Contacts of the helix formed by residues 281 - 299 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A VAL 2.9 12.1 + - - +
279A ARG 4.0 2.5 - - - -
280A LYS* 1.3 77.6 - - - +
282A ASN* 1.3 63.4 + - - +
283A ARG* 3.1 39.2 + - - +
284A ALA* 3.2 16.6 + - + +
285A VAL* 3.1 18.0 + - - +
312A PHE 4.7 3.1 - - - +
313A TYR* 3.8 27.2 - - + -
314A GLU 5.5 1.6 + - - -
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Residues in contact with ASN 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A THR* 3.1 22.0 + - - +
86A SER* 4.6 8.6 + - - +
88A PRO* 3.5 35.4 - - - +
279A ARG 4.4 2.4 + - - -
280A LYS 4.0 2.4 + - - -
281A ASP* 1.3 70.1 + - - +
283A ARG* 1.3 55.8 + - + +
285A VAL* 3.2 9.2 + - - +
286A GLN* 2.7 40.5 + - - +
289A ARG* 5.6 3.5 + - - +
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Residues in contact with ARG 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 4.2 15.3 - - + +
85A THR* 3.9 24.0 - - - +
86A SER* 3.9 18.6 + - - +
281A ASP* 3.1 22.6 + - - +
282A ASN* 1.3 78.4 - - - +
284A ALA* 1.3 57.5 + - - +
286A GLN* 3.3 7.9 + - - +
287A LYS* 2.8 42.7 + - - +
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Residues in contact with ALA 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A VAL* 4.1 9.6 - - + +
281A ASP* 3.2 26.7 + - + +
282A ASN 3.2 0.6 - - - -
283A ARG* 1.3 79.6 - - - +
285A VAL* 1.3 62.1 + - - +
287A LYS* 3.2 6.0 + - - +
288A LEU* 2.9 19.9 + - - +
312A PHE* 3.3 48.4 - - + +
313A TYR* 4.3 6.1 - - + -
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Residues in contact with VAL 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A MET* 3.4 16.9 - - + +
267A ILE* 5.0 4.9 - - + -
278A VAL* 3.9 9.0 - - + +
279A ARG* 3.7 36.8 - - + +
281A ASP 3.1 13.8 + - - +
282A ASN* 3.2 10.1 + - - +
284A ALA* 1.3 76.0 - - - +
286A GLN* 1.3 57.1 + - - +
288A LEU* 3.3 3.3 + - - -
289A ARG* 2.9 52.5 + - - +
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Residues in contact with GLN 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LYS 3.7 17.1 + - - +
82A ASN* 4.2 2.6 - - - +
83A GLN 2.7 27.9 + - - -
84A LEU* 3.3 19.1 - - + +
85A THR* 3.0 38.1 + - - +
282A ASN* 2.7 23.8 + - - +
283A ARG* 3.5 5.4 - - - +
285A VAL* 1.3 73.9 - - - +
287A LYS* 1.3 61.0 + - - +
289A ARG* 3.4 18.2 + - - +
290A ARG* 3.1 23.0 + - + +
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Residues in contact with LYS 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LEU* 3.8 33.0 - - + +
283A ARG* 2.8 31.6 + - - +
284A ALA* 3.5 8.5 - - - +
286A GLN* 1.3 73.6 - - - +
288A LEU* 1.3 60.8 + - - +
290A ARG* 3.3 7.5 + - - +
291A GLU* 3.1 27.6 + - + +
309A ILE* 4.0 31.0 - - + -
310A GLU 4.3 5.7 + - - -
311A SER* 3.5 26.3 + - - +
312A PHE* 5.0 2.2 - - + +
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Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A MET* 3.7 23.3 - - + +
266A PHE* 4.3 15.7 - - + -
267A ILE* 3.8 25.6 - - + +
278A VAL* 5.0 1.3 - - + -
284A ALA 2.9 15.6 + - - +
285A VAL* 3.8 4.5 - - - +
287A LYS* 1.3 72.7 - - - +
289A ARG* 1.3 61.1 + - - +
291A GLU* 3.3 1.2 + - - +
292A VAL* 2.7 48.1 + - + +
307A ILE* 4.3 4.3 - - + -
309A ILE* 3.8 16.1 - - + +
312A PHE* 4.0 19.3 - - + -
318A PHE* 4.2 26.9 - - + -
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Residues in contact with ARG 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A LYS* 6.4 3.8 - - - +
259A ASP* 5.1 14.8 - - + +
260A GLN* 3.2 30.7 - - - +
263A MET* 3.4 20.3 - - + +
282A ASN* 5.4 4.4 + - - +
285A VAL* 2.9 44.4 + - - +
286A GLN* 3.7 22.1 - - - +
288A LEU* 1.3 76.9 - - - +
290A ARG* 1.3 56.5 + - - +
292A VAL* 3.7 1.2 - - - +
293A GLU* 2.9 31.0 + - + +
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Residues in contact with ARG 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ASN* 3.4 56.1 + - - +
286A GLN* 3.1 14.9 + - + +
287A LYS* 3.6 10.1 - - - +
288A LEU 3.2 0.2 - - - -
289A ARG* 1.3 76.8 - - - +
291A GLU* 1.3 75.2 + - - +
293A GLU* 3.5 6.0 + - - +
294A LYS* 3.2 27.0 + - + +
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Residues in contact with GLU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A LYS* 3.1 20.1 + - + +
288A LEU 4.0 2.0 - - - +
290A ARG* 1.3 89.4 + - - +
292A VAL* 1.3 58.5 + - - +
294A LYS* 2.7 39.1 + - - +
295A ALA* 2.9 30.4 + - - +
306A ARG 5.5 0.5 - - - +
307A ILE* 3.6 25.3 - - + +
308A GLU 4.0 14.8 + - - +
309A ILE* 3.8 21.8 - - + -
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Residues in contact with VAL 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ASP* 3.8 25.4 - - + +
262A VAL* 3.5 43.1 - - + -
263A MET* 4.0 12.6 - - - +
266A PHE* 4.3 2.2 - - + -
288A LEU* 2.7 43.0 + - + +
289A ARG 3.7 2.7 - - - +
291A GLU* 1.3 73.7 - - - +
293A GLU* 1.3 57.1 + - - +
295A ALA* 3.3 7.0 + - - +
296A LYS* 2.9 29.9 + - + +
307A ILE* 4.0 10.1 - - + -
322A LEU* 5.8 0.9 - - - +
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Residues in contact with GLU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A TYR* 3.7 10.0 + - - +
81A LYS* 5.0 8.5 - - - +
259A ASP* 3.8 24.7 - - - +
289A ARG* 2.9 19.7 + - + +
290A ARG* 3.8 6.6 - - - +
292A VAL* 1.3 76.4 - - - +
294A LYS* 1.3 64.8 + - - +
296A LYS* 3.4 4.8 + - - +
297A ARG* 2.9 63.2 + - - +
501A ACP 2.5 31.5 + - - +
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Residues in contact with LYS 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A ARG* 3.2 15.1 + - - +
291A GLU* 2.7 42.7 + - - +
293A GLU* 1.3 82.1 + - - +
295A ALA* 1.3 66.9 + - - +
297A ARG* 3.1 12.2 + - + +
298A ALA* 3.1 22.3 + - + +
306A ARG 5.5 4.4 + - - -
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Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A GLU 2.9 20.5 + - - +
292A VAL* 3.6 4.7 - - - +
294A LYS* 1.3 74.0 - - - +
296A LYS* 1.3 63.5 + - - +
298A ALA* 3.1 5.3 + - - +
299A LEU* 2.9 29.0 + - - +
305A ALA* 4.1 20.5 - - + +
306A ARG 4.9 2.9 - - - +
307A ILE* 3.9 25.1 - - + -
322A LEU* 4.9 10.1 - - + -
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Residues in contact with LYS 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A GLY* 3.2 16.2 + - - -
258A PHE* 4.5 7.0 - - + -
259A ASP* 2.6 29.3 + - - +
262A VAL* 6.1 0.7 - - + -
292A VAL* 2.9 15.0 + - + +
293A GLU* 3.4 13.0 - - - +
294A LYS 3.2 0.2 - - - -
295A ALA* 1.3 75.4 - - - +
297A ARG* 1.3 62.0 + - - +
299A LEU* 3.1 22.7 + - - +
300A SER* 3.4 12.1 + - - -
322A LEU* 5.4 2.6 - - + +
327A PHE* 3.5 41.7 - - + -
368A ILE* 4.9 3.1 - - + -
501A ACP 2.7 59.2 + - + +
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Residues in contact with ARG 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A TYR* 3.3 31.3 + - - -
59A ASN* 5.8 3.2 + - - +
61A ILE* 4.0 18.5 - - - +
293A GLU* 2.9 44.6 + - - +
294A LYS* 3.1 11.8 + - + +
296A LYS* 1.3 77.5 - - - +
298A ALA* 1.3 64.0 + - - +
300A SER* 3.1 19.2 + - - -
301A SER* 4.1 3.3 + - - -
501A ACP 3.6 53.6 + - + +
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Residues in contact with ALA 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A LYS* 3.1 13.2 + - + +
295A ALA* 3.1 9.6 + - - +
297A ARG* 1.3 76.7 - - - +
299A LEU* 1.3 57.8 + - - +
301A SER* 3.0 11.5 + - - -
302A GLN* 2.9 52.5 + - - +
305A ALA* 4.4 7.9 - - + -
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Residues in contact with LEU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ALA 2.9 19.1 + - - +
296A LYS* 3.1 11.6 + - - +
298A ALA* 1.3 77.1 - - - +
300A SER* 1.3 56.5 + - - +
301A SER 3.2 0.7 - - - -
302A GLN 3.3 15.7 - - - +
303A HIS 3.7 5.4 - - - +
304A GLN* 3.6 33.7 - - - +
305A ALA* 3.8 3.6 - - + +
322A LEU* 3.6 44.4 - - + +
323A THR 4.0 2.9 - - - +
324A ARG* 2.9 37.7 + - - +
327A PHE* 3.9 25.0 - - + -
369A PRO* 4.4 3.2 - - - +
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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