Contacts of the helix formed by residues 343 - 354 (chain A) in PDB entry 3FZF
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 ILE 343 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A PHE* 3.6 36.8 - - + -
271A LYS* 4.8 1.1 - - + -
275A SER* 3.7 3.1 - - - +
302A PHE* 4.1 21.1 - - + -
303A GLU* 5.7 0.7 - - + -
310A PHE* 3.8 31.0 - - + -
340A SER* 3.2 15.6 + - - +
342A ARG* 1.3 75.3 - - - +
344A PRO* 1.3 75.1 - - + +
345A LYS* 4.0 8.7 - - + +
346A ILE* 3.0 20.2 + - + +
347A GLN* 3.2 9.9 + - - +
401A ATP 3.6 24.7 - - + +
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Residues in contact with PRO 344 (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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274A LEU 4.2 3.4 - - - +
275A SER* 3.4 32.5 - - - +
299A ARG* 3.8 34.5 - - - +
303A GLU* 5.1 1.8 - - - +
342A ARG 3.3 7.6 - - - +
343A ILE* 1.3 84.9 - - + +
345A LYS* 1.3 57.4 + - - +
347A GLN* 2.9 18.2 + - + +
348A LYS* 2.9 27.5 + - - +
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Residues in contact with LYS 345 (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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303A GLU* 3.4 43.0 + - + +
307A ALA* 6.1 3.4 - - - +
310A PHE* 3.5 33.9 - - + -
311A ARG* 6.2 0.2 - - - +
343A ILE* 3.2 2.6 - - + -
344A PRO* 1.3 79.1 - - - +
346A ILE* 1.3 61.7 + - - +
348A LYS* 3.3 25.5 + - + +
349A LEU* 3.1 48.6 + - + +
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Residues in contact with ILE 346 (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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198A PHE* 4.0 26.9 - - + -
200A LEU* 3.3 28.3 - - + -
233A PHE* 4.2 6.7 - - + -
310A PHE* 3.9 39.3 - - + -
313A THR* 4.4 7.9 - - + +
336A LEU* 6.1 0.2 - - + -
340A SER 4.4 7.0 - - - +
341A THR* 4.9 9.4 - - - -
343A ILE* 3.0 16.6 + - + +
345A LYS* 1.3 74.0 - - - +
347A GLN* 1.3 66.6 + - + +
349A LEU* 3.4 12.6 + - + +
350A LEU* 3.2 27.8 + - + +
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Residues in contact with GLN 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A LEU* 3.7 15.7 - - + +
341A THR 2.8 30.1 + - - +
342A ARG* 4.0 11.5 + - - +
343A ILE 3.2 7.4 + - - +
344A PRO* 2.9 15.8 + - - +
346A ILE* 1.3 77.4 - - + +
348A LYS* 1.3 56.9 + - - +
350A LEU* 3.4 4.3 + - - +
351A GLN* 2.9 25.7 + - - +
359A LEU* 3.6 17.2 - - + +
361A LYS* 2.9 39.9 - - + +
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Residues in contact with LYS 348 (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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344A PRO 2.9 11.7 + - - +
345A LYS* 3.6 28.5 - - + +
346A ILE 3.2 0.2 - - - -
347A GLN* 1.3 75.8 - - - +
349A LEU* 1.3 63.7 + - - +
351A GLN* 3.5 5.5 + - + +
352A ASP* 3.1 46.7 + - - +
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Residues in contact with LEU 349 (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 ALA 5.9 0.4 - - - +
310A PHE* 3.3 44.2 - - + +
311A ARG* 4.2 28.7 - - - +
313A THR* 3.8 10.3 - - - +
314A LEU* 4.7 17.5 - - + +
345A LYS* 3.1 45.4 + - - +
346A ILE* 3.4 14.3 + - + +
348A LYS* 1.3 76.6 - - - +
350A LEU* 1.3 58.7 + - + +
352A ASP* 3.4 5.8 + - - +
353A PHE* 2.9 32.0 + - - +
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Residues in contact with LEU 350 (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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196A LEU* 6.0 0.2 - - + -
198A PHE* 3.7 41.7 - - + -
313A THR* 5.1 1.3 - - - +
314A LEU* 3.9 24.5 - - + -
317A VAL* 5.0 1.6 - - + -
334A ILE* 4.7 6.3 - - + -
336A LEU* 3.7 28.5 - - + -
346A ILE* 3.2 23.1 + - + +
347A GLN* 3.6 5.6 - - - +
349A LEU* 1.3 79.2 - - + +
351A GLN* 1.3 64.2 + - - +
353A PHE* 4.3 1.8 - - - -
354A PHE* 3.0 43.7 + - + +
359A LEU* 4.2 15.7 - - + +
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Residues in contact with GLN 351 (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 ILE* 6.2 0.2 - - - +
347A GLN 2.9 16.8 + - - +
348A LYS* 3.5 7.4 + - + +
349A LEU 3.3 0.2 - - - -
350A LEU* 1.3 76.3 - - - +
352A ASP* 1.3 62.7 + - - +
354A PHE* 3.0 27.7 + - - +
355A ASN* 3.1 3.5 + - - -
356A GLY* 3.6 11.1 - - - +
357A LYS 3.1 27.1 + - - +
358A GLU* 5.2 0.3 - - - -
359A LEU* 4.0 25.8 + - + +
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Residues in contact with ASP 352 (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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328A LYS* 4.9 1.6 + - - -
348A LYS* 3.1 35.5 + - - +
349A LEU* 3.9 5.3 - - - +
351A GLN* 1.3 81.7 - - - +
353A PHE* 1.3 61.2 + - - +
355A ASN* 3.1 25.8 + - - +
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Residues in contact with PHE 353 (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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311A ARG* 6.0 2.0 - - - -
314A LEU* 3.9 37.7 - - + -
317A VAL* 3.6 22.4 - - + -
318A GLU* 4.2 31.9 - - + -
321A LEU* 4.4 2.2 - - + -
328A LYS* 2.7 63.4 + - + +
349A LEU 2.9 19.4 + - - +
350A LEU* 3.8 4.9 - - - +
352A ASP* 1.3 75.7 - - - +
354A PHE* 1.3 80.7 + + - +
355A ASN 3.5 1.9 + - - -
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Residues in contact with PHE 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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196A LEU* 4.0 20.6 - - + -
317A VAL* 3.8 20.9 - - + -
321A LEU* 4.7 0.7 - - + -
328A LYS* 3.7 39.3 - - + -
331A ILE* 4.1 23.3 - - + -
334A ILE* 3.5 40.4 - - + -
350A LEU* 3.0 31.4 + - + +
351A GLN* 3.0 12.6 + - - +
353A PHE* 1.3 95.2 - + + +
355A ASN* 1.3 68.1 + - - +
356A GLY 2.9 3.5 + - - -
357A LYS* 2.9 17.2 + - + -
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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