Contacts of the helix formed by residues 297 - 310 (chain B) in PDB entry 5FWP
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 THR 297 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B ASP 4.7 5.4 - - - +
296B ILE* 1.3 75.3 - - - +
298B GLN* 1.3 60.2 + - - +
299B GLU* 3.6 10.6 + - - +
300B GLU* 2.8 42.5 + - - +
301B TYR* 3.0 31.1 + - - -
128E MET* 5.4 0.7 - - - -
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Residues in contact with GLN 298 (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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297B THR* 1.3 71.7 - - - +
299B GLU* 1.3 63.4 + - + +
301B TYR* 3.2 2.4 + - - +
302B GLY* 2.7 19.5 + - - +
315B HIS* 2.9 36.7 + - - -
128E MET* 3.1 37.1 - - + +
130E ASN* 3.5 36.2 - - - +
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Residues in contact with GLU 299 (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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297B THR* 3.2 9.0 + - - +
298B GLN* 1.3 80.1 - - + +
300B GLU* 1.3 59.7 + - + +
302B GLY* 3.3 1.6 + - - -
303B GLU* 2.8 39.1 + - + +
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Residues in contact with GLU 300 (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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288B ILE* 5.1 7.5 - - + +
291B ARG* 2.8 39.5 + - - +
295B ASP 3.9 1.6 - - - +
296B ILE* 3.6 14.8 - - + -
297B THR* 2.8 45.9 + - - +
299B GLU* 1.3 76.7 - - + +
301B TYR* 1.3 58.6 + - - +
303B GLU* 3.4 5.5 + - - +
304B PHE* 2.9 29.6 + - - +
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Residues in contact with TYR 301 (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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288B ILE* 4.2 7.4 - - + -
293B PRO* 3.3 37.1 + - - +
296B ILE* 3.4 38.8 - - + +
297B THR 3.0 21.8 + - - -
298B GLN* 3.7 5.2 - - - +
300B GLU* 1.3 76.3 - - - +
302B GLY* 1.3 59.0 + - - +
304B PHE* 3.4 3.3 + - - +
305B TYR* 2.9 29.3 + - - +
315B HIS* 3.6 17.9 - - + +
318B VAL* 3.8 22.2 - - + -
320B HIS* 4.6 5.2 - - + +
332B LEU* 3.7 23.8 - - + -
334B PHE* 3.6 9.5 - + - -
126E LYS* 4.3 5.7 + - - +
128E MET* 3.7 31.2 - - + -
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Residues in contact with GLY 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B GLN* 2.7 25.6 + - - +
299B GLU* 3.7 1.6 - - - -
301B TYR* 1.3 74.5 - - - +
303B GLU* 1.3 58.8 + - - +
305B TYR* 3.2 2.3 + - - +
306B LYS* 2.8 41.0 + - - +
314B ASP* 4.2 12.1 - - - +
315B HIS* 3.9 9.2 - - - -
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Residues in contact with GLU 303 (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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299B GLU* 2.8 24.8 + - + +
300B GLU* 3.9 5.2 - - - +
302B GLY* 1.3 70.8 - - - +
304B PHE* 1.3 61.0 + - - +
306B LYS* 2.8 34.4 + - - +
307B SER* 2.8 36.4 + - - +
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Residues in contact with PHE 304 (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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208B PHE* 3.9 25.6 - + - -
285B THR* 5.0 5.4 - - + -
286B LYS 4.0 6.7 - - - -
288B ILE* 3.3 28.3 - - + -
289B TRP* 3.8 24.2 - + - -
300B GLU 2.9 17.0 + - - +
301B TYR* 3.6 6.3 - - - +
303B GLU* 1.3 77.4 - - - +
305B TYR* 1.3 51.3 + - - +
307B SER* 3.1 6.6 + - - -
308B LEU* 2.6 57.7 + - + +
332B LEU* 4.0 10.1 - - + -
334B PHE* 3.5 33.7 - + - -
380B VAL* 3.9 15.7 - - + -
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Residues in contact with TYR 305 (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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301B TYR 2.9 18.3 + - - +
302B GLY 3.2 3.6 + - - +
304B PHE* 1.3 80.7 - - - +
306B LYS* 1.3 55.8 + - - +
308B LEU* 3.9 5.4 - - + -
309B THR* 2.7 69.5 + - + +
311B ASP* 4.1 11.9 + - + +
313B GLU 3.3 22.4 - - - -
314B ASP* 3.6 5.1 + - - -
315B HIS* 3.3 40.2 - - + -
334B PHE* 3.5 37.9 - + + -
336B PRO* 3.2 30.6 - - + +
337B ARG 4.6 0.9 + - - -
378B ARG* 4.4 6.6 - - + +
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Residues in contact with LYS 306 (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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302B GLY* 2.8 21.9 + - - +
303B GLU* 2.8 42.9 + - - +
305B TYR* 1.3 76.5 - - - +
307B SER* 1.3 53.7 + - - +
309B THR* 3.9 1.3 - - - -
310B ASN* 2.7 34.5 + - - -
311B ASP 3.1 19.6 + - - +
312B TRP* 3.1 26.9 + - - +
313B GLU 3.8 0.2 - - - +
314B ASP* 3.8 23.8 - - + +
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Residues in contact with SER 307 (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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285B THR* 5.2 18.4 - - - -
303B GLU* 2.8 26.3 + - - +
304B PHE* 3.4 8.2 - - - -
306B LYS* 1.3 74.8 - - - +
308B LEU* 1.3 64.9 + - - +
310B ASN* 3.3 19.0 + - - +
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Residues in contact with LEU 308 (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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208B PHE* 5.6 3.6 - - + -
304B PHE* 2.6 36.8 + - + +
305B TYR* 3.3 5.2 - - - +
307B SER* 1.3 75.7 - - - +
309B THR* 1.3 64.3 + - + +
310B ASN* 4.5 4.7 + - - -
334B PHE* 3.8 20.2 - - + -
352B ASN 5.4 0.2 - - - +
354B LYS* 6.0 6.3 - - + -
378B ARG* 3.3 30.5 + - + +
379B GLY* 3.7 34.3 - - - +
380B VAL* 3.8 25.1 - - + -
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Residues in contact with THR 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B TYR* 2.7 51.7 + - + +
308B LEU* 1.3 81.1 - - + +
310B ASN* 1.3 72.3 + - - +
311B ASP* 3.1 27.4 + - - +
378B ARG* 3.6 45.7 + - + +
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Residues in contact with ASN 310 (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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306B LYS 2.7 18.4 + - - +
307B SER* 3.3 17.6 + - - +
308B LEU 4.5 3.8 + - - -
309B THR* 1.3 81.2 + - - +
311B ASP* 1.3 58.3 + - - +
312B TRP 3.6 2.4 + - - -
176E SER 5.1 4.6 - - - +
177E ASP 5.7 1.8 - - - +
179E VAL* 4.5 10.9 - - - +
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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