Contacts of the helix formed by residues 320 - 336 (chain A) in PDB entry 3ZFW
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 HIS 320 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A LEU* 3.8 44.8 - - + +
317A GLY 3.5 14.5 + - - +
318A LYS 3.7 1.4 - - - -
319A PHE* 1.3 76.2 - - - +
321A PRO* 1.4 72.7 - - + +
322A ASP* 3.1 44.6 + - - +
323A VAL* 2.8 29.1 + - + +
324A ALA 3.3 4.0 + - - -
353A ILE* 3.6 3.9 - - - +
357A ARG* 3.9 19.3 - - - +
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Residues in contact with PRO 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A PHE 4.2 2.0 - - - +
320A HIS* 1.4 99.7 - - + +
322A ASP* 1.4 63.3 + - - +
324A ALA* 3.4 7.3 + - + +
325A LYS* 3.2 19.4 + - - +
353A ILE* 3.7 10.3 - - + -
354A TYR* 4.1 8.3 - - + -
357A ARG* 4.1 23.6 - - + +
358A LEU* 3.9 39.5 - - + -
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Residues in contact with ASP 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ARG* 3.8 24.8 + - - +
316A LEU* 3.8 22.0 - - + +
320A HIS* 2.9 26.2 + - - +
321A PRO* 1.4 75.8 - - - +
323A VAL* 1.3 64.6 + - - +
325A LYS* 3.2 11.8 + - + +
326A GLN 3.2 16.6 + - - -
208X ASP* 6.1 0.7 - - - -
210X SER* 5.4 3.3 + - - -
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Residues in contact with VAL 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LEU* 3.7 19.5 - - + -
312A ARG* 4.0 28.9 - - + +
313A GLU* 3.8 14.6 - - + +
316A LEU* 4.9 1.1 - - + -
317A GLY 3.1 25.1 - - - +
318A LYS 3.7 20.0 - - - +
320A HIS* 2.8 19.1 + - + +
322A ASP* 1.3 73.6 - - - +
324A ALA* 1.4 57.1 + - - +
326A GLN* 3.3 8.7 + - - +
327A LEU* 3.0 35.9 + - + +
353A ILE* 4.2 4.9 - - + -
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Residues in contact with ALA 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A HIS 3.3 1.8 + - - -
321A PRO 3.4 10.1 - - - +
322A ASP 3.3 0.4 - - - -
323A VAL* 1.4 76.5 - - - +
325A LYS* 1.4 58.5 + - - +
327A LEU* 3.4 12.6 + - - +
328A SER* 2.9 32.2 + - - -
350A ALA* 3.8 16.5 - - - +
353A ILE* 3.8 19.6 - - + +
354A TYR* 3.5 26.9 - - + -
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Residues in contact with LYS 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ASN* 4.1 2.7 - - - +
312A ARG* 5.1 2.2 - - - +
321A PRO 3.2 12.2 + - - +
322A ASP* 3.2 12.9 + - + +
324A ALA* 1.4 73.1 - - - +
326A GLN* 1.4 71.8 + - - +
328A SER* 3.5 6.6 + - - -
329A ASN* 3.2 42.6 + - - +
354A TYR* 3.4 13.6 + - - +
206X GLU* 3.4 40.4 + - + +
207X TRP 3.5 18.0 + - - -
208X ASP* 3.4 33.9 + - - +
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Residues in contact with GLN 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ASN* 2.8 25.5 + - - +
305A CYS* 3.2 45.7 + - - -
308A ALA* 3.8 9.2 - - - +
309A LEU* 3.8 24.9 - - + +
312A ARG* 3.1 45.4 + - - +
322A ASP 3.2 8.2 + - - +
323A VAL 3.3 8.5 + - - +
325A LYS* 1.4 79.6 - - - +
327A LEU* 1.4 50.1 + - - +
329A ASN* 3.0 7.2 + - - +
330A LEU* 2.8 35.8 + - + +
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Residues in contact with LEU 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LEU* 3.8 21.5 - - + -
323A VAL* 3.0 23.5 + - + +
324A ALA* 3.6 7.0 - - - +
326A GLN* 1.4 74.6 - - - +
328A SER* 1.3 50.6 + - - +
330A LEU* 3.2 7.2 + - + +
331A ALA* 2.8 34.3 + - - +
346A TYR* 3.5 42.3 - - + +
349A ARG* 3.8 59.7 - - + +
350A ALA* 3.9 2.9 - - + +
353A ILE* 4.1 14.1 - - + -
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Residues in contact with SER 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ALA 2.9 15.5 + - - -
325A LYS* 3.5 12.1 - - - -
326A GLN 3.3 0.2 - - - -
327A LEU* 1.3 73.4 - - - +
329A ASN* 1.4 58.8 + - - +
331A ALA* 3.4 4.0 - - - +
332A LEU* 3.2 31.1 + - - +
347A TYR* 3.9 21.4 + - - -
350A ALA* 3.8 11.5 - - - +
354A TYR* 3.8 13.3 + - - -
368A THR* 4.3 4.7 + - - -
371A ASN* 5.8 1.6 - - - -
206X GLU* 6.1 0.9 - - - -
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Residues in contact with ASN 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ASN* 2.8 29.3 + - - +
305A CYS* 4.2 4.3 - - - -
325A LYS* 3.2 21.2 + - - +
326A GLN* 3.0 10.6 + - - +
328A SER* 1.4 76.7 - - - +
330A LEU* 1.3 65.0 + - - +
332A LEU* 3.4 10.6 + - - +
333A LEU* 3.3 17.7 + - - +
205X LEU* 3.5 29.6 - - + +
206X GLU* 2.8 47.3 + - - +
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Residues in contact with LEU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A GLU* 4.3 16.2 - - + -
305A CYS* 3.6 30.5 - - + +
306A LYS* 4.0 28.5 - - + +
309A LEU* 4.0 22.4 - - + -
326A GLN 2.8 13.2 + - - +
327A LEU* 3.4 11.4 - - + +
329A ASN* 1.3 72.8 - - - +
331A ALA* 1.4 63.5 + - - +
333A LEU* 3.4 9.0 + - + +
334A CYS* 3.3 25.3 + - - -
346A TYR* 3.7 38.8 - - + +
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Residues in contact with ALA 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LEU 2.8 13.5 + - - +
328A SER 3.4 10.3 - - - +
330A LEU* 1.4 76.2 - - - +
332A LEU* 1.4 56.1 + - - +
334A CYS* 3.2 5.4 + - - +
335A GLN* 3.0 27.9 + - - +
343A VAL* 3.7 11.8 - - - +
346A TYR* 3.7 23.1 - - + -
347A TYR* 3.6 33.0 - - + -
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Residues in contact with LEU 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A SER 3.2 14.4 + - - +
329A ASN* 3.5 16.2 - - - +
330A LEU 3.3 0.4 - - - -
331A ALA* 1.4 78.5 - - - +
333A LEU* 1.4 55.4 + - - +
335A GLN* 3.4 13.2 + - - +
336A ASN* 3.1 38.6 + - - +
347A TYR* 3.8 14.8 + - - +
203X THR* 3.5 34.5 - - + +
204X ASN 3.9 22.9 - - - +
205X LEU* 3.9 21.5 - - + -
206X GLU* 4.9 0.7 - - + +
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Residues in contact with LEU 333 (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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289A ALA* 4.7 0.7 - - + +
293A GLY* 4.6 4.3 - - - -
298A TYR* 3.9 26.2 - - + +
301A ALA* 3.7 47.8 - - + +
302A GLU* 3.9 9.0 - - + +
305A CYS* 3.8 26.5 - - + -
329A ASN 3.3 9.9 + - - +
330A LEU* 3.6 12.6 - - + +
331A ALA 3.4 0.2 - - - -
332A LEU* 1.4 78.1 - - - +
334A CYS* 1.4 61.2 + - - +
336A ASN* 3.5 10.4 + - - +
337A GLN* 3.2 30.6 + - - +
205X LEU* 3.8 23.1 - - + -
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Residues in contact with CYS 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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302A GLU* 3.9 15.0 - - - -
330A LEU 3.3 13.2 + - - -
331A ALA 3.2 9.0 + - - +
333A LEU* 1.4 76.1 - - - +
335A GLN* 1.3 52.7 + - - +
336A ASN 3.2 0.2 - - - -
337A GLN* 2.9 10.2 + - - +
338A GLY 2.8 29.1 + - - -
339A LYS* 2.9 20.5 + - + -
342A GLU* 3.7 24.7 - - + -
343A VAL* 3.8 15.0 - - + +
346A TYR* 3.6 24.5 - - - -
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Residues in contact with GLN 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ALA 3.0 11.7 + - - +
332A LEU* 3.4 17.1 - - - +
334A CYS* 1.3 75.3 - - - +
336A ASN* 1.3 59.8 + - - +
338A GLY* 3.1 18.7 + - - +
343A VAL* 3.4 19.7 - - + +
347A TYR* 3.9 30.7 + - - -
371A ASN* 4.9 7.3 + - - +
374A SER* 6.1 1.2 - - - -
375A CYS* 5.5 2.6 - - - +
378A LYS* 5.3 19.7 + - - +
203X THR* 3.3 26.9 - - - +
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Residues in contact with ASN 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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298A TYR* 3.2 55.8 + - + -
332A LEU* 3.1 19.0 + - - +
333A LEU* 3.9 4.0 - - - +
334A CYS 3.2 0.6 - - - -
335A GLN* 1.3 77.7 - - - +
337A GLN* 1.3 58.7 + - - +
203X THR* 3.1 55.7 + - - +
205X LEU* 5.3 3.4 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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