Contacts of the helix formed by residues 324 - 341 (chain A) in PDB entry 3ZRH
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 ARG 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A VAL 3.0 22.6 + - - +
274A VAL 2.6 25.2 + - - -
275A GLU* 3.9 4.2 + - - +
276A GLY* 3.7 25.3 - - - +
319A ALA* 3.2 27.5 + - - +
322A PHE* 4.0 16.6 - - + +
323A GLN* 1.3 78.9 - - - +
325A GLN* 1.3 58.7 + - - +
326A ASP* 3.5 12.6 - - - +
327A MET* 3.2 26.8 + - + +
328A LEU* 3.0 25.1 + - - +
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Residues in contact with GLN 325 (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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323A GLN* 3.2 17.9 + - - +
324A ARG* 1.3 69.4 - - - +
326A ASP* 1.3 72.6 + - - +
328A LEU* 2.8 29.4 + - + +
329A ALA* 3.0 13.4 + - - +
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Residues in contact with ASP 326 (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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278A LEU* 4.7 12.5 - - + +
323A GLN 4.6 1.6 - - - +
324A ARG* 3.7 13.5 - - - +
325A GLN* 1.3 81.1 + - - +
327A MET* 1.3 93.1 + - + +
329A ALA* 3.2 12.7 + - - +
330A ILE* 3.2 18.8 + - - +
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Residues in contact with MET 327 (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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272A GLY 4.1 4.5 - - - +
273A VAL* 3.9 18.2 - - - -
276A GLY* 3.6 37.9 - - - +
277A ASP 3.7 7.9 - - - +
278A LEU* 4.0 11.0 - - + +
281A ILE* 3.5 35.9 - - + -
319A ALA* 4.7 2.5 - - + -
324A ARG* 3.5 26.9 - - + +
325A GLN 3.2 0.4 - - - -
326A ASP* 1.3 100.2 + - - +
328A LEU* 1.3 59.3 + - - +
330A ILE* 3.0 13.3 - - - +
331A LEU* 2.7 39.1 + - + +
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Residues in contact with LEU 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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316A VAL* 3.9 38.4 - - + +
319A ALA* 4.0 16.8 - - + +
320A ILE* 3.8 26.0 - - + +
324A ARG 3.0 8.3 + - - +
325A GLN* 2.8 31.7 + - + +
327A MET* 1.3 72.0 - - - +
329A ALA* 1.3 56.1 + - - +
331A LEU* 3.3 5.7 + - - +
332A LEU* 2.8 54.3 + - + +
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Residues in contact with ALA 329 (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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325A GLN 3.0 10.3 + - - +
326A ASP* 3.6 9.6 - - - +
328A LEU* 1.3 73.5 - - - +
330A ILE* 1.3 66.0 + - - +
332A LEU* 4.0 4.2 - - - +
333A THR* 2.9 28.1 + - - +
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Residues in contact with ILE 330 (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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278A LEU* 3.6 35.0 - - + -
281A ILE* 3.9 15.5 - - + -
282A GLU* 6.5 0.2 - - + -
326A ASP 3.2 12.1 + - - +
327A MET* 3.0 20.9 - - - +
329A ALA* 1.3 75.0 - - - +
331A LEU* 1.3 63.9 + - + +
333A THR* 2.9 24.8 - - + +
334A GLU* 3.0 11.0 + - - +
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Residues in contact with LEU 331 (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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273A VAL* 6.0 2.5 - - + -
281A ILE* 4.4 20.6 - - + +
285A LYS* 5.9 3.1 - - + -
291A ILE* 3.7 29.1 - - + +
315A LEU* 3.9 43.5 - - + +
316A VAL* 3.9 19.7 - - + +
319A ALA* 4.3 7.4 - - + -
327A MET* 2.7 34.0 + - + +
328A LEU* 3.6 4.7 - - - +
330A ILE* 1.3 73.9 - - + +
332A LEU* 1.3 58.0 + - - +
334A GLU* 3.3 6.9 + - + +
335A VAL* 2.9 32.3 + - - +
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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
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316A VAL* 4.2 27.8 - - + -
328A LEU* 2.8 41.8 + - + +
329A ALA* 4.2 4.0 - - - +
331A LEU* 1.3 70.4 - - - +
333A THR* 1.3 67.2 + - - +
335A VAL* 3.2 11.9 + - + +
336A SER* 3.0 28.6 + - - +
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Residues in contact with THR 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 ALA 2.9 18.6 + - - +
330A ILE* 2.9 32.5 - - + +
332A LEU* 1.3 75.1 - - - +
334A GLU* 1.3 68.6 + - - +
336A SER* 3.2 7.4 + - - -
337A GLN* 3.0 41.5 + - - +
438A ARG* 5.9 3.4 + - - +
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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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285A LYS* 5.4 15.9 - - + +
291A ILE* 4.0 26.7 - - + -
330A ILE 3.0 13.6 + - - +
331A LEU* 3.3 11.9 - - + +
333A THR* 1.3 80.4 - - + +
335A VAL* 1.3 61.9 + - - +
337A GLN* 3.4 13.4 + - - +
338A GLN* 3.0 52.0 + - - +
346A MET* 5.0 4.0 - - - +
438A ARG* 5.8 2.1 + - - -
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Residues in contact with VAL 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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291A ILE* 3.9 30.3 - - + -
292A ALA* 5.2 4.0 - - + +
316A VAL* 5.4 6.1 - - + -
331A LEU 2.9 20.5 + - - +
332A LEU* 3.8 13.5 - - + +
333A THR 3.2 0.4 - - - -
334A GLU* 1.3 75.0 - - - +
336A SER* 1.3 66.7 + - - +
338A GLN* 3.5 6.5 + - - +
339A ALA* 3.3 22.4 + - + +
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Residues in contact with SER 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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332A LEU* 3.0 19.0 + - - +
333A THR* 3.5 7.1 - - - -
335A VAL* 1.3 78.9 - - - +
337A GLN* 1.3 63.7 + - - +
339A ALA* 3.4 5.5 + - - +
340A ALA* 3.2 22.2 + - - +
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Residues in contact with GLN 337 (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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333A THR* 3.0 31.5 + - - +
334A GLU* 4.0 15.6 - - - +
336A SER* 1.3 74.6 - - - +
338A GLN* 1.3 60.9 + - - +
339A ALA 3.0 2.2 - - - -
340A ALA* 2.9 3.0 + - - +
341A LYS* 2.5 41.9 + - + +
346A MET* 5.1 6.4 - - + +
436A TRP* 3.8 28.5 - - + -
438A ARG* 3.7 37.1 + - - +
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Residues in contact with GLN 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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288A GLY* 4.9 13.1 + - - -
289A GLY 5.0 3.6 + - - -
290A ASP* 5.6 1.8 - - - +
291A ILE* 4.8 10.7 - - - +
334A GLU* 3.0 43.3 + - - +
335A VAL* 3.7 8.3 - - - +
337A GLN* 1.3 77.2 - - - +
339A ALA* 1.3 59.2 + - - +
341A LYS 3.5 13.3 + - - +
342A CYS* 5.3 2.3 - - - +
346A MET* 3.1 31.3 - - + +
686A ARG* 5.7 2.6 + - - -
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Residues in contact with ALA 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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335A VAL* 3.3 15.4 + - + +
336A SER* 3.4 4.7 + - - +
337A GLN 3.0 0.8 - - - -
338A GLN* 1.3 79.1 - - - +
340A ALA* 1.3 61.7 + - - +
341A LYS 3.5 0.2 - - - -
401A GLU* 4.9 8.0 - - - +
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Residues in contact with ALA 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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336A SER 3.2 14.4 + - - +
337A GLN* 2.9 4.6 + - - +
339A ALA* 1.3 77.6 - - - +
341A LYS* 1.3 77.3 + - + +
400A ASP* 3.9 4.9 - - - +
401A GLU* 3.5 21.1 - - - +
1694A EDO 6.2 2.0 - - - -
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Residues in contact with LYS 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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337A GLN* 2.5 30.6 + - + +
338A GLN 3.5 8.6 + - - +
339A ALA 3.5 1.2 - - - -
340A ALA* 1.3 88.1 + - + +
342A CYS* 1.3 63.1 + - - +
343A ILE 4.2 0.4 - - - -
346A MET* 3.4 15.5 - - - +
400A ASP 3.0 27.7 + - - -
401A GLU* 3.7 12.7 - - - +
403A LEU 3.1 20.9 + - - -
436A TRP* 3.3 59.4 - - + +
1694A EDO 3.0 36.8 + - - +
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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