Contacts of the helix formed by residues 296 - 310 (chain A) in PDB entry 2FBW
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 SER 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A GLY 5.0 2.5 - - - -
132A GLY* 4.6 5.8 - - - +
295A ALA* 1.3 77.1 - - - +
297A ARG* 1.3 66.6 + - - +
298A ASP* 2.6 23.2 + - - -
299A VAL* 3.0 12.8 + - - +
300A VAL* 3.0 20.1 + - - +
407A ASN* 3.9 7.4 - - - -
409A LEU* 5.1 6.1 - - - -
619A ARG* 3.4 6.0 + - - -
621A TYR* 3.3 39.6 - - - -
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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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130A PHE* 3.6 16.2 - - - -
251A GLN* 3.0 43.8 + - - +
252A PHE 4.3 6.7 - - - +
253A HIS* 3.5 32.5 + - - -
254A PRO* 3.9 24.0 - - + -
266A GLU* 2.9 30.7 + - - +
269A ARG* 5.8 0.2 - - - +
295A ALA 4.6 1.6 - - - +
296A SER* 1.3 74.3 - - - +
298A ASP* 1.3 63.6 + - - +
300A VAL* 4.1 0.6 - - - +
301A SER* 2.9 30.1 + - - -
364A HIS* 3.9 3.4 + - - -
407A ASN* 4.0 3.4 + - - +
408A ARG* 3.7 22.6 + - - +
410A GLY* 3.6 28.5 - - - +
411A ALA 4.8 0.8 - - - +
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Residues in contact with ASP 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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252A PHE 5.5 0.7 - - - -
296A SER* 2.6 29.0 + - - -
297A ARG* 1.3 72.2 - - - +
299A VAL* 1.3 60.9 + - - +
301A SER* 4.0 4.1 - - - -
302A ARG* 2.9 60.6 + - - +
407A ASN* 3.2 19.1 + - - +
547A GLY* 3.4 10.2 - - - +
548A ALA* 3.8 18.8 - - + +
619A ARG* 2.9 31.3 + - - -
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Residues in contact with VAL 299 (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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284A MET* 4.4 5.2 - - + -
287A TYR* 5.0 10.3 - - + +
288A ALA* 5.0 2.9 - - + -
295A ALA* 4.2 16.2 - - + -
296A SER* 3.0 24.0 + - - +
298A ASP* 1.3 78.8 - - - +
300A VAL* 1.3 61.3 + - - +
302A ARG* 3.4 21.1 + - - +
303A SER* 2.7 41.4 + - - +
619A ARG* 4.4 7.0 - - - +
621A TYR* 4.4 11.4 - - + -
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Residues in contact with VAL 300 (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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254A PRO* 3.6 30.5 - - + -
269A ARG* 4.1 14.1 - - - +
275A LEU* 3.7 26.7 - - + -
284A MET* 3.9 17.5 - - + -
292A LYS 4.6 0.4 - - - +
293A ASP 4.4 3.4 - - - +
295A ALA* 3.6 31.2 - - + +
296A SER 3.0 16.0 + - - +
297A ARG* 4.8 0.2 - - - -
299A VAL* 1.3 75.5 - - - +
301A SER* 1.3 57.6 + - - +
303A SER* 3.3 1.2 + - - -
304A MET* 2.8 31.2 + - + +
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Residues in contact with SER 301 (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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252A PHE* 2.8 34.2 + - - -
253A HIS 3.7 0.5 - - - -
254A PRO* 3.5 16.6 - - - +
297A ARG 2.9 16.4 + - - -
298A ASP* 4.0 4.0 - - - -
300A VAL* 1.3 77.8 - - - +
302A ARG* 1.3 53.9 + - - +
304A MET* 3.3 1.5 + - - -
305A THR* 2.7 38.2 + - - -
361A PRO* 3.7 21.3 - - - +
482A VAL* 4.4 6.1 - - - -
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Residues in contact with ARG 302 (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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298A ASP* 2.9 51.5 + - - +
299A VAL* 3.9 16.2 - - - +
301A SER* 1.3 75.0 - - - +
303A SER* 1.3 57.4 + - - +
305A THR* 3.1 2.6 + - - -
306A ILE* 2.8 37.0 + - + +
482A VAL* 3.7 22.4 + - + +
483A PHE* 3.7 32.0 - - + -
547A GLY* 2.9 23.8 + - - +
548A ALA* 4.2 5.5 + - - +
550A ALA* 4.0 20.5 - - - +
619A ARG* 4.7 1.8 - - - +
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Residues in contact with SER 303 (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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283A PHE* 4.5 0.7 - - - -
284A MET* 3.5 23.3 - - - +
287A TYR* 3.4 42.1 + - - +
299A VAL* 2.7 27.7 + - - +
300A VAL 3.5 3.8 - - - -
302A ARG* 1.3 76.2 - - - +
304A MET* 1.3 63.8 + - - +
306A ILE* 3.1 4.4 + - - +
307A GLU* 3.0 28.0 + - - +
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Residues in contact with MET 304 (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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254A PRO* 2.9 50.7 - - - +
255A THR* 4.3 3.1 - - + -
275A LEU* 4.0 8.3 - - + -
283A PHE* 3.9 27.3 - - + -
300A VAL* 2.8 26.5 + - - +
301A SER 3.7 3.6 - - - +
303A SER* 1.3 73.1 - - - +
305A THR* 1.3 62.0 + - - +
307A GLU* 3.3 5.1 + - - +
308A ILE* 3.1 29.8 + - + +
321A VAL* 3.4 30.2 - - + +
359A VAL* 4.0 12.8 - - + -
360A LEU* 4.1 10.5 - - - -
361A PRO* 3.9 10.8 - - + -
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Residues in contact with THR 305 (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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301A SER 2.7 21.5 + - - -
302A ARG* 3.1 6.9 + - - -
304A MET* 1.3 75.4 - - - +
306A ILE* 1.3 58.2 + - - +
308A ILE* 3.4 9.7 + - + +
309A ARG* 2.9 43.7 + - + +
361A PRO* 3.9 11.5 - - - +
482A VAL* 3.7 20.3 - - + +
483A PHE* 3.9 24.2 - - + -
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Residues in contact with ILE 306 (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 TYR* 3.2 34.5 - - + +
302A ARG* 2.8 21.4 + - + +
303A SER* 3.1 6.7 + - - +
305A THR* 1.3 73.9 - - - +
307A GLU* 1.3 65.4 + - - +
309A ARG* 3.1 23.5 + - - +
310A GLU* 2.8 49.2 + - + +
483A PHE* 4.0 23.1 - - + -
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Residues in contact with GLU 307 (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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277A ASN* 2.8 22.2 + - + -
283A PHE* 3.6 26.5 - - + -
286A ARG* 3.0 14.6 + - - -
287A TYR* 2.5 26.1 + - - +
303A SER 3.0 17.1 + - - +
304A MET* 3.5 10.1 - - - +
306A ILE* 1.3 76.0 - - - +
308A ILE* 1.3 60.6 + - - +
310A GLU* 3.4 4.5 + - - +
311A GLY 3.5 0.2 + - - -
312A ARG* 2.7 71.9 + - + +
321A VAL* 4.8 11.7 - - + -
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Residues in contact with ILE 308 (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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304A MET* 3.1 18.8 + - + +
305A THR* 3.7 9.0 - - + +
307A GLU* 1.3 72.4 - - - +
309A ARG* 1.3 66.6 + - + +
310A GLU 3.1 2.4 + - - -
311A GLY* 3.1 13.5 + - - -
312A ARG 4.3 0.2 + - - -
313A GLY* 4.3 7.4 - - - +
318A LYS 3.8 20.6 - - - +
319A ASP* 3.7 25.8 - - + +
320A HIS* 3.9 17.3 - - - +
321A VAL* 4.0 17.7 - - + +
360A LEU* 4.7 11.9 - - + -
361A PRO* 4.8 6.3 - - + -
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Residues in contact with ARG 309 (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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305A THR* 2.9 31.6 + - + +
306A ILE* 3.6 29.3 - - - +
308A ILE* 1.3 77.0 - - + +
310A GLU* 1.3 62.6 + - + +
311A GLY 3.3 1.9 + - - -
483A PHE* 3.7 24.5 - - - +
552A GLU* 2.7 35.8 + - - -
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Residues in contact with GLU 310 (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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286A ARG* 5.3 0.9 + - - -
287A TYR* 4.4 1.2 + - - -
306A ILE* 2.8 38.6 + - + +
307A GLU 4.1 0.4 - - - +
308A ILE 3.1 0.2 - - - -
309A ARG* 1.3 82.7 + - + +
311A GLY* 1.3 59.0 + - - +
312A ARG* 2.7 54.2 + - - +
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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
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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