Contacts of the helix formed by residues 327 - 343 (chain A) in PDB entry 1ZMD
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A ASP* 3.9 1.3 + - - +
325A PRO* 2.9 29.8 + - + +
326A MET* 1.3 84.3 - - - +
328A ALA* 1.3 65.5 + - - +
329A HIS* 3.4 13.9 - - + +
330A LYS* 3.2 9.2 + - + +
331A ALA* 3.1 21.7 + - - +
354A VAL* 4.4 4.3 - - + +
355A PRO 3.7 23.1 - - - +
356A SER* 3.9 16.6 - - - +
357A VAL 6.0 0.2 - - - +
480A FAD 3.2 16.3 + - - +
481A NAI 3.7 44.9 - - + +
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Residues in contact with ALA 328 (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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16A PRO* 3.8 10.9 - - + +
45A CYS* 3.4 33.4 - - - -
50A CYS* 3.8 2.2 - - - -
327A LEU* 1.3 71.3 - - - +
329A HIS* 1.3 61.7 + - - +
331A ALA* 3.3 4.2 + - - +
332A GLU* 3.0 28.2 + - - +
480A FAD 2.8 32.8 + - - +
452B HIS* 3.6 14.1 - - + -
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Residues in contact with HIS 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LEU* 3.8 17.2 - - + +
328A ALA* 1.3 75.9 - - - +
330A LYS* 1.3 63.5 + - - +
332A GLU* 3.8 7.8 - - - +
333A ASP* 3.0 33.3 + - - +
354A VAL* 3.8 10.5 - - + +
355A PRO* 2.8 30.9 + - + -
356A SER* 5.3 1.8 - - - -
357A VAL* 5.7 1.6 - - + -
480A FAD 3.3 19.2 + + - -
481A NAI 5.4 1.8 - - - -
449B CYS* 3.6 25.8 - - - -
450B HIS 3.2 25.1 - - - +
451B ALA* 4.0 9.5 - - + -
452B HIS* 3.1 30.5 + - + +
457B GLU* 5.3 0.9 - - - +
460B ARG* 5.3 1.6 - - - +
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Residues in contact with LYS 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A GLY* 3.0 23.1 + - - -
320A ASP* 5.1 0.8 - - - +
322A VAL* 3.6 3.8 + - - +
323A ALA 3.0 25.1 + - - -
324A GLY* 3.7 11.3 + - - -
325A PRO* 3.2 33.9 + - + +
326A MET* 6.2 0.2 - - - +
327A LEU* 3.2 15.2 + - + +
328A ALA 3.2 0.2 - - - -
329A HIS* 1.3 81.5 - - - +
331A ALA* 1.3 59.4 + - - +
333A ASP* 3.4 3.0 + - - +
334A GLU* 2.9 65.7 + - - +
349A ILE* 4.5 4.0 - - + +
351A TYR* 3.9 18.4 - - + -
354A VAL* 4.3 11.4 - - + -
449B CYS* 4.7 7.0 - - - -
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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
----------------------------------------------------------
16A PRO* 4.5 0.2 - - + -
17A GLY* 3.3 21.8 - - - +
318A ILE* 3.7 2.8 - - - +
319A GLY* 3.6 32.1 - - - +
320A ASP 4.6 0.2 - - - +
327A LEU 3.1 9.6 + - - +
328A ALA 3.3 7.6 + - - +
330A LYS* 1.3 81.6 - - - +
332A GLU* 1.3 62.7 + - - +
334A GLU* 3.4 0.9 + - - +
335A GLY 3.0 18.2 + - - -
480A FAD 3.8 22.7 - - - +
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Residues in contact with GLU 332 (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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16A PRO* 3.4 37.5 - - + +
17A GLY* 4.3 0.7 - - - -
19A TYR* 4.7 7.1 + - - -
20A VAL* 3.7 25.0 - - + +
328A ALA 3.0 19.7 + - - +
329A HIS* 3.8 7.6 - - - +
330A LYS 3.3 0.2 - - - -
331A ALA* 1.3 76.8 - - - +
333A ASP* 1.3 65.5 + - - +
335A GLY* 3.2 3.3 + - - -
336A ILE* 3.1 29.2 + - + +
452B HIS* 3.7 28.6 + - - -
457B GLU* 4.5 8.8 - - - +
460B ARG* 5.8 1.4 + - - -
473B ASN* 5.2 6.4 + - - -
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Residues in contact with ASP 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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329A HIS* 3.0 18.4 + - - +
330A LYS 3.8 3.4 - - - +
332A GLU* 1.3 76.8 - - - +
334A GLU* 1.3 65.5 + - - +
336A ILE* 3.3 9.9 + - - +
337A ILE* 3.0 34.3 + - + +
349A ILE* 4.3 14.0 - - + +
447B ARG 4.5 3.5 - - - +
449B CYS* 3.2 24.3 + - - +
460B ARG* 2.9 42.9 + - - -
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Residues in contact with GLU 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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308A PHE* 3.4 24.1 - - + -
318A ILE* 3.6 12.4 - - + +
319A GLY 2.7 31.0 + - - -
322A VAL* 3.5 4.6 - - - +
323A ALA 4.0 0.2 - - - +
330A LYS* 2.9 48.0 + - - +
331A ALA 3.8 4.0 - - - +
332A GLU 3.3 0.2 - - - -
333A ASP* 1.3 76.1 - - - +
335A GLY* 1.3 59.3 + - - +
337A ILE* 3.6 8.3 - - - +
338A CYS* 3.0 31.2 + - - +
349A ILE* 4.0 11.7 - - + -
351A TYR* 2.4 28.6 + - - -
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Residues in contact with GLY 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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17A GLY 4.2 4.5 - - - -
21A ALA* 3.8 24.9 - - - +
318A ILE* 4.2 10.3 - - - +
331A ALA 3.0 14.5 + - - -
332A GLU 3.2 3.6 + - - -
333A ASP 3.2 0.2 - - - -
334A GLU* 1.3 77.0 - - - +
336A ILE* 1.3 62.4 + - - +
338A CYS* 3.4 3.2 + - - +
339A VAL* 3.1 29.5 + - - +
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Residues in contact with ILE 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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20A VAL* 3.4 30.7 - - + -
24A LYS* 4.1 29.6 - - + +
332A GLU* 3.1 12.9 + - + +
333A ASP* 3.3 12.8 + - - +
335A GLY* 1.3 75.9 - - - +
337A ILE* 1.3 60.9 + - + +
339A VAL* 3.2 4.0 + - - +
340A GLU* 2.8 49.6 + - - +
447B ARG* 5.3 2.2 - - - +
460B ARG* 5.6 6.1 - - - +
464B LEU* 5.4 6.7 - - + -
472B ILE* 4.3 13.2 - - + -
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Residues in contact with ILE 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A PHE* 3.7 18.4 - - + -
333A ASP* 3.0 23.9 + - + +
334A GLU* 3.6 10.5 - - - +
336A ILE* 1.3 75.6 - - + +
338A CYS* 1.3 68.7 + - - +
340A GLU* 3.7 18.4 - - - +
341A GLY 2.9 17.7 + - - -
346A ALA 5.2 0.4 - - - +
347A VAL* 3.5 33.4 - - + +
348A HIS 3.8 16.8 - - - +
349A ILE* 3.7 31.6 - - + -
447B ARG* 4.6 9.0 - - - +
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Residues in contact with CYS 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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145A LEU* 4.1 10.3 - - + -
307A ARG 4.0 4.9 - - - +
308A PHE* 3.9 18.2 - - + -
316A TYR* 3.5 37.9 - - - -
318A ILE* 3.9 8.7 - - + -
334A GLU 3.0 21.9 + - - +
335A GLY* 3.6 5.2 - - - +
337A ILE* 1.3 80.8 - - - +
339A VAL* 1.3 57.6 + - - +
341A GLY* 3.2 3.1 + - - -
342A MET* 3.0 38.8 + - - +
347A VAL* 5.1 1.1 - - - -
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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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9A VAL* 5.1 1.8 - - + -
21A ALA* 3.6 25.4 - - + +
24A LYS* 3.8 6.3 - - + -
25A ALA* 3.3 33.9 - - + +
28A LEU* 3.2 28.0 - - + +
30A PHE* 4.0 4.9 - - + -
145A LEU* 4.3 11.2 - - + -
335A GLY 3.1 16.6 + - - +
336A ILE 3.7 2.5 - - - +
338A CYS* 1.3 78.1 - - - +
340A GLU* 1.3 64.5 + - - +
342A MET* 3.2 21.5 + - + +
343A ALA* 3.1 15.9 + - - +
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Residues in contact with GLU 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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24A LYS* 3.9 25.5 + - - -
28A LEU* 3.9 12.6 - - + -
336A ILE* 2.8 31.4 + - + +
337A ILE* 3.7 16.6 - - - +
338A CYS 3.3 0.2 - - - -
339A VAL* 1.3 76.1 - - - +
341A GLY* 1.3 60.5 + - - +
343A ALA* 3.0 12.0 + - - +
344A GLY 3.3 0.5 + - - -
345A GLY* 2.9 25.2 + - - -
346A ALA 4.7 9.5 - - - +
447B ARG* 2.8 44.8 + - - -
468B PHE* 5.9 1.2 - - - -
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Residues in contact with GLY 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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307A ARG* 5.1 7.9 - - - +
316A TYR* 5.5 1.8 - - - -
337A ILE 2.9 10.5 + - - -
338A CYS 3.6 3.1 - - - -
339A VAL 3.1 0.4 - - - -
340A GLU* 1.3 73.3 - - - +
342A MET* 1.3 56.0 + - - +
343A ALA 3.0 1.6 - - - -
344A GLY* 2.7 24.6 + - - -
345A GLY 3.4 17.4 - - - +
347A VAL* 3.5 18.1 - - - +
444E ASP* 5.7 1.0 - - - +
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Residues in contact with MET 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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9A VAL* 3.8 33.4 - - + -
30A PHE* 3.7 17.1 - - + -
143A ASN* 4.2 16.6 - - + +
145A LEU* 4.3 19.1 - - + -
316A TYR* 3.6 47.9 + - + +
338A CYS* 3.0 33.7 + - - +
339A VAL* 3.4 21.1 - - + +
341A GLY* 1.3 75.7 - - - +
343A ALA* 1.3 57.4 + - - +
344A GLY 3.4 2.4 + - - -
412E THR* 4.1 11.4 - - - +
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Residues in contact with ALA 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 4.2 20.9 - - + +
30A PHE* 4.0 16.6 - - + -
339A VAL 3.1 10.0 + - - +
340A GLU 3.0 11.5 + - - +
341A GLY 3.0 1.2 - - - -
342A MET* 1.3 74.2 - - - +
344A GLY* 1.3 58.4 + - - +
345A GLY 3.6 1.0 + - - -
411E SER 4.7 4.5 - - - +
412E THR* 3.1 24.7 - - - +
413E ASP* 4.7 2.1 - - - +
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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
------------------------------------------------------------
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