Contacts of the helix formed by residues 312 - 329 (chain J) in PDB entry 1ZUM
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 GLU 312 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310J VAL 3.4 1.0 + - - -
311J GLN* 1.3 72.2 - - + +
313J ASP* 1.3 74.5 + - - +
314J ILE 3.1 1.4 + - - -
315J TYR* 3.3 14.9 + - - +
316J ASP* 4.8 2.6 + - - +
409J LYS* 4.0 27.8 - - + +
410J PHE 2.8 18.6 + - - +
411J LYS* 3.7 41.2 - - + +
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Residues in contact with ASP 313 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279J SER* 4.3 21.3 + - - -
311J GLN* 3.1 5.6 + - - +
312J GLU* 1.3 88.0 - - - +
314J ILE* 1.3 62.3 + - + +
315J TYR 3.7 0.2 - - - -
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Residues in contact with ILE 314 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277J ILE* 3.8 21.3 - - + +
278J MET 3.5 27.1 - - - +
279J SER* 3.7 30.1 - - - +
281J ALA* 5.4 1.8 - - + +
283J MET* 3.8 23.6 - - + -
310J VAL* 3.7 10.5 - - + -
311J GLN 3.2 13.5 - - - +
313J ASP* 1.3 82.4 - - + +
315J TYR* 1.3 65.3 + - - +
316J ASP 3.5 2.0 - - - -
317J GLU* 3.4 10.6 + - - +
318J PHE* 2.9 23.6 + - + +
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Residues in contact with TYR 315 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310J VAL* 3.8 20.4 - - + -
311J GLN 3.2 4.7 + - - +
312J GLU* 3.3 22.9 + - - +
314J ILE* 1.3 77.4 - - - +
316J ASP* 1.3 73.5 + - - +
318J PHE* 3.6 1.2 - - - +
319J VAL* 2.8 53.0 + - + +
387J GLY* 3.7 7.4 - - - -
388J ASP* 2.8 46.2 + - - -
407J ILE* 3.9 19.0 + - + +
408J LEU 4.1 0.9 - - - -
409J LYS* 3.6 54.3 - - + -
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Residues in contact with ASP 316 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312J GLU 4.8 2.3 + - - +
314J ILE 3.5 0.6 - - - -
315J TYR* 1.3 94.5 - - - +
317J GLU* 1.3 62.5 + - - +
319J VAL* 3.7 3.7 - - - +
320J GLU* 3.0 27.5 + - - +
409J LYS* 5.5 2.4 + - - -
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Residues in contact with GLU 317 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283J MET* 3.8 22.1 - - + +
314J ILE* 3.4 12.2 + - - +
315J TYR 3.3 0.6 - - - -
316J ASP* 1.3 78.3 - - - +
318J PHE* 1.3 64.6 + - - +
320J GLU* 3.3 10.6 + - - +
321J ARG* 3.1 56.4 + - + +
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Residues in contact with PHE 318 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277J ILE* 4.0 25.4 - - + -
283J MET* 4.0 18.5 - - + +
286J ALA* 3.9 18.2 - - + -
287J VAL* 3.8 20.4 - - + -
290J ALA* 3.6 26.7 - - + -
308J THR* 3.9 14.6 - - + -
310J VAL* 3.7 29.8 - - + -
314J ILE* 2.9 18.7 + - + +
315J TYR 3.6 3.1 - - - +
317J GLU* 1.3 76.5 - - - +
319J VAL* 1.3 60.8 + - - +
321J ARG* 3.3 3.5 + - - +
322J SER* 2.8 51.0 + - - -
405J MET* 5.3 2.0 - - + -
407J ILE* 4.3 9.9 - - + -
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Residues in contact with VAL 319 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315J TYR* 2.8 59.2 + - + +
316J ASP* 3.7 4.7 - - - +
318J PHE* 1.3 79.4 - - + +
320J GLU* 1.3 58.2 + - - +
322J SER* 3.2 4.9 + - - -
323J VAL* 2.9 38.8 + - + +
368J LEU* 3.5 33.0 - - + -
407J ILE* 3.9 20.0 - - + -
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Residues in contact with GLU 320 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316J ASP* 3.0 19.2 + - - +
317J GLU* 3.5 9.2 - - - +
318J PHE 3.3 0.2 - - - -
319J VAL* 1.3 78.5 - - - +
321J ARG* 1.3 62.7 + - + +
323J VAL* 3.5 5.7 + - - +
324J ALA* 3.1 22.2 + - - +
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Residues in contact with ARG 321 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283J MET* 3.6 29.9 - - - +
284J ASP* 2.7 33.8 + - - +
287J VAL* 3.8 19.4 - - + +
317J GLU* 3.1 47.8 + - + +
318J PHE 3.7 3.4 - - - +
320J GLU* 1.3 74.6 - - + +
322J SER* 1.3 60.6 + - - +
324J ALA* 3.4 6.9 + - - +
325J ARG* 3.0 29.3 + - - +
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Residues in contact with SER 322 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287J VAL* 4.2 12.1 + - - +
290J ALA* 5.6 0.3 - - - +
291J HIS* 5.0 3.5 + - - -
318J PHE* 2.8 49.1 + - - -
319J VAL 3.6 4.3 - - - -
321J ARG* 1.3 73.4 - - - +
323J VAL* 1.3 60.6 + - - +
325J ARG* 3.3 4.6 + - - +
326J ALA* 2.9 30.2 + - - +
405J MET* 3.4 29.2 - - - +
407J ILE* 4.2 5.6 - - - -
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Residues in contact with VAL 323 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319J VAL* 2.9 23.3 + - + +
320J GLU* 3.8 6.7 - - - +
322J SER* 1.3 75.0 - - - +
324J ALA* 1.3 63.1 + - - +
326J ALA* 3.2 7.4 + - - +
327J LYS* 2.9 44.0 + - + +
368J LEU* 3.7 55.0 - - + +
369J CYS* 4.2 5.4 - - + -
385J VAL* 4.4 8.7 - - + -
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Residues in contact with ALA 324 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320J GLU 3.1 12.0 + - - +
321J ARG* 3.5 12.6 - - - +
323J VAL* 1.3 80.5 - - - +
325J ARG* 1.3 61.5 + - - +
327J LYS* 3.3 10.8 + - - +
328J SER* 3.1 23.3 + - - -
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Residues in contact with ARG 325 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287J VAL* 4.6 9.6 - - + -
288J GLU* 3.0 38.3 + - - +
291J HIS* 3.3 48.8 + - + +
321J ARG 3.0 17.3 + - - +
322J SER* 3.6 7.2 - - - +
324J ALA* 1.3 73.1 - - - +
326J ALA* 1.3 65.2 + - - +
328J SER* 2.9 26.4 + - - -
329J ARG* 3.2 19.8 + - - +
340J GLU* 2.6 40.4 + - - -
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Residues in contact with ALA 326 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291J HIS* 3.9 10.3 - - - -
295J PHE* 4.3 14.6 - - + -
322J SER 2.9 17.8 + - - +
323J VAL 3.6 4.7 - - - +
325J ARG* 1.3 77.6 - - - +
327J LYS* 1.3 62.6 + - - +
329J ARG* 3.3 17.0 + - - +
369J CYS* 3.8 8.3 - - - -
383J PRO* 3.5 18.4 - - + +
385J VAL* 3.6 27.1 - - + -
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Residues in contact with LYS 327 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323J VAL* 2.9 32.9 + - + +
324J ALA* 3.7 7.9 - - - +
325J ARG 3.3 0.4 - - - -
326J ALA* 1.3 77.1 - - - +
328J SER* 1.3 61.9 + - - +
329J ARG 3.5 4.0 + - - +
368J LEU 4.4 3.9 + - - -
369J CYS* 3.9 29.2 - - + +
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Residues in contact with SER 328 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324J ALA 3.1 12.7 + - - -
325J ARG* 2.9 33.1 + - - -
327J LYS* 1.3 76.0 - - - +
329J ARG* 1.3 63.6 + - - +
330J VAL* 3.2 13.2 + - - +
340J GLU* 3.6 6.4 - - - +
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Residues in contact with ARG 329 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291J HIS* 3.0 41.0 + - + +
292J PHE* 5.7 1.4 - - - +
295J PHE* 3.4 37.8 + - - +
296J PHE* 4.4 4.8 - - - +
297J ASN 4.9 2.6 - - - +
298J GLN 5.0 1.0 - - - +
325J ARG* 3.2 13.7 + - - +
326J ALA 3.3 15.5 + - - +
327J LYS 4.3 3.3 - - - +
328J SER* 1.3 73.9 - - - +
330J VAL* 1.3 63.6 + - - +
331J VAL* 3.4 10.6 + - - +
340J GLU* 3.3 48.7 + - + +
341J GLN* 3.1 32.6 + - + +
383J PRO* 4.0 14.3 - - + +
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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