Contacts of the helix formed by residues 327 - 343 (chain F) in PDB entry 1ZMC
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 LEU 327 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188F VAL* 6.2 4.0 - - + -
320F ASP* 3.8 1.6 + - - +
325F PRO* 3.0 28.5 + - + -
326F MET* 1.3 83.0 - - - +
328F ALA* 1.3 64.3 + - - +
329F HIS* 3.7 13.0 - - + +
330F LYS* 3.6 9.2 - - + +
331F ALA* 3.3 21.1 + - - +
354F VAL* 4.0 7.4 - - + -
355F PRO 3.5 24.7 - - - +
356F SER* 4.0 17.5 - - - +
357F VAL 6.1 1.1 - - - +
480F FAD 3.2 32.9 + - + +
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Residues in contact with ALA 328 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452E HIS* 3.6 29.6 - - + -
16F PRO* 3.7 16.6 - - + +
45F CYS* 3.7 17.0 - - - -
50F CYS* 3.9 3.4 - - - -
327F LEU* 1.3 68.5 - - - +
329F HIS* 1.3 64.0 + - - +
330F LYS 3.1 2.1 + - - -
331F ALA* 3.3 3.3 + - - +
332F GLU* 3.0 29.7 + - - +
480F FAD 2.9 25.9 + - - +
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Residues in contact with HIS 329 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449E CYS* 3.7 19.9 - - - -
450E HIS 2.9 30.1 - - - +
451E ALA* 3.7 10.0 - - + -
452E HIS* 3.0 30.4 + - + +
457E GLU* 5.2 1.3 - - - +
460E ARG* 5.2 2.9 - - - +
327F LEU* 3.7 14.8 - - + +
328F ALA* 1.3 76.7 - - - +
330F LYS* 1.3 62.5 + - - +
332F GLU* 3.8 7.6 - - - +
333F ASP* 3.2 29.0 + - - +
354F VAL* 4.1 5.4 - - + -
355F PRO* 2.6 34.2 + - + -
356F SER* 5.3 2.0 - - - -
357F VAL* 5.6 2.2 - - + -
480F FAD 3.3 22.1 + + - -
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Residues in contact with LYS 330 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449E CYS* 4.9 2.0 - - - -
319F GLY 3.3 19.8 + - - +
320F ASP* 5.8 0.2 - - - +
322F VAL* 3.3 5.5 + - - +
323F ALA 2.7 28.3 + - - -
324F GLY* 3.7 10.9 + - - -
325F PRO* 3.3 34.7 + - + +
326F MET* 6.0 0.2 - - - +
327F LEU* 3.4 14.9 + - + +
328F ALA 3.1 0.4 - - - -
329F HIS* 1.3 80.8 - - - +
331F ALA* 1.3 64.9 + - - +
333F ASP* 3.4 5.1 + - - +
334F GLU* 2.8 62.3 + - + +
349F ILE* 5.5 2.1 - - + +
351F TYR* 3.8 17.0 - - + -
354F VAL* 4.4 14.8 - - + -
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Residues in contact with ALA 331 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F PRO* 4.4 0.4 - - + -
17F GLY* 3.4 27.6 - - - +
318F ILE* 3.7 3.3 - - - +
319F GLY* 3.7 30.3 - - - -
327F LEU 3.3 7.9 + - - +
328F ALA 3.3 7.4 + - - +
330F LYS* 1.3 75.8 - - - +
332F GLU* 1.3 67.2 + - - +
334F GLU* 3.5 3.0 + - - +
335F GLY 3.0 18.0 + - - -
480F FAD 3.7 17.0 - - - +
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Residues in contact with GLU 332 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452E HIS* 3.9 25.3 + - - -
457E GLU* 4.3 9.9 - - - +
460E ARG* 5.4 5.1 + - - +
473E ASN* 5.4 5.5 + - - -
16F PRO* 3.4 34.4 - - + +
17F GLY* 4.3 0.7 - - - -
19F TYR* 4.6 7.4 + - - -
20F VAL* 3.8 26.0 - - + +
328F ALA 3.0 18.4 + - - +
329F HIS* 3.8 8.9 - - - +
330F LYS 3.3 0.2 - - - -
331F ALA* 1.3 77.4 - - - +
333F ASP* 1.3 67.4 + - - +
335F GLY* 3.0 3.3 + - - -
336F ILE* 2.9 29.5 + - + +
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Residues in contact with ASP 333 (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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447E ARG 4.4 3.8 - - - +
449E CYS* 3.2 26.8 + - - +
460E ARG* 2.9 41.6 + - - -
329F HIS 3.2 19.3 + - - +
330F LYS* 3.8 3.4 - - - +
332F GLU* 1.3 81.0 - - - +
334F GLU* 1.3 57.5 + - - +
336F ILE* 3.3 9.1 + - - +
337F ILE* 2.9 39.5 + - + +
349F ILE* 3.8 22.9 - - + +
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Residues in contact with GLU 334 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308F PHE* 3.4 25.9 - - + -
318F ILE* 3.7 11.3 - - + +
319F GLY* 2.8 30.4 + - - -
322F VAL* 3.7 4.4 - - - +
323F ALA 4.0 0.2 - - - +
330F LYS* 2.8 50.0 + - + +
331F ALA 3.8 3.1 - - - +
333F ASP* 1.3 77.6 - - + +
335F GLY* 1.3 58.4 + - - +
337F ILE* 3.6 10.3 - - + +
338F CYS* 2.8 34.3 + - - +
349F ILE* 5.2 4.3 - - + -
351F TYR* 2.6 27.6 + - + +
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Residues in contact with GLY 335 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F GLY 4.1 2.2 - - - -
21F ALA* 3.7 20.6 - - - +
318F ILE* 3.9 19.7 - - - +
331F ALA 3.0 15.0 + - - -
332F GLU 3.0 3.6 + - - -
334F GLU* 1.3 77.3 - - - +
336F ILE* 1.3 61.6 + - - +
338F CYS* 3.8 1.5 - - - +
339F VAL* 3.4 29.6 + - - +
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Residues in contact with ILE 336 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447E ARG* 5.0 3.4 - - - +
460E ARG* 5.6 6.3 - - - +
464E LEU* 5.5 6.7 - - + -
472E ILE* 4.6 15.0 - - + -
20F VAL* 3.3 30.5 - - + -
24F LYS* 4.2 25.6 - - + +
332F GLU* 2.9 13.5 + - + +
333F ASP* 3.6 12.6 - - - +
335F GLY* 1.3 79.3 - - - +
337F ILE* 1.3 63.0 + - + +
339F VAL* 3.9 1.9 - - - +
340F GLU* 3.0 47.8 + - - +
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Residues in contact with ILE 337 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447E ARG* 4.5 9.0 - - - +
308F PHE* 3.7 19.7 - - + -
333F ASP* 2.9 23.6 + - + +
334F GLU* 3.6 7.4 - - - +
336F ILE* 1.3 79.8 - - + +
338F CYS* 1.3 68.2 + - - +
340F GLU* 3.7 16.7 - - - +
341F GLY 2.8 19.1 + - - -
346F ALA 5.1 0.7 - - - +
347F VAL* 3.5 30.6 - - + +
348F HIS 3.4 32.1 - - - +
349F ILE* 3.7 20.2 - - + -
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Residues in contact with CYS 338 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145F LEU* 3.8 16.4 - - + -
307F ARG 4.0 10.5 - - - +
308F PHE* 4.0 14.1 - - + -
316F TYR* 3.5 44.5 - - - -
318F ILE* 3.8 9.0 - - + -
334F GLU 2.8 19.6 + - - +
335F GLY 3.8 4.9 - - - +
337F ILE* 1.3 79.1 - - - +
339F VAL* 1.3 57.1 + - - +
341F GLY* 3.0 4.2 + - - -
342F MET* 2.9 35.2 + - - +
347F VAL* 4.7 0.9 - - - -
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Residues in contact with VAL 339 (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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9F VAL* 4.9 1.8 - - + -
21F ALA 3.9 12.6 - - - +
24F LYS* 4.1 3.8 - - + -
25F ALA* 3.3 42.8 - - + +
28F LEU* 3.6 15.4 - - + +
30F PHE* 3.9 5.6 - - + -
145F LEU* 4.2 18.2 - - + -
335F GLY 3.4 17.8 + - - +
336F ILE* 4.0 2.7 - - - +
338F CYS* 1.3 76.7 - - + +
340F GLU* 1.3 66.5 + - - +
342F MET* 3.2 25.9 + - - +
343F ALA* 3.2 16.1 + - - +
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Residues in contact with GLU 340 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447E ARG* 2.9 44.5 + - - -
464E LEU* 6.1 0.2 - - - +
468E PHE* 5.9 1.0 - - - -
24F LYS* 3.8 21.3 + - - -
28F LEU* 3.9 19.2 - - + +
336F ILE* 3.0 33.9 + - + +
337F ILE* 3.2 11.3 + - - +
339F VAL* 1.3 78.0 - - - +
341F GLY* 1.3 57.7 + - - +
343F ALA* 3.0 15.9 + - - +
344F GLY 3.3 0.2 + - - -
345F GLY* 2.9 24.3 + - - -
346F ALA 4.7 9.7 - - - +
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Residues in contact with GLY 341 (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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438A TYR* 5.7 0.5 + - - -
444B ASP* 5.5 2.4 - - - +
307F ARG* 4.9 9.1 - - - +
316F TYR* 5.6 1.3 - - - -
337F ILE 2.8 10.3 + - - -
338F CYS 3.4 3.6 - - - -
340F GLU* 1.3 74.9 - - - +
342F MET* 1.3 56.3 + - - +
344F GLY* 2.7 24.6 + - - -
345F GLY 3.4 18.1 - - - +
347F VAL* 3.4 18.3 - - - +
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Residues in contact with MET 342 (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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412B THR* 4.1 12.8 - - - +
9F VAL* 3.1 37.5 - - + -
30F PHE* 3.8 16.2 - - + -
143F ASN* 3.4 34.8 - - + +
145F LEU* 5.5 3.6 - - - -
316F TYR* 3.7 37.0 + - + +
338F CYS* 2.9 21.7 + - - +
339F VAL* 3.2 34.3 + - - +
341F GLY* 1.3 76.0 - - - +
343F ALA* 1.3 56.3 + - - +
344F GLY 3.3 2.8 + - - -
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Residues in contact with ALA 343 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B SER 4.6 6.0 - - - +
412B THR* 3.1 24.2 - - + +
413B ASP* 4.5 2.9 - - - +
28F LEU* 4.1 22.4 - - + +
30F PHE* 3.8 12.5 - - + -
339F VAL 3.2 10.1 + - - +
340F GLU* 3.0 10.7 + - - +
342F MET* 1.3 75.1 - - - +
344F GLY* 1.3 59.5 + - - +
345F GLY 3.4 2.2 + - - +
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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
------------------------------------------------------------
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