Contacts of the helix formed by residues 314 - 329 (chain G) 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 ILE 314 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277G ILE* 3.9 22.2 - - + +
278G MET 3.6 25.1 - - - +
279G SER* 3.6 30.3 - - - +
281G ALA* 5.5 1.1 - - + +
283G MET* 3.9 23.8 - - + -
310G VAL* 3.7 11.7 - - + -
311G GLN 3.1 15.5 - - - +
313G ASP* 1.3 83.5 - - + +
315G TYR* 1.3 60.5 + - - +
316G ASP 3.5 2.0 - - - -
317G GLU* 3.4 11.5 + - - +
318G PHE* 2.9 30.2 + - + +
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Residues in contact with TYR 315 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310G VAL* 3.7 20.0 - - + -
311G GLN 3.2 9.3 + - - +
312G GLU* 3.3 19.6 + - - +
314G ILE* 1.3 78.6 - - - +
316G ASP* 1.3 73.4 + - - +
318G PHE* 3.7 0.9 - - - +
319G VAL* 2.9 52.5 + - + +
387G GLY* 3.7 6.9 - - - -
388G ASP* 2.7 48.5 + - - -
407G ILE* 3.8 19.1 + - + +
408G LEU 4.0 0.4 - - - -
409G LYS* 3.6 51.1 - - + -
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Residues in contact with ASP 316 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312G GLU 4.8 1.7 + - - -
313G ASP 5.7 0.2 - - - -
314G ILE 3.5 0.4 - - - -
315G TYR* 1.3 92.4 - - - +
317G GLU* 1.3 62.9 + - - +
319G VAL* 3.4 4.5 + - - +
320G GLU* 3.0 30.8 + - + +
409G LYS* 5.1 2.8 + - - -
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Residues in contact with GLU 317 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283G MET* 3.8 17.6 - - + +
314G ILE* 3.4 13.3 + - - +
315G TYR 3.3 0.4 - - - -
316G ASP* 1.3 75.1 - - - +
318G PHE* 1.3 67.6 + - - +
320G GLU* 3.3 6.5 + - - +
321G ARG* 2.9 67.0 + - + +
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Residues in contact with PHE 318 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277G ILE* 4.0 30.5 - - + -
283G MET* 3.8 20.4 - - + +
286G ALA* 3.9 5.8 - - + -
287G VAL* 3.7 32.0 - - + +
290G ALA* 3.6 25.8 - - + -
308G THR* 3.9 9.2 - - + -
310G VAL* 3.6 31.9 - - + -
314G ILE* 2.9 18.8 + - + +
315G TYR 3.7 3.1 - - - +
317G GLU* 1.3 77.4 - - - +
319G VAL* 1.3 61.2 + - + +
321G ARG* 3.4 2.3 + - - +
322G SER* 2.8 53.6 + - - -
405G MET* 5.5 0.9 - - + -
407G ILE* 4.6 9.0 - - + -
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Residues in contact with VAL 319 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315G TYR* 2.9 57.6 + - + +
316G ASP* 3.7 5.6 - - - +
318G PHE* 1.3 78.3 - - + +
320G GLU* 1.3 61.6 + - + +
322G SER* 3.1 2.1 + - - -
323G VAL* 2.8 37.5 + - + +
368G LEU* 3.5 31.6 - - + -
407G ILE* 3.9 25.4 - - + -
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Residues in contact with GLU 320 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316G ASP* 3.0 23.3 + - + +
317G GLU* 3.3 7.2 + - - +
319G VAL* 1.3 77.5 - - + +
321G ARG* 1.3 64.4 + - + +
323G VAL* 3.4 9.6 + - - +
324G ALA* 3.0 23.6 + - - +
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Residues in contact with ARG 321 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283G MET* 3.4 32.9 - - - +
284G ASP* 4.3 18.6 + - - +
287G VAL* 3.9 21.8 - - + +
317G GLU* 2.9 52.0 + - + +
318G PHE 3.9 2.7 - - - +
320G GLU* 1.3 77.3 - - + +
322G SER* 1.3 58.6 + - - +
324G ALA* 3.4 6.7 + - - +
325G ARG* 3.0 27.5 + - - +
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Residues in contact with SER 322 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287G VAL* 4.2 13.8 + - - +
290G ALA* 5.3 0.7 - - - +
291G HIS* 4.9 4.0 + - - -
318G PHE* 2.8 47.3 + - - -
319G VAL 3.6 3.6 - - - -
321G ARG* 1.3 78.5 - - - +
323G VAL* 1.3 56.8 + - - +
325G ARG* 3.2 4.3 + - - +
326G ALA* 2.9 29.1 + - - +
405G MET* 3.4 30.4 - - - +
407G ILE* 4.2 5.4 - - - -
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Residues in contact with VAL 323 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319G VAL* 2.8 23.9 + - + +
320G GLU* 3.8 10.3 - - - +
322G SER* 1.3 74.1 - - - +
324G ALA* 1.3 65.2 + - - +
326G ALA* 3.2 6.6 + - - +
327G LYS* 3.0 55.2 + - + +
368G LEU* 3.7 45.8 - - + +
369G CYS* 4.0 4.7 - - + -
385G VAL* 4.2 11.0 - - + -
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Residues in contact with ALA 324 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320G GLU 3.0 17.6 + - - +
321G ARG* 3.7 7.9 - - - +
323G VAL* 1.3 75.7 - - - +
325G ARG* 1.3 62.5 + - - +
327G LYS* 3.4 8.7 + - - +
328G SER* 3.2 23.0 + - - -
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Residues in contact with ARG 325 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287G VAL* 4.7 9.6 - - + -
288G GLU* 5.5 13.4 - - - +
291G HIS* 3.3 52.2 + - + +
321G ARG 3.0 17.5 + - - +
322G SER* 3.5 7.9 - - - +
323G VAL 3.2 0.2 - - - -
324G ALA* 1.3 79.6 - - - +
326G ALA* 1.3 61.4 + - - +
328G SER* 3.2 28.7 + - - -
329G ARG* 3.3 10.9 + - - +
340G GLU* 3.2 31.5 + - - -
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Residues in contact with ALA 326 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291G HIS* 3.8 10.7 - - - -
295G PHE* 4.3 16.6 - - + -
322G SER 2.9 16.8 + - - +
323G VAL 3.2 4.0 + - - +
325G ARG* 1.3 78.5 - - - +
327G LYS* 1.3 61.6 + - - +
329G ARG* 3.3 16.5 + - - +
369G CYS* 3.7 8.5 - - - -
383G PRO* 3.4 19.1 - - + +
385G VAL* 3.6 25.8 - - + -
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Residues in contact with LYS 327 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323G VAL* 3.0 35.2 + - + +
324G ALA* 3.9 6.5 - - - +
325G ARG 3.3 0.2 - - - -
326G ALA* 1.3 77.2 - - - +
328G SER* 1.3 61.5 + - - +
329G ARG 3.5 4.7 + - - +
368G LEU 3.8 7.1 + - - -
369G CYS* 3.4 33.9 - - + +
383G PRO 5.9 0.2 - - - -
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Residues in contact with SER 328 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324G ALA 3.2 14.0 + - - -
325G ARG* 3.2 25.1 + - - -
326G ALA 3.2 0.2 - - - -
327G LYS* 1.3 74.8 - - - +
329G ARG* 1.3 65.0 + - - +
330G VAL* 3.2 11.8 + - - +
340G GLU* 3.5 5.2 + - - +
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Residues in contact with ARG 329 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291G HIS* 2.8 49.0 + - + +
292G PHE* 5.8 1.2 - - - +
295G PHE* 3.4 37.2 + - - +
296G PHE* 4.5 4.4 - - - +
297G ASN 5.0 1.6 - - - +
298G GLN 5.2 1.2 - - - +
325G ARG* 3.3 13.8 + - - +
326G ALA 3.3 16.9 + - - +
327G LYS 4.2 5.2 - - - +
328G SER* 1.3 75.9 - - - +
330G VAL* 1.3 62.6 + - - +
331G VAL* 3.5 9.9 + - - +
340G GLU* 3.2 48.0 + - + +
341G GLN* 3.1 34.1 + - + +
383G PRO* 3.9 11.8 - - + +
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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