + - + +
280B GLU* 2.9 42.2 + - - +
281B CYS* 2.8 27.7 + - - -
311B HIS* 4.3 13.7 - - + +
312B GLN 3.5 11.0 - - - +
313B ARG* 4.2 18.1 - - + +
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Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B LEU 3.8 1.4 + - - -
276B ARG* 1.3 72.8 - - - +
278B LEU* 1.3 63.0 + - + +
279B TYR 3.5 0.2 + - - -
281B CYS* 3.9 5.4 - - - -
282B ASN* 2.9 53.9 + - - +
302B VAL* 4.2 7.2 - - + -
305B VAL* 3.6 43.1 - - + +
307B PRO* 3.8 23.6 - - + -
312B GLN* 2.9 44.7 + - + +
314B ALA* 3.9 22.0 - - + +
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Residues in contact with LEU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B VAL* 4.4 2.7 - - + -
116B CYS* 3.7 28.9 - - - +
137B GLY* 5.4 0.9 - - - -
139B TYR* 3.6 29.7 + - + +
152B ALA* 3.2 29.4 - - + +
153B LEU* 5.0 0.7 - - + -
154B GLN 4.3 1.8 - - - +
276B ARG* 3.6 2.0 - - - +
277B LEU* 1.3 82.4 - - + +
279B TYR* 1.3 62.7 + - + +
280B GLU 3.8 0.2 - - - -
282B ASN* 4.8 2.0 - - - +
283B PRO* 3.7 13.0 - - - +
307B PRO* 3.8 27.4 - - + -
309B ASP 5.1 0.7 - - - +
310B ILE* 3.6 50.5 + - + +
312B GLN 4.7 1.0 + - - +
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Residues in contact with TYR 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B VAL* 4.1 27.1 - - + -
97B GLU* 3.7 33.8 + - + -
116B CYS* 3.9 3.4 - - + -
117B PHE 3.7 29.4 - - - +
118B ASP* 3.8 10.6 + - + +
135B ILE* 3.6 21.7 - - - +
276B ARG* 3.4 47.3 + - + +
278B LEU* 1.3 78.4 - - + +
280B GLU* 1.3 66.5 + - + +
283B PRO* 4.1 9.2 - - - -
310B ILE 3.5 19.3 - - - -
311B HIS* 2.6 31.3 + + - -
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Residues in contact with GLU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ASP* 3.0 16.8 - - - +
121B ASP* 2.9 23.2 - - - +
135B ILE* 3.8 16.5 - - + +
248B MET* 3.3 23.3 - - + +
275B LEU* 3.5 21.9 - - + +
276B ARG* 2.9 58.1 + - - +
278B LEU 3.8 0.6 - - - -
279B TYR* 1.3 82.4 - - + +
281B CYS* 1.3 66.3 + - - +
282B ASN 3.6 0.2 - - - -
283B PRO* 3.7 2.8 - - - +
284B MET* 3.4 17.8 + - - +
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Residues in contact with CYS 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B MET* 4.2 2.2 - - - -
275B LEU* 3.6 34.5 - - - -
276B ARG 2.8 22.8 + - - +
277B LEU* 3.9 8.7 - - + -
280B GLU* 1.3 73.6 - - - +
282B ASN* 1.3 59.3 + - - +
284B MET* 3.5 1.6 + - - +
285B ALA* 2.8 31.2 + - - +
302B VAL* 4.0 17.0 - - + -
314B ALA* 4.3 12.3 - - + -
316B ILE* 4.0 29.8 - - + +
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Residues in contact with ASN 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B TYR* 3.3 17.6 + - - +
154B GLN 4.9 0.9 - - - +
155B PRO* 4.9 0.3 - - - +
156B GLY* 3.2 30.7 + - - -
159B LEU* 4.3 5.8 - - + -
277B LEU* 2.9 36.3 + - - +
278B LEU* 4.3 1.8 - - - +
281B CYS* 1.3 74.1 - - - +
283B PRO* 1.4 61.2 - - + +
285B ALA* 3.1 1.9 + - - +
286B TYR* 2.8 30.8 + - - +
302B VAL* 3.0 41.6 + - - +
303B LEU* 3.7 10.6 - - + +
305B VAL 5.2 1.0 - - - +
307B PRO* 5.8 0.7 - - - +
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Residues in contact with PRO 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ILE* 3.4 25.8 - - + -
136B PHE 3.6 31.6 - - - +
137B GLY* 3.9 9.2 - - - +
159B LEU* 4.7 1.3 - - + -
162B ALA* 4.0 11.8 - - + +
163B GLY 4.2 4.9 - - - +
278B LEU 3.7 14.6 - - - +
279B TYR* 4.3 3.6 - - - -
280B GLU 3.7 11.2 - - - +
282B ASN* 1.4 90.3 - - + +
284B MET* 1.3 63.6 + - - +
285B ALA 3.1 0.2 + - - -
286B TYR* 3.2 3.3 + - - +
287B VAL* 3.0 29.7 + - - +
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Residues in contact with MET 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ILE* 4.1 14.1 - - + -
164B TYR* 3.8 28.9 - - + -
248B MET* 3.6 14.4 - - + -
249B VAL* 3.6 45.1 - - + +
252B VAL* 3.5 27.8 - - + -
280B GLU 3.4 18.4 + - - +
281B CYS 3.5 2.8 + - - +
283B PRO* 1.3 75.9 - - - +
285B ALA* 1.3 61.4 + - - +
287B VAL* 3.7 4.1 - - - +
288B MET* 3.1 28.4 + - - +
318B LEU* 3.9 19.5 - - + -
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Residues in contact with ALA 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B CYS 2.8 19.5 + - - +
282B ASN 3.1 4.9 + - - +
284B MET* 1.3 73.5 - - - +
286B TYR* 1.3 66.1 + - - +
288B MET* 3.1 3.8 + - - +
289B GLU* 2.9 27.5 + - - +
295B ALA* 3.7 28.9 - - + -
302B VAL* 4.0 13.9 - - + -
303B LEU* 3.8 17.3 - - + -
316B ILE* 4.7 1.1 - - + -
318B LEU* 4.7 1.3 - - - +
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Residues in contact with TYR 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B GLY 4.2 2.2 - - - -
157B ARG 5.5 2.7 - - - -
159B LEU* 3.4 47.7 + - + -
160B VAL 3.7 9.0 + - - -
161B ALA* 4.3 7.0 - - - -
162B ALA* 3.7 16.8 - - + -
176B ALA* 3.7 29.2 - - + -
177B MET* 3.8 8.9 - - - -
178B ASP* 3.8 6.8 + - - +
282B ASN 2.8 16.3 + - - +
283B PRO 3.6 4.3 - - - +
285B ALA* 1.3 76.3 - - - +
287B VAL* 1.3 61.7 + - - +
289B GLU* 3.2 2.7 + - + +
290B LYS* 3.0 60.3 + - + +
303B LEU* 3.7 23.5 - - + +
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Residues in contact with VAL 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ALA* 4.7 1.1 - - + +
163B GLY* 4.2 21.8 - - - +
164B TYR* 4.4 18.6 - - + -
174B VAL* 4.4 7.6 - - + -
176B ALA* 3.9 23.3 - - + -
181B VAL* 3.6 8.5 - - + +
252B VAL* 5.7 1.6 - - + -
256B LEU* 4.3 27.6 - - + -
283B PRO 3.0 21.4 + - - +
284B MET* 3.7 7.6 - - - +
286B TYR* 1.3 72.9 - - - +
288B MET* 1.3 70.8 + - + +
290B LYS 3.3 2.9 + - - -
291B ALA* 2.9 22.0 + - - +
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Residues in contact with MET 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ILE* 3.9 20.9 - - - -
252B VAL* 3.8 36.6 - - + +
255B THR* 4.2 12.1 - - + -
256B LEU* 4.1 24.9 - - + +
284B MET 3.1 16.5 + - - +
285B ALA* 3.1 7.7 + - - +
287B VAL* 1.3 80.4 - - + +
289B GLU* 1.3 55.6 + - - +
291B ALA* 3.0 10.9 + - - +
292B GLY 3.2 0.2 + - - -
293B GLY* 2.6 29.8 + - - -
294B MET 4.3 17.0 - - - +
318B LEU* 4.2 23.3 - - + -
319B GLY* 4.5 9.4 - - - +
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Residues in contact with GLU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ARG* 3.0 34.2 + - - -
285B ALA 2.9 22.4 + - - +
286B TYR* 3.2 5.6 + - + +
288B MET* 1.3 70.8 - - - +
290B LYS* 1.3 66.0 + - + +
292B GLY* 3.1 14.2 + - - -
293B GLY 3.7 18.0 + - - +
294B MET* 4.5 3.6 - - - +
295B ALA* 4.5 18.2 + - + +
301B ALA* 5.1 6.5 - - - +
303B LEU* 3.6 18.2 - - + +
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Residues in contact with LYS 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ALA* 4.5 3.1 - - + -
177B MET 3.9 18.6 - - - +
178B ASP* 3.5 32.7 + - - +
180B GLY* 4.2 9.6 - - - -
181B VAL* 3.9 16.8 - - + +
200B VAL 4.2 0.2 - - - +
201B LYS* 2.9 22.7 + - - -
286B TYR* 3.0 52.7 + - + +
287B VAL 3.6 3.6 - - - +
289B GLU* 1.3 79.2 - - + +
291B ALA* 1.3 57.1 + - - +
292B GLY 3.3 0.2 - - - -
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Residues in contact with ALA 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B VAL* 4.1 5.4 - - + -
200B VAL 3.7 15.5 - - - +
201B LYS* 3.2 11.9 - - - +
202B ILE* 2.8 32.6 + - + +
256B LEU* 3.7 28.3 - - + -
287B VAL 2.9 15.5 + - - +
288B MET* 3.0 8.0 + - - +
290B LYS* 1.3 76.0 - - - +
292B GLY* 1.3 57.7 + - - +
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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