Contacts of the strand formed by residues 296 - 309 (chain A) in PDB entry 1FPQ
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 LEU 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A GLN* 5.8 0.6 + - - -
268A GLY 3.6 3.6 - - - +
269A ASP 3.5 33.9 - - - +
270A ALA* 3.8 4.3 - - - +
271A MSE 3.9 10.3 - - + +
292A CYS 3.0 13.7 + - - +
293A HIS 3.1 6.1 + - - +
294A LYS 3.9 3.1 - - - +
295A ALA* 1.3 80.2 - - - +
297A SER* 1.3 64.0 + - - +
298A PRO* 4.7 0.2 - - - +
300A GLY* 3.9 3.4 - - - -
301A LYS 3.6 30.3 - - - +
302A VAL* 3.9 4.0 - - + -
352A PHE* 3.6 24.5 - - + -
372A LYS* 3.0 49.2 + - + -
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Residues in contact with SER 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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212A THR* 5.7 0.2 - - - +
268A GLY* 3.1 21.6 + - - -
269A ASP* 3.2 24.4 + - - +
295A ALA 3.7 0.4 + - - -
296A LEU* 1.3 74.8 - - - +
298A PRO* 1.3 81.5 - - - +
299A ASN 3.5 2.5 - - - -
300A GLY 3.2 8.2 + - - -
372A LYS* 2.8 19.1 - - - +
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Residues in contact with PRO 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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297A SER* 1.3 90.6 - - - +
299A ASN* 1.3 72.7 + - - +
300A GLY 3.6 1.0 + - - -
372A LYS* 3.7 21.9 - - + +
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Residues in contact with ASN 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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269A ASP* 6.0 0.4 - - - -
297A SER* 3.5 1.7 - - - -
298A PRO* 1.3 87.8 + - - +
300A GLY* 1.3 62.4 + - - +
371A TYR* 5.0 6.6 - - - -
372A LYS* 5.5 0.7 - - - -
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Residues in contact with GLY 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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269A ASP* 3.1 23.1 - - - -
296A LEU* 3.9 14.8 - - - -
297A SER* 3.2 13.0 + - - -
298A PRO 3.4 1.0 + - - -
299A ASN* 1.3 81.0 - - - +
301A LYS* 1.3 63.5 + - - +
371A TYR* 3.8 4.7 - - - +
372A LYS* 3.4 22.7 + - - +
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Residues in contact with LYS 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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204A TYR* 3.3 5.5 + - - -
206A GLY* 2.8 33.8 + - - -
210A ILE* 4.4 10.8 - - - -
269A ASP 3.3 4.1 + - - +
270A ALA* 3.3 8.3 - - + +
271A MSE 3.3 21.1 + - - +
296A LEU* 3.6 10.2 - - - +
300A GLY* 1.3 76.3 - - - +
302A VAL* 1.3 61.5 + - - +
303A ILE* 4.3 13.9 - - + -
369A GLU* 2.9 34.3 + - + +
370A PHE 3.1 13.0 - - - +
371A TYR* 3.7 33.5 + - + +
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Residues in contact with VAL 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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271A MSE 3.6 9.4 - - + -
273A LEU* 4.2 11.4 - - + -
289A LEU* 4.6 4.9 - - + -
292A CYS* 4.1 16.4 - - + -
296A LEU* 3.9 10.8 - - + -
301A LYS* 1.3 74.3 - - - +
303A ILE* 1.3 66.0 + - - +
304A ILE* 3.5 31.2 - - + -
352A PHE* 3.5 29.2 - - + -
368A MSE 3.6 0.5 - - - +
369A GLU* 3.1 7.1 - - - +
370A PHE* 2.6 53.6 + - + -
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Residues in contact with ILE 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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204A TYR* 3.2 26.0 - - + +
207A PHE* 3.8 28.0 - - + -
210A ILE* 4.6 7.2 - - + -
213A LEU* 4.7 6.5 - - + -
270A ALA* 5.1 1.1 - - + -
271A MSE 2.7 18.9 + - - +
272A ILE* 3.2 16.5 - - + +
273A LEU 2.8 27.2 + - - -
301A LYS* 4.3 20.9 - - + +
302A VAL* 1.3 77.1 - - - +
304A ILE* 1.3 64.4 + - - +
305A VAL* 4.4 4.9 - - + -
367A VAL* 3.7 28.0 - - + -
368A MSE 3.3 4.3 - - - +
369A GLU* 4.8 1.8 - - + -
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Residues in contact with ILE 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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273A LEU* 3.6 31.0 - - + +
277A CYS* 4.2 13.0 - - - -
289A LEU* 4.4 5.6 - - + -
302A VAL* 3.5 24.2 - - + -
303A ILE* 1.3 72.7 - - - +
305A VAL* 1.3 63.7 + - - +
306A GLU* 3.8 23.3 + - + -
343A TYR* 4.5 11.7 - - + -
366A GLY 3.5 2.1 - - - +
367A VAL* 3.4 2.8 - - - -
368A MSE 2.7 59.3 + - + +
370A PHE* 3.7 28.9 - - + -
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Residues in contact with VAL 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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200A MSE 3.3 35.7 - - + -
272A ILE* 4.2 19.5 - - + -
273A LEU 3.0 8.9 + - - -
274A LYS* 3.6 25.2 + - + +
275A ALA* 3.2 24.6 + - - +
303A ILE* 4.4 8.1 - - + -
304A ILE* 1.3 73.7 - - - +
306A GLU* 1.3 62.2 + - - +
365A LEU* 4.1 24.7 - - + +
366A GLY 3.4 8.5 - - - +
367A VAL* 4.5 9.9 - - + -
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Residues in contact with GLU 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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273A LEU 5.0 0.7 - - - +
275A ALA* 4.0 5.9 - - - +
276A VAL 3.4 2.9 + - - -
277A CYS* 3.3 11.9 + - + +
278A HIS* 2.9 55.0 + - - +
304A ILE* 3.8 19.6 + - + -
305A VAL* 1.3 80.1 - - - +
307A PHE* 1.3 64.9 + - - +
308A ILE* 3.9 2.9 - - - +
337A GLU* 3.9 6.4 - - - +
343A TYR* 3.3 32.7 + - + +
365A LEU* 3.6 8.7 - - - -
366A GLY* 2.8 30.2 + - - +
368A MSE 4.2 7.2 - - + +
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Residues in contact with PHE 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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29A MSE 4.3 18.8 - - + -
192A VAL* 6.1 0.7 - - + -
196A GLU* 3.3 27.4 - - - -
306A GLU* 1.3 83.7 + - - +
308A ILE* 1.3 63.3 + - - +
309A LEU 3.9 0.3 + - - -
321A LEU* 3.8 15.0 - - + -
322A VAL* 4.1 16.8 - - + +
325A LEU* 3.5 27.6 - - + -
337A GLU* 3.9 21.0 + - - +
338A ARG 3.8 8.8 + - - +
343A TYR* 4.1 3.6 + - - -
364A SER* 3.3 35.2 - - - -
365A LEU* 3.8 22.0 - - + -
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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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306A GLU 3.9 3.6 - - - +
307A PHE* 1.3 76.5 - - - +
309A LEU* 1.3 69.1 + - - +
310A PRO* 3.5 5.7 - - + +
318A GLU* 5.8 1.4 - - - +
322A VAL* 3.6 14.6 - - - +
338A ARG 3.8 1.8 - - - +
339A THR 4.2 1.3 - - - -
340A GLU* 3.6 28.9 - - + +
343A TYR* 5.2 0.2 - - + -
357A VAL* 4.4 13.5 - - + -
360A ARG* 3.7 45.0 + - - +
364A SER* 2.9 14.0 + - - +
366A GLY* 3.7 24.7 - - - +
368A MSE 3.9 29.6 - - + -
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Residues in contact with LEU 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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90A ARG* 3.9 28.9 - - - +
308A ILE* 1.3 76.7 - - - +
310A PRO* 1.3 74.0 - - + +
311A GLU 3.5 0.5 + - - -
322A VAL* 3.6 29.0 - - + +
323A SER* 3.9 24.9 - - - +
326A ASP* 4.5 11.2 - - + +
337A GLU* 3.4 34.1 - - + +
338A ARG* 3.1 19.7 + - - +
339A THR* 3.3 24.4 - - + +
340A GLU 4.0 0.9 + - - -
342A GLN* 5.0 1.8 - - - +
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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