Contacts of the helix formed by residues 344 - 358 (chain F) in PDB entry 3CB4
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 GLY 344 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83F ASP* 3.1 17.6 + - - -
294F GLN* 4.1 11.4 - - - -
295F VAL* 4.1 15.8 - - - +
342F PHE* 3.3 5.0 - - - +
343F LEU* 1.3 80.2 - - - +
345F LEU* 1.3 65.0 + - - +
347F HIS* 3.7 0.9 - - - +
348F MET* 3.2 21.7 + - - +
470F TYR* 4.3 0.4 - - - -
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Residues in contact with LEU 345 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F ASP* 3.3 1.6 + - - -
295F VAL* 4.9 1.7 - - + +
344F GLY* 1.3 70.9 - - - -
346F LEU* 1.3 61.7 + - + +
348F MET* 3.1 35.1 + - + +
349F GLU* 2.8 47.5 + - - +
368F PRO* 4.9 0.2 - - + -
450F VAL 3.8 14.8 - - - +
451F VAL* 3.6 42.6 - - + +
453F ASP* 4.9 8.5 - - - +
455F PHE* 4.6 21.5 - - + -
470F TYR* 3.4 23.5 + - + +
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Residues in contact with LEU 346 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F HIS* 3.2 45.3 - - + +
83F ASP* 3.4 29.6 - - + +
84F PHE* 3.8 23.6 - - + -
345F LEU* 1.3 76.6 - - + +
347F HIS* 1.3 61.0 + - - +
349F GLU* 3.6 15.5 - - + +
350F ILE* 2.8 40.4 + - + +
470F TYR* 5.1 3.8 - - + +
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Residues in contact with HIS 347 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F ASP* 2.8 19.9 + - + +
84F PHE* 4.0 15.4 - + + -
321F ASP* 3.1 37.7 + - - -
323F SER 4.4 0.2 - - - -
324F LEU* 4.2 12.3 + - - -
342F PHE* 3.5 17.9 - + + -
343F LEU* 3.0 44.4 - - + +
344F GLY 3.7 10.1 - - - +
346F LEU* 1.3 79.4 - - - +
348F MET* 1.3 61.1 + - - +
350F ILE* 3.7 10.1 - - - +
351F ILE* 3.2 42.1 + - + +
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Residues in contact with MET 348 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295F VAL* 5.0 3.8 - - + -
297F ALA* 4.3 18.2 - - - -
299F LEU* 6.1 0.9 - - + -
342F PHE* 3.6 42.8 - - + -
344F GLY 3.2 9.6 + - - +
345F LEU* 3.1 38.5 + - + +
347F HIS* 1.3 80.2 - - - +
349F GLU* 1.3 62.6 + - + +
351F ILE* 3.5 2.8 + - - +
352F GLN* 2.9 54.1 + - + +
365F THR* 5.2 1.8 - - - +
366F THR 5.7 0.2 - - - +
368F PRO* 4.4 22.9 - - + -
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Residues in contact with GLU 349 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345F LEU* 2.8 43.9 + - - +
346F LEU* 4.0 12.3 - - + +
347F HIS 3.3 0.4 - - - -
348F MET* 1.3 79.8 - - + +
350F ILE* 1.3 60.3 + - - +
352F GLN* 3.9 16.2 - - - +
353F GLU* 3.0 30.5 + - - +
453F ASP* 4.9 9.0 - - - +
455F PHE* 5.5 9.6 - - - -
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Residues in contact with ILE 350 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F PHE* 3.8 29.4 - - + -
346F LEU* 2.8 37.1 + - + +
347F HIS* 3.7 8.5 - - - +
349F GLU* 1.3 69.9 - - - +
351F ILE* 1.3 67.0 + - + +
353F GLU* 3.3 6.3 + - - +
354F ARG* 2.9 43.8 + - - +
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Residues in contact with ILE 351 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299F LEU* 5.5 1.1 - - + -
314F LEU* 5.3 4.5 - - + -
317F LEU* 4.1 18.8 - - + -
321F ASP* 4.1 4.9 - - - +
324F LEU* 4.0 22.2 - - + -
342F PHE* 3.6 31.4 - - + -
347F HIS* 3.2 47.1 + - + +
348F MET 3.8 2.5 - - - +
350F ILE* 1.3 84.6 - - + +
352F GLN* 1.3 52.1 + - + +
354F ARG* 3.1 9.6 + - - +
355F LEU* 2.7 54.4 + - + +
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Residues in contact with GLN 352 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299F LEU* 4.0 18.7 - - + +
342F PHE* 5.9 0.4 - - + -
348F MET* 2.9 46.7 + - + +
349F GLU* 3.9 14.5 - - - +
351F ILE* 1.3 75.9 - - + +
353F GLU* 1.3 55.7 + - - +
355F LEU* 3.3 9.2 + - + +
356F GLU* 2.9 33.0 + - - +
363F LEU* 6.2 0.9 - - + -
365F THR* 3.2 42.4 + - - +
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Residues in contact with GLU 353 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349F GLU 3.0 20.2 + - - +
350F ILE* 3.6 5.9 - - - +
352F GLN* 1.3 76.7 - - - +
354F ARG* 1.3 61.9 + - - +
356F GLU* 3.6 14.9 + - - +
357F ARG* 2.8 71.2 + - + +
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Residues in contact with ARG 354 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317F LEU* 3.0 43.6 + - + +
320F ASN* 6.2 2.4 - - - +
350F ILE* 2.9 29.9 + - - +
351F ILE* 3.4 9.4 - - - +
353F GLU* 1.3 80.3 + - - +
355F LEU* 1.3 60.9 + - - +
357F ARG* 5.3 0.4 - - - -
358F GLU* 3.1 75.4 + - + +
359F TYR* 3.5 7.3 + - + -
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Residues in contact with LEU 355 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299F LEU* 4.5 10.8 - - + -
310F PHE* 3.9 19.1 - - + -
313F ALA* 4.3 14.4 - - + -
314F LEU* 5.0 4.0 - - + -
317F LEU* 3.6 29.2 - - + -
351F ILE* 2.7 35.7 + - + +
352F GLN* 3.5 9.4 - - - +
354F ARG* 1.3 73.0 - - - +
356F GLU* 1.3 59.4 + - - +
359F TYR* 3.6 16.8 - - + +
360F ASP 3.3 7.8 + - - -
361F LEU* 3.1 28.4 + - + +
363F LEU* 3.9 30.3 - - + -
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Residues in contact with GLU 356 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554C TYR* 3.6 25.7 + - - +
352F GLN 2.9 17.8 + - - +
353F GLU* 3.7 14.0 - - - +
355F LEU* 1.3 78.1 - - - +
357F ARG* 1.3 68.6 + - + +
360F ASP* 3.2 22.0 - - - +
361F LEU 3.6 15.5 + - - +
362F ASP* 5.7 1.8 - - - +
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Residues in contact with ARG 357 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353F GLU* 2.8 52.6 + - - +
354F ARG* 5.3 0.4 - - - -
356F GLU* 1.3 91.5 - - + +
358F GLU* 1.3 70.3 + - + +
359F TYR 3.4 0.6 + - - -
360F ASP* 3.5 11.4 + - - +
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Residues in contact with GLU 358 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354F ARG* 3.1 58.6 + - + +
357F ARG* 1.3 83.9 - - + +
359F TYR* 1.3 80.5 + - + +
360F ASP* 3.8 1.6 + - - +
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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