Contacts of the helix formed by residues 333 - 342 (chain A) in PDB entry 5FI2
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 VAL 333 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A LYS* 3.8 2.0 - - - -
313A SER* 5.5 8.5 - - - +
318A ASN 6.2 0.4 - - - +
320A LEU 6.1 0.7 - - - +
321A PHE 5.5 0.9 - - - +
329A HIS* 4.3 13.2 - - + +
330A ASN* 3.3 41.5 - - - +
332A MET* 1.3 81.3 - - - +
334A ASN* 1.3 56.6 + - - +
335A ALA* 4.3 7.0 - - + +
336A GLY* 3.0 11.8 + - - +
337A ALA* 2.7 31.5 + - - +
462A CYS 5.7 2.5 - - - +
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Residues in contact with ASN 334 (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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285A SER* 4.3 2.8 + - - -
288A LYS* 3.2 26.7 + - - +
333A VAL* 1.3 73.7 - - - +
335A ALA* 1.3 52.9 + - - +
337A ALA* 3.6 0.7 - - - +
338A ILE* 2.7 42.1 + - - +
386A ARG* 5.1 13.5 - - - +
387A ASN* 3.9 21.6 + - - +
390A ILE* 4.1 13.7 - - + +
413A TYR* 3.4 14.1 + - - +
465A TYR* 5.8 2.8 - - - -
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Residues in contact with ALA 335 (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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321A PHE* 3.9 34.1 - - + +
328A PRO* 3.7 5.3 - - + +
333A VAL* 3.3 5.9 - - + +
334A ASN* 1.3 77.9 - - - +
336A GLY* 1.3 61.0 + - - +
338A ILE* 3.5 0.4 + - - -
339A VAL* 3.2 28.9 + - - +
390A ILE* 3.7 32.9 - - + +
394A LEU* 3.7 6.9 - - + +
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Residues in contact with GLY 336 (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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308A VAL* 4.1 5.0 - - - +
328A PRO* 3.4 17.2 - - - +
330A ASN 3.2 22.7 - - - -
331A PRO* 4.0 7.2 - - - -
333A VAL* 3.0 6.3 + - - +
335A ALA* 1.3 77.1 - - - +
337A ALA* 1.3 58.4 + - - +
339A VAL* 3.3 3.6 + - - +
340A VAL* 2.9 31.7 + - - +
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Residues in contact with ALA 337 (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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288A LYS* 3.6 35.7 - - + -
291A LYS* 3.8 13.7 - - - +
331A PRO 3.5 8.9 + - - +
333A VAL 2.7 19.4 + - - +
334A ASN 3.6 3.4 - - - +
336A GLY* 1.3 72.2 - - - +
338A ILE* 1.3 53.0 + - - +
340A VAL* 3.2 6.0 + - - +
341A THR* 2.7 38.2 + - - -
413A TYR* 3.9 6.7 - - + -
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Residues in contact with ILE 338 (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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334A ASN 2.7 28.6 + - - +
335A ALA 3.8 4.7 - - - +
336A GLY 3.3 0.2 - - - -
337A ALA* 1.3 71.4 - - - +
339A VAL* 1.3 62.2 + - - +
341A THR* 3.5 5.3 - - - -
342A SER* 3.3 15.8 + - - -
387A ASN* 3.8 24.9 - - + +
390A ILE* 3.7 22.0 - - + -
391A GLY* 5.2 1.3 - - - -
394A LEU* 3.9 16.2 - - + -
400A PHE* 4.0 13.6 - - + -
409A ILE* 3.6 13.9 - - + +
410A LEU* 3.9 28.7 - - + -
413A TYR* 3.6 27.6 - - + -
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Residues in contact with VAL 339 (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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307A TYR* 3.5 41.1 - - + +
308A VAL* 4.7 3.8 - - + -
328A PRO* 3.7 15.5 - - + -
335A ALA 3.2 15.3 + - - +
336A GLY 3.7 7.0 - - - +
337A ALA 3.2 0.4 - - - -
338A ILE* 1.3 73.6 - - - +
340A VAL* 1.3 64.8 + - - +
342A SER* 2.7 27.8 + - - +
343A LEU* 3.2 7.2 - - + +
394A LEU* 3.6 22.2 - - + -
399A CYS* 4.2 16.4 - - + +
400A PHE* 4.2 8.7 - - + -
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Residues in contact with VAL 340 (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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288A LYS 5.3 0.2 - - - +
291A LYS* 3.6 32.8 - - + +
292A TYR* 3.7 22.9 - - + +
295A ALA* 4.1 7.9 - - + -
304A VAL* 4.8 4.5 - - + -
308A VAL* 4.1 15.3 - - + -
331A PRO* 3.9 24.0 - - + +
336A GLY 2.9 17.6 + - - +
337A ALA* 3.6 9.2 - - - +
339A VAL* 1.3 74.3 - - - +
341A THR* 1.3 64.8 - - - +
343A LEU* 2.9 24.6 + - - +
344A ILE* 3.5 8.0 + - + +
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Residues in contact with THR 341 (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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291A LYS* 2.8 24.1 + - - -
337A ALA 2.7 24.2 + - - -
338A ILE* 3.5 10.1 - - - -
340A VAL* 1.3 78.3 - - - +
342A SER* 1.3 59.0 + - - +
343A LEU 3.2 1.6 + - - -
344A ILE* 3.6 16.8 + - - +
353A LYS* 5.6 0.3 + - - -
409A ILE* 4.0 12.2 - - + +
412A PHE* 3.6 36.9 - - + -
413A TYR* 3.8 18.1 - - - +
416A LEU* 3.9 13.7 - - + -
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Residues in contact with SER 342 (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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338A ILE 3.3 5.8 + - - -
339A VAL* 2.7 17.4 + - - +
341A THR* 1.3 78.1 - - - +
343A LEU* 1.3 59.4 + - - +
344A ILE 5.0 1.1 - - - -
346A GLN* 3.6 13.9 - - - +
353A LYS* 5.7 1.5 + - - -
400A PHE* 3.3 27.8 - - - -
401A PRO* 3.3 28.3 - - - +
404A THR* 4.4 4.7 + - - +
409A ILE* 3.8 26.1 - - - +
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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