Contacts of the helix formed by residues 281 - 299 (chain B) in PDB entry 5F2R
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 ASP 281 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B VAL 2.9 15.0 + - - +
279B ARG 4.0 2.5 - - - -
280B LYS* 1.3 78.5 - - - +
282B ASN* 1.3 62.8 + - - +
283B ARG* 3.0 27.8 + - - +
284B ALA* 3.2 16.4 + - + +
285B VAL* 3.1 14.6 + - - +
312B PHE 4.7 3.3 - - - +
313B TYR* 3.7 26.9 - - + -
314B GLU 5.5 1.6 + - - -
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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
----------------------------------------------------------
279B ARG 4.4 6.8 - - - +
280B LYS 4.0 2.2 + - - -
281B ASP* 1.3 71.8 + - - +
283B ARG* 1.3 58.0 + - + +
285B VAL* 3.2 17.3 + - - +
286B GLN* 2.7 37.1 + - - +
289B ARG* 5.4 1.6 + - - -
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Residues in contact with ARG 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B THR* 3.8 21.8 - - - +
86B SER* 4.1 33.2 + - - +
281B ASP* 3.0 15.2 + - - +
282B ASN* 1.3 78.2 - - - +
284B ALA* 1.3 58.6 + - - +
286B GLN* 3.3 12.3 + - - +
287B LYS* 2.9 44.1 + - - +
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Residues in contact with ALA 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B VAL* 3.2 26.7 - - + -
281B ASP* 3.2 21.1 + - + +
283B ARG* 1.3 79.1 - - - +
285B VAL* 1.3 61.5 + - - +
287B LYS* 3.2 6.2 + - - +
288B LEU* 3.0 19.4 + - - +
312B PHE* 3.4 40.8 - - + +
313B TYR* 4.3 1.8 - - + -
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Residues in contact with VAL 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B MET* 3.4 18.2 - - + +
267B ILE* 4.9 6.7 - - + -
278B VAL* 3.9 7.4 - - + +
279B ARG* 3.7 34.3 - - + +
281B ASP 3.1 14.0 + - - +
282B ASN* 3.2 20.8 + - - +
284B ALA* 1.3 75.7 - - - +
286B GLN* 1.3 57.6 + - - +
288B LEU* 3.4 2.3 + - - -
289B ARG* 2.9 52.7 + - - +
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Residues in contact with GLN 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LYS 4.8 6.3 + - - -
82B ASN* 5.1 1.4 - - - +
83B GLN 2.7 31.6 + - - +
85B THR 4.6 0.5 + - - +
86B SER* 3.9 25.0 + - - +
282B ASN 2.7 20.3 + - - +
283B ARG* 3.5 13.6 + - - +
285B VAL* 1.3 73.5 - - - +
287B LYS* 1.3 63.0 + - + +
289B ARG* 3.4 18.6 + - - +
290B ARG* 3.1 23.4 + - + +
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Residues in contact with LYS 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ARG* 2.9 30.0 + - - +
284B ALA* 3.5 8.5 - - - +
286B GLN* 1.3 78.1 - - + +
288B LEU* 1.3 60.7 + - - +
290B ARG* 3.3 7.2 + - - +
291B GLU* 3.1 26.9 + - - +
309B ILE* 3.9 30.1 - - + -
310B GLU 4.3 5.9 + - - -
311B SER* 3.5 25.5 + - - +
312B PHE* 5.0 2.2 + - + +
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Residues in contact with LEU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B MET* 3.7 23.8 - - + +
266B PHE* 4.3 15.7 - - + -
267B ILE* 3.8 25.6 - - + +
278B VAL* 5.2 0.7 - - + -
284B ALA 3.0 15.6 + - - +
285B VAL* 3.8 5.6 - - - +
287B LYS* 1.3 72.3 - - - +
289B ARG* 1.3 60.8 + - - +
291B GLU 3.3 0.8 + - - +
292B VAL* 2.7 48.5 + - + +
307B ILE* 4.3 4.5 - - + -
309B ILE* 3.8 13.6 - - + +
312B PHE* 4.0 18.8 - - + -
318B PHE* 4.2 28.9 - - + -
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Residues in contact with ARG 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ASP* 5.2 13.8 - - + +
260B GLN* 3.2 30.5 - - - +
263B MET* 3.4 20.7 - - + +
282B ASN* 5.4 1.2 + - - -
285B VAL* 2.9 44.4 + - - +
286B GLN* 3.7 20.3 - - - +
287B LYS 3.3 0.2 - - - -
288B LEU* 1.3 75.7 - - - +
290B ARG* 1.3 56.0 + - - +
292B VAL* 3.3 1.6 + - - +
293B GLU* 2.9 31.3 + - + +
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Residues in contact with ARG 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ASN* 3.4 56.8 + - - +
286B GLN* 3.1 14.0 + - + +
287B LYS* 3.7 9.6 - - - +
288B LEU 3.2 0.4 - - - -
289B ARG* 1.3 77.9 - - - +
291B GLU* 1.3 75.3 + - - +
293B GLU* 3.5 6.2 + - - +
294B LYS* 3.3 30.8 + - + +
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Residues in contact with GLU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B LYS 3.1 16.5 + - - +
288B LEU 4.0 2.0 - - - +
290B ARG* 1.3 86.5 + - - +
292B VAL* 1.3 58.9 + - - +
294B LYS* 3.3 36.9 + - - +
295B ALA* 2.9 30.3 + - - +
306B ARG 5.5 1.2 - - - +
307B ILE* 3.6 24.7 - - + +
308B GLU 4.1 15.6 + - - +
309B ILE* 3.8 22.4 - - + -
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Residues in contact with VAL 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ASP* 3.8 24.5 - - + +
262B VAL* 3.5 43.3 - - + -
263B MET* 4.0 12.8 - - - +
266B PHE* 4.3 2.5 - - + -
288B LEU* 2.7 44.5 + - + +
289B ARG 3.7 3.1 - - - +
291B GLU* 1.3 73.4 - - - +
293B GLU* 1.3 63.9 + - - +
295B ALA* 3.3 6.2 + - - +
296B LYS* 2.9 23.9 + - + +
307B ILE* 4.0 9.4 - - + -
322B LEU* 5.8 0.7 - - + +
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Residues in contact with GLU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TYR* 3.7 8.2 + - - -
81B LYS* 5.0 9.8 + - - +
259B ASP* 3.7 28.7 - - - +
289B ARG* 2.9 19.5 + - + +
290B ARG* 3.8 6.2 - - - +
291B GLU 3.4 0.2 - - - -
292B VAL* 1.3 76.1 - - - +
294B LYS* 1.3 66.6 + - - +
296B LYS* 3.4 4.6 + - - +
297B ARG* 3.0 62.1 + - - +
501B ACP 2.7 27.4 + - - +
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Residues in contact with LYS 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B ARG* 3.3 19.5 + - - +
291B GLU* 3.3 43.0 + - - +
293B GLU* 1.3 82.7 + - - +
295B ALA* 1.3 66.8 + - - +
297B ARG* 3.1 11.0 + - + +
298B ALA* 3.1 22.2 + - + +
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Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B GLU 2.9 20.5 + - - +
292B VAL 3.3 4.5 + - - +
294B LYS* 1.3 72.8 - - - +
296B LYS* 1.3 62.7 + - - +
298B ALA* 3.2 5.5 + - - +
299B LEU* 2.9 28.9 + - - +
305B ALA* 4.1 20.4 - - + +
306B ARG 4.9 2.9 - - - +
307B ILE* 3.9 26.5 - - + -
322B LEU* 4.9 9.9 - - + -
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Residues in contact with LYS 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B GLY* 3.2 19.3 + - - +
258B PHE* 4.4 4.9 - - + -
259B ASP* 2.6 30.8 + - - +
262B VAL* 6.1 1.3 - - + -
292B VAL* 2.9 15.2 + - + +
293B GLU* 3.4 13.9 - - - +
295B ALA* 1.3 75.0 - - - +
297B ARG* 1.3 61.4 + - - +
299B LEU* 3.1 22.4 + - - +
300B SER* 3.4 12.0 + - - -
322B LEU* 5.4 1.7 - - + +
327B PHE* 3.5 40.6 - - + -
368B ILE* 5.0 2.7 - - + -
501B ACP 2.7 58.0 + - + +
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Residues in contact with ARG 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TYR* 3.1 33.7 + - - -
59B ASN* 6.3 0.8 - - - -
61B ILE* 4.2 15.6 - - - +
293B GLU* 3.0 44.5 + - - +
294B LYS* 3.1 12.2 + - + +
296B LYS* 1.3 77.7 - - - +
298B ALA* 1.3 63.9 + - - +
300B SER* 3.1 19.2 + - - -
301B SER* 4.1 3.1 + - - -
501B ACP 3.6 56.1 + - + +
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Residues in contact with ALA 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B LYS* 3.1 14.5 + - + +
295B ALA* 3.6 9.4 - - - +
297B ARG* 1.3 76.6 - - - +
299B LEU* 1.3 57.1 + - - +
300B SER 3.1 0.2 - - - -
301B SER* 3.0 11.8 + - - -
302B GLN* 2.9 52.2 + - - +
305B ALA* 4.4 8.3 - - + -
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Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ALA 2.9 18.2 + - - +
296B LYS* 3.1 11.4 + - - +
298B ALA* 1.3 76.3 - - - +
300B SER* 1.3 57.0 + - - +
301B SER 3.2 0.4 - - - -
302B GLN 3.3 15.3 - - - +
303B HIS 3.7 5.2 - - - +
304B GLN* 3.6 24.7 - - - +
305B ALA* 4.1 3.4 - - + -
322B LEU* 3.6 54.7 - - + +
323B THR 4.0 2.5 - - - +
324B ARG* 2.9 36.9 + - - +
327B PHE* 3.9 25.2 - - + -
369B PRO* 4.4 2.6 - - - +
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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