Contacts of the strand formed by residues 353 - 366 (chain A) in PDB entry 2FO1
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 MET 353 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A VAL* 3.9 13.5 - - + -
259A LEU* 3.7 31.4 - - + -
260A TYR* 6.1 2.2 - - - +
263A LEU* 5.9 2.7 - - + -
348A PHE* 3.0 5.4 - - - +
349A TYR* 2.5 44.7 + - + +
351A CYS* 2.7 30.4 + - - +
352A GLY* 1.3 75.7 - - - +
354A GLU* 1.3 63.7 + - - +
554A GLN* 3.2 28.0 - - - +
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Residues in contact with GLU 354 (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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348A PHE* 3.9 7.9 - - + -
349A TYR* 4.5 0.2 - - - -
352A GLY 4.6 7.0 - - - +
353A MET* 1.3 79.9 - - - +
355A ILE* 1.3 66.2 + - - +
554A GLN* 3.1 24.3 + - - -
556A ALA 3.3 23.0 - - - +
557A ASN 4.1 6.1 - - - +
558A PRO* 4.1 21.6 - - + +
93D ARG* 3.2 39.6 + - - +
96D THR* 3.2 35.3 - - + +
97D ALA* 6.4 0.4 - - + -
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Residues in contact with ILE 355 (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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249A TRP* 4.6 15.9 - - + -
252A LYS* 4.3 6.3 - - - -
286A LEU* 5.3 4.0 - - + -
347A PHE* 3.0 34.0 + - + +
348A PHE* 3.6 13.9 - - - +
349A TYR* 3.1 37.0 - - + +
354A GLU* 1.3 81.7 - - - +
356A GLY* 1.3 59.4 + - - +
358A PHE* 4.9 5.8 - - + -
548A PHE* 4.3 23.3 - - + -
554A GLN* 4.2 9.0 - - - +
558A PRO* 3.7 4.8 - - - +
559A ILE* 2.7 39.7 + - - +
96D THR* 5.5 0.2 + - - -
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Residues in contact with GLY 356 (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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346A GLN* 3.6 6.8 - - - +
347A PHE 3.1 26.1 + - - +
355A ILE* 1.3 86.7 - - - +
357A GLY* 1.3 57.1 + - - -
358A PHE* 4.2 13.5 - - - -
558A PRO* 4.3 5.6 - - - +
559A ILE* 4.2 1.6 - - - -
560A SER* 3.7 15.3 - - - -
92D GLN* 5.0 4.5 - - - -
96D THR* 5.0 3.4 + - - -
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Residues in contact with GLY 357 (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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345A ALA 3.3 3.4 - - - -
346A GLN* 3.0 24.7 - - - -
356A GLY* 1.3 74.1 - - - -
358A PHE* 1.3 64.7 + - - -
359A VAL* 5.3 1.5 - - - +
560A SER* 3.3 38.6 + - - +
92D GLN* 4.9 2.2 - - - +
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Residues in contact with PHE 358 (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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217A ILE* 4.7 17.0 - - + -
219A ILE* 4.4 17.9 - - + -
344A ASN* 3.4 5.2 - - - +
345A ALA* 2.8 39.7 + - + +
347A PHE* 3.4 35.7 - + + -
355A ILE* 4.9 8.5 - - + -
356A GLY* 4.2 14.4 - - - -
357A GLY* 1.3 84.0 - - - -
359A VAL* 1.3 71.4 + - - +
546A TYR* 4.1 44.9 - + + -
548A PHE* 5.1 11.7 - + - -
559A ILE* 5.6 0.9 - - + -
560A SER* 4.5 9.6 - - - -
562A CYS* 4.5 9.9 - - + -
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Residues in contact with VAL 359 (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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219A ILE* 5.9 3.4 - - - -
342A ASP* 3.9 16.4 - - - +
343A LEU 3.0 15.3 - - - +
344A ASN* 4.6 13.9 - - - +
357A GLY 5.3 2.0 - - - +
358A PHE* 1.3 84.6 - - - +
360A SER* 1.3 67.1 + - - +
362A ARG* 5.9 2.5 - - - +
546A TYR* 3.5 18.3 + - - -
584A ARG* 5.3 4.7 + - - +
585A ASP* 5.4 7.6 - - - +
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Residues in contact with SER 360 (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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219A ILE* 5.2 10.5 - - - +
221A HIS* 3.5 27.5 + - - -
342A ASP* 3.3 14.4 - - - +
343A LEU* 3.2 40.5 + - - +
359A VAL* 1.3 79.7 - - - +
361A GLN* 1.3 76.9 + - - +
362A ARG* 4.7 4.3 + - - -
363A ILE* 4.5 0.3 - - - +
544A ALA* 5.5 8.3 - - - -
546A TYR* 5.3 0.9 - - - -
584A ARG* 5.2 3.9 + - - -
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Residues in contact with GLN 361 (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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221A HIS* 3.8 8.2 + - - +
223A LYS* 4.0 16.3 - - - +
342A ASP* 3.7 4.6 - - - +
360A SER* 1.3 92.3 + - - +
362A ARG* 1.3 90.7 + - - +
363A ILE* 3.7 1.9 + - - +
542A ASP* 3.2 26.9 - - - +
543A LYS 5.4 1.3 - - - +
584A ARG* 2.8 37.8 + - - +
1240E ASP* 5.2 2.0 + - - -
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Residues in contact with ARG 362 (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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221A HIS* 4.6 0.5 + - - -
223A LYS* 3.6 14.0 - - - +
340A TYR* 4.5 17.3 - - + -
341A PHE 4.0 3.8 - - - -
342A ASP* 4.3 19.1 + - - -
359A VAL* 5.9 2.6 - - - +
360A SER 4.7 5.5 + - - -
361A GLN* 1.3 95.7 - - - +
363A ILE* 1.3 62.5 + - - +
383A TYR* 3.1 27.5 + - + +
1239E GLU* 5.4 4.3 - - - +
1240E ASP* 3.4 29.6 + - - +
1242E LYS* 5.6 6.2 - - - +
1271E ASP* 4.6 5.7 + - - -
1272E ALA* 4.6 9.8 - - + +
1273E THR* 3.3 38.8 + - + +
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Residues in contact with ILE 363 (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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221A HIS* 3.4 18.6 - - + -
222A ALA* 3.3 24.5 - - + +
223A LYS 3.9 3.8 - - - -
224A VAL* 3.8 9.4 - - - +
225A ALA* 3.8 15.0 - - + +
236A PHE* 5.5 3.8 - - + -
240A PRO* 5.9 1.6 - - + -
340A TYR* 3.3 8.1 - - - -
341A PHE* 2.9 68.3 + - + +
343A LEU* 4.2 16.6 - - + -
360A SER* 4.5 0.7 - - - +
361A GLN 3.9 2.9 - - - +
362A ARG* 1.3 80.2 - - - +
364A LYS* 1.3 73.4 + - - +
383A TYR* 4.4 0.2 - - - -
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Residues in contact with LYS 364 (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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223A LYS 3.2 14.8 + - - +
224A VAL* 3.4 7.4 - - + -
225A ALA* 2.8 25.8 + - - +
339A LYS* 4.1 10.8 + - - +
340A TYR* 3.3 38.2 + - + +
363A ILE* 1.3 79.4 - - - +
365A VAL* 1.3 78.2 + - - +
366A ILE* 4.6 6.1 - - + +
380A ASP* 5.3 4.5 - - - -
383A TYR* 3.7 28.4 - - + +
384A LEU* 4.0 27.8 - - + -
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Residues in contact with VAL 365 (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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225A ALA 3.5 4.3 - - - +
227A LYS* 3.9 39.5 - - + +
332A ILE* 3.9 17.3 - - + -
336A ASP 5.9 1.8 - - - +
338A ARG 4.0 15.0 - - - +
339A LYS* 3.2 17.5 + - - +
340A TYR 5.0 0.2 - - - -
341A PHE* 3.6 34.5 - - + -
364A LYS* 1.3 91.7 + - - +
366A ILE* 1.3 67.6 + - - +
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Residues in contact with ILE 366 (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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224A VAL* 3.3 33.2 - - + -
225A ALA 2.9 17.9 + - - +
226A GLN* 3.4 5.5 - - + -
227A LYS* 3.0 25.7 + - - -
364A LYS* 4.6 12.6 - - + +
365A VAL* 1.3 78.3 - - - +
367A SER* 1.3 62.3 + - - +
368A LYS 4.4 9.2 - - - +
369A PRO* 4.6 15.3 - - + -
384A LEU* 4.8 11.4 - - + -
492A GLN* 5.5 4.9 - - + -
493A LEU* 4.1 25.6 - - + -
6C T 5.2 3.1 - - - +
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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