Contacts of the helix formed by residues 327 - 343 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B ASP* 3.8 1.6 + - - +
325B PRO* 3.0 25.5 + - + +
326B MET* 1.3 82.2 - - - +
328B ALA* 1.3 64.4 + - - +
329B HIS* 3.7 12.3 - - + +
330B LYS* 3.4 12.1 + - + +
331B ALA* 3.1 21.1 + - - +
354B VAL* 4.3 5.2 - - + -
355B PRO 3.5 24.5 - - - +
356B SER* 4.0 17.0 - - - +
480B FAD 3.2 16.2 + - - +
481B NAI 3.6 45.8 - - + +
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Residues in contact with ALA 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A HIS* 3.7 10.8 - - + -
16B PRO* 3.7 11.6 - - + +
45B CYS* 3.5 32.3 - - - -
50B CYS* 3.9 0.2 - - - -
327B LEU* 1.3 69.8 - - - +
329B HIS* 1.3 63.9 + - - +
331B ALA* 3.1 4.0 + - - +
332B GLU* 3.0 28.4 + - - +
480B FAD 2.8 36.7 + - + +
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Residues in contact with HIS 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A CYS* 3.7 22.6 - - - -
450A HIS 3.1 19.5 - - - +
451A ALA* 3.7 17.2 - - + -
452A HIS* 2.9 35.9 + - + +
457A GLU* 5.4 0.2 - - - +
460A ARG* 5.2 1.1 - - - +
327B LEU* 3.7 16.8 - - + +
328B ALA* 1.3 75.5 - - - +
330B LYS* 1.3 63.0 + - - +
332B GLU* 4.0 8.5 - - - +
333B ASP* 3.0 33.5 + - - +
354B VAL* 3.9 5.8 - - + -
355B PRO* 2.7 31.0 + - + -
356B SER* 5.3 1.8 - - - -
357B VAL* 5.6 1.6 - - + -
480B FAD 3.2 18.5 + + - -
481B NAI 5.2 2.2 - - - -
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Residues in contact with LYS 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A CYS* 4.7 6.5 - - - -
319B GLY* 3.1 21.8 + - - +
320B ASP* 5.2 0.6 - - - +
322B VAL* 3.8 3.2 + - - +
323B ALA 2.8 27.8 + - - -
324B GLY 3.9 4.9 + - - -
325B PRO* 3.2 40.1 + - + +
327B LEU* 3.4 17.0 + - + +
328B ALA 3.1 0.6 - - - -
329B HIS* 1.3 80.0 - - - +
331B ALA* 1.3 64.4 + - - +
333B ASP* 3.6 3.1 + - - +
334B GLU* 2.9 64.8 + - + +
349B ILE* 4.7 1.5 - - + +
351B TYR* 3.8 19.1 - - + -
354B VAL* 4.3 10.1 - - + -
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Residues in contact with ALA 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PRO* 4.3 0.2 - - + -
17B GLY* 3.3 26.7 - - - +
318B ILE* 4.1 1.9 - - - +
319B GLY* 3.7 29.8 - - - -
327B LEU 3.1 12.7 + - - +
328B ALA 3.1 8.4 + - - +
330B LYS* 1.3 75.8 - - - +
332B GLU* 1.3 63.9 + - - +
334B GLU* 3.3 4.0 + - - +
335B GLY 3.0 18.0 + - - -
480B FAD 3.8 15.7 - - - +
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Residues in contact with GLU 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A HIS* 4.4 18.1 + - - -
457A GLU* 4.3 12.3 - - - +
460A ARG* 5.6 3.1 + - - -
473A ASN* 5.4 5.2 + - - -
16B PRO* 3.5 34.4 - - + +
17B GLY* 4.2 0.7 - - - -
19B TYR* 4.3 8.8 + - - -
20B VAL* 3.8 27.4 - - + +
328B ALA 3.0 20.1 + - - +
329B HIS* 4.0 8.1 - - - +
330B LYS 3.4 0.2 - - - -
331B ALA* 1.3 73.5 - - - +
333B ASP* 1.3 69.9 + - - +
335B GLY* 3.0 2.6 + - - -
336B ILE* 2.9 28.6 + - + +
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Residues in contact with ASP 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A ARG 4.3 4.5 - - - +
449A CYS* 3.5 22.9 + - - +
460A ARG* 2.7 45.6 + - - -
329B HIS* 3.0 21.0 + - - +
330B LYS 3.9 4.0 - - - +
332B GLU* 1.3 79.5 - - - +
334B GLU* 1.3 62.0 + - - +
336B ILE* 3.4 8.1 + - - +
337B ILE* 3.0 33.9 + - + +
349B ILE* 4.5 14.2 - - + +
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Residues in contact with GLU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B PHE* 3.5 25.6 - - + -
318B ILE* 3.7 11.6 - - + +
319B GLY* 2.9 25.6 + - - -
322B VAL* 5.2 0.9 - - - +
323B ALA 4.2 0.7 - - - +
330B LYS* 2.9 48.7 + - - +
331B ALA 3.7 3.4 - - - +
332B GLU 3.2 0.4 - - - -
333B ASP* 1.3 73.0 - - - +
335B GLY* 1.3 61.8 + - - +
337B ILE* 3.5 8.3 - - - +
338B CYS* 2.8 33.3 + - - +
349B ILE* 4.1 9.9 - - + -
351B TYR* 2.4 30.7 + - - +
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Residues in contact with GLY 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLY 4.0 2.2 - - - -
21B ALA* 3.8 16.2 - - - -
318B ILE* 3.4 26.2 - - - +
331B ALA 3.0 12.0 + - - -
332B GLU 3.0 4.0 + - - -
334B GLU* 1.3 77.4 - - - +
336B ILE* 1.3 61.1 + - - +
338B CYS* 3.6 1.1 - - - +
339B VAL* 3.1 29.5 + - - +
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Residues in contact with ILE 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A ARG* 5.1 3.4 - - - +
460A ARG* 5.6 6.7 - - - +
464A LEU* 5.3 6.1 - - + -
472A ILE* 3.9 18.6 - - + -
20B VAL* 3.5 28.6 - - + +
24B LYS* 4.2 25.1 - - + +
332B GLU* 2.9 12.1 + - + +
333B ASP* 3.7 11.9 - - - +
335B GLY* 1.3 77.2 - - - +
337B ILE* 1.3 63.1 + - + +
339B VAL* 3.4 4.1 - - - +
340B GLU* 3.0 54.1 + - - +
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Residues in contact with ILE 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A ARG* 4.9 6.7 - - - +
308B PHE* 3.5 26.5 - - + -
333B ASP* 3.0 21.3 + - + +
334B GLU* 3.5 8.1 - - - +
336B ILE* 1.3 78.4 - - + +
338B CYS* 1.3 62.8 + - - +
340B GLU* 3.6 18.1 - - - +
341B GLY 2.8 23.7 + - - -
346B ALA 5.3 1.3 - - - +
347B VAL* 3.4 27.9 - - + +
348B HIS 4.1 14.1 - - - +
349B ILE* 3.8 25.8 - - + -
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Residues in contact with CYS 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LEU* 3.9 10.1 - - + -
307B ARG 4.5 5.4 - - - +
308B PHE* 4.0 16.8 - - + -
316B TYR* 3.5 39.2 - - - -
318B ILE* 3.8 10.8 - - + -
334B GLU 2.8 21.2 + - - +
335B GLY* 3.6 4.3 - - - +
337B ILE* 1.3 78.6 - - - +
339B VAL* 1.3 57.9 + - + +
341B GLY* 3.1 4.2 + - - -
342B MET* 2.9 39.7 + - - +
347B VAL* 4.9 0.7 - - - -
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Residues in contact with VAL 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 5.0 2.0 - - + -
21B ALA* 3.9 13.9 - - + +
24B LYS* 3.8 10.1 - - + -
25B ALA* 3.8 28.7 - - + +
28B LEU* 3.5 23.6 - - + +
30B PHE* 3.8 2.9 - - + -
145B LEU* 4.1 13.9 - - + -
335B GLY 3.1 13.8 + - - +
336B ILE 3.4 10.3 - - - +
338B CYS* 1.3 73.5 - - - +
340B GLU* 1.3 66.4 + - - +
342B MET* 3.2 33.6 + - + +
343B ALA* 3.1 16.1 + - - +
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Residues in contact with GLU 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A ARG* 3.1 39.7 + - - -
24B LYS* 3.6 23.4 + - - -
28B LEU* 3.9 19.5 - - + -
336B ILE* 3.0 33.7 + - + +
337B ILE* 3.6 16.2 - - - +
338B CYS 3.2 0.2 - - - -
339B VAL* 1.3 76.6 - - - +
341B GLY* 1.3 61.5 + - - +
343B ALA* 3.0 12.4 + - - +
344B GLY 3.2 0.3 + - - -
345B GLY* 3.0 26.3 + - - -
346B ALA 5.0 8.5 - - - +
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Residues in contact with GLY 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ARG* 2.8 36.1 + - - -
316B TYR* 5.4 2.7 - - - -
337B ILE 2.8 9.9 + - - -
338B CYS 3.1 3.3 + - - -
340B GLU* 1.3 74.6 - - - +
342B MET* 1.3 64.2 + - - +
344B GLY* 3.0 8.3 + - - -
345B GLY 3.5 3.1 - - - -
347B VAL* 3.3 20.1 - - - +
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Residues in contact with MET 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 3.8 39.0 - - + -
30B PHE* 3.9 15.5 - - + -
143B ASN* 4.2 16.4 + - + +
145B LEU* 4.2 11.4 - - + -
316B TYR* 3.6 42.1 + - + +
338B CYS* 2.9 36.0 + - - +
339B VAL* 3.2 28.0 - - + +
341B GLY* 1.3 77.2 - - - +
343B ALA* 1.3 60.2 + - - +
344B GLY 3.2 1.1 + - - -
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Residues in contact with ALA 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 4.3 19.3 - - + +
30B PHE* 4.0 18.2 - - + -
339B VAL 3.1 10.6 + - - +
340B GLU* 3.0 11.6 + - - +
342B MET* 1.3 77.1 - - - +
344B GLY* 1.3 57.1 + - - +
345B GLY 3.6 0.6 + - - -
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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
------------------------------------------------------------
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