Contacts of the helix formed by residues 345 - 359 (chain B) in PDB entry 5FS9
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 PRO 345 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344B LEU* 1.4 86.8 - - + +
346B GLU* 1.3 67.2 + - - +
347B TYR* 3.4 2.9 - - + +
348B LEU* 3.1 8.2 + - + +
349B SER 3.0 19.4 + - - -
500B SER* 4.6 5.8 - - - -
504B THR* 4.1 17.5 - - + +
506B GLY* 5.7 2.7 - - - -
508B PHE* 5.1 6.5 - - + -
565B ILE* 3.6 43.5 - - + -
567B TYR* 3.7 11.4 - - + +
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Residues in contact with GLU 346 (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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337B LYS* 5.0 10.3 + - - -
338B GLU* 4.0 20.3 - - - +
345B PRO* 1.3 73.7 - - - +
347B TYR* 1.3 65.5 + - - +
349B SER* 3.5 7.9 - - - -
350B ASN* 3.0 26.5 + - + +
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Residues in contact with TYR 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B PRO* 3.3 3.7 + - + +
346B GLU* 1.3 79.3 - - - +
348B LEU* 1.3 62.2 + - - +
350B ASN* 4.0 3.5 - - - +
351B TRP* 3.1 36.8 + + + +
508B PHE* 4.1 30.3 - + + -
558B GLU* 3.0 31.7 + - + -
559B ASP 4.6 0.5 + - - -
560B TYR* 3.6 30.8 + + - +
579B TRP* 4.4 22.0 - + - -
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Residues in contact with LEU 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LEU* 3.9 21.1 - - + -
345B PRO* 3.1 7.7 + - + +
347B TYR* 1.3 78.2 - - - +
349B SER* 1.3 57.5 + - - +
350B ASN 3.2 1.3 - - - -
351B TRP* 4.2 4.5 - - + -
352B THR* 2.7 44.1 + - - +
492B TYR* 4.1 10.5 - - + -
508B PHE* 4.6 8.7 - - + -
565B ILE* 3.7 30.5 - - + -
577B VAL* 4.8 1.3 - - + -
579B TRP* 3.4 67.3 - - + +
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Residues in contact with SER 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B GLU* 2.7 38.9 + - - +
339B ASN 3.2 24.7 - - - +
341B GLY* 4.1 7.7 - - - -
344B LEU* 4.0 18.1 + - - +
345B PRO 3.0 10.4 + - - -
346B GLU* 3.3 13.0 + - - -
348B LEU* 1.3 76.1 - - - +
350B ASN* 1.3 64.6 + - - +
352B THR* 3.4 4.5 + - - -
353B MET* 3.1 18.4 + - - +
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Residues in contact with ASN 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B GLU* 3.8 16.7 + - + +
346B GLU* 3.0 18.6 + - + +
347B TYR* 4.0 3.9 - - - +
349B SER* 1.3 81.1 + - - +
351B TRP* 1.3 66.4 + - - +
353B MET* 3.3 22.4 + - - +
354B GLU* 3.2 33.6 + - - +
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Residues in contact with TRP 351 (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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347B TYR* 3.1 37.3 + + + +
348B LEU* 3.3 8.9 + - + +
350B ASN* 1.3 77.4 + - - +
352B THR* 1.3 68.0 + - - +
354B GLU* 3.4 8.0 + - + +
355B LYS* 3.0 39.7 + - + +
358B ARG* 4.2 19.7 + - - +
490B VAL* 3.7 30.7 - - + -
492B TYR* 3.8 11.7 - - - -
560B TYR 4.3 7.4 + - - -
561B GLY* 5.7 2.0 - - - -
579B TRP* 3.5 47.5 - + - -
580B ASN* 5.1 2.0 - - - -
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Residues in contact with THR 352 (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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339B ASN* 3.9 12.3 - - + -
340B MET* 3.4 29.4 - - + -
344B LEU* 4.1 2.6 - - - +
348B LEU* 2.7 24.1 + - - +
349B SER* 3.6 8.3 - - - -
350B ASN 3.1 0.2 - - - -
351B TRP* 1.3 83.0 - - - +
353B MET* 1.3 59.6 + - - +
355B LYS* 3.2 4.2 + - - +
356B VAL* 2.9 31.8 + - + +
486B LEU* 3.9 12.6 - - + -
492B TYR* 2.6 28.2 + - - +
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Residues in contact with MET 353 (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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334B PHE* 4.4 0.2 - - - -
337B LYS 3.8 23.8 - - - +
338B GLU* 4.0 9.9 - - + -
339B ASN* 3.2 28.8 + - - +
349B SER 3.1 12.9 + - - +
350B ASN* 3.3 28.2 + - - +
352B THR* 1.3 77.8 - - - +
354B GLU* 1.3 58.0 + - - +
356B VAL* 3.4 3.9 + - - +
357B ARG* 3.0 60.6 + - - +
363B VAL* 3.9 19.7 - - + +
365B PRO* 4.2 9.2 - - + -
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Residues in contact with GLU 354 (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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350B ASN* 3.2 23.3 + - - +
351B TRP* 3.4 9.4 + - + +
353B MET* 1.3 79.2 - - - +
355B LYS* 1.3 59.5 + - - +
357B ARG* 2.8 43.5 + - - +
358B ARG* 2.9 48.3 + - - +
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Residues in contact with LYS 355 (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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317B CYS* 4.6 0.9 - - - -
351B TRP* 3.0 36.0 + - + +
352B THR* 3.2 8.7 + - - +
354B GLU* 1.3 72.8 - - - +
356B VAL* 1.3 67.2 + - - +
358B ARG* 3.2 35.2 + - + +
359B GLU* 2.8 46.5 + - + +
486B LEU* 3.4 42.3 + - + -
489B ASP* 3.2 23.8 + - - -
490B VAL* 3.6 14.4 - - + -
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Residues in contact with VAL 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B SER* 4.5 6.7 - - - -
316B ALA* 4.0 7.2 - - + -
317B CYS* 3.9 23.8 - - - -
332B GLN* 3.6 19.7 - - - +
339B ASN* 3.9 18.4 - - - +
352B THR* 2.9 24.7 + - + +
353B MET 3.4 4.9 + - - +
355B LYS* 1.3 70.7 - - - +
357B ARG* 1.3 63.6 + - - +
359B GLU* 2.9 18.7 + - - +
361B VAL* 3.6 29.5 - - + +
363B VAL* 3.8 5.8 - - + -
486B LEU* 4.3 13.7 - - + -
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Residues in contact with ARG 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B MET* 3.0 39.2 + - - +
354B GLU* 2.8 48.7 + - - +
355B LYS 3.3 0.2 - - - -
356B VAL* 1.3 75.4 - - - +
358B ARG* 1.3 58.6 + - + +
360B GLY* 2.9 22.0 + - - -
361B VAL 3.4 16.2 + - - +
363B VAL* 3.1 44.5 + - + +
365B PRO* 3.8 17.0 - - - +
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Residues in contact with ARG 358 (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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324B ARG* 2.8 19.9 + - - -
351B TRP* 4.2 21.4 + - - +
354B GLU* 2.9 39.0 + - - +
355B LYS* 3.2 36.1 + - + +
357B ARG* 1.3 71.4 - - + +
359B GLU* 1.3 61.6 + - - +
360B GLY 3.1 5.4 - - - -
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Residues in contact with GLU 359 (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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181B PHE* 6.0 2.9 - - - -
317B CYS* 3.9 44.0 - - + +
320B GLY* 3.7 16.7 - - - +
321B ARG* 5.1 7.8 + - - +
324B ARG* 3.4 19.0 + - - +
355B LYS* 2.8 37.2 + - - +
356B VAL 2.9 11.5 + - - +
358B ARG* 1.3 79.3 - - - +
360B GLY* 1.3 62.4 + - - +
361B VAL* 4.5 2.9 - - + -
486B LEU 5.9 0.4 - - - -
489B ASP* 4.5 2.8 - - - +
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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