Contacts of the helix formed by residues 312 - 329 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310C VAL 3.5 0.4 + - - -
311C GLN* 1.3 72.8 - - + +
313C ASP* 1.3 77.3 + - - +
314C ILE 3.2 0.7 + - - -
315C TYR* 3.3 15.1 + - - +
316C ASP* 4.8 2.3 + - - -
409C LYS* 4.0 28.0 - - + +
410C PHE 2.9 19.6 + - - +
411C LYS* 3.4 42.1 - - + +
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Residues in contact with ASP 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C SER* 4.4 19.2 + - - -
311C GLN* 3.1 5.0 + - - +
312C GLU* 1.3 89.9 - - - +
314C ILE* 1.3 62.0 + - + +
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Residues in contact with ILE 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C ILE* 3.9 20.9 - - + +
278C MET 3.5 24.9 - - - +
279C SER* 3.5 30.3 - - - +
281C ALA* 5.3 3.4 - - + +
283C MET* 3.8 26.5 - - + -
310C VAL* 3.8 11.2 - - + -
311C GLN 3.0 12.1 + - - +
313C ASP* 1.3 82.0 - - + +
315C TYR* 1.3 66.0 + - - +
316C ASP 3.5 1.8 - - - -
317C GLU* 3.4 9.2 + - - +
318C PHE* 2.9 24.3 + - + +
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Residues in contact with TYR 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C VAL* 3.8 20.0 - - + -
311C GLN 3.2 7.5 + - - +
312C GLU* 3.3 20.5 + - - +
314C ILE* 1.3 78.0 - - - +
316C ASP* 1.3 82.2 + - - +
318C PHE* 3.2 0.9 + - - +
319C VAL* 2.9 47.7 + - + +
387C GLY* 3.8 5.9 - - - -
388C ASP* 2.8 34.5 + - + +
407C ILE* 3.7 20.2 + - + +
408C LEU 4.1 0.4 - - - -
409C LYS* 3.6 57.2 - - + -
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Residues in contact with ASP 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C GLU 4.8 2.1 + - - -
313C ASP 5.6 0.2 + - - -
314C ILE 3.5 0.6 - - - -
315C TYR* 1.3 92.5 - - - +
317C GLU* 1.3 63.9 + - - +
319C VAL* 3.5 3.9 + - - +
320C GLU* 3.0 27.3 + - - +
409C LYS* 4.9 4.3 + - - -
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Residues in contact with GLU 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C MET* 3.9 22.3 - - + +
314C ILE* 3.4 11.4 + - - +
315C TYR 3.3 0.2 - - - -
316C ASP* 1.3 76.6 - - - +
318C PHE* 1.3 67.6 + - - +
320C GLU* 3.3 11.6 + - + +
321C ARG* 3.0 50.1 + - + +
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Residues in contact with PHE 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C ILE* 4.1 24.2 - - + -
283C MET* 3.9 19.0 - - + -
286C ALA* 3.8 7.4 - - + -
287C VAL* 3.7 32.8 - - + -
290C ALA* 3.6 26.2 - - + -
308C THR* 3.8 14.1 - - + -
310C VAL* 3.5 32.1 - - + -
314C ILE* 2.9 17.9 + - + +
315C TYR 3.6 3.1 - - - +
317C GLU* 1.3 76.9 - - - +
319C VAL* 1.3 61.1 + - + +
321C ARG* 3.3 3.3 + - - +
322C SER* 2.8 51.1 + - - -
405C MET* 5.2 0.9 - - + -
407C ILE* 4.5 9.6 - - + -
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Residues in contact with VAL 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C TYR* 2.9 53.4 + - + +
316C ASP* 3.8 4.0 - - - +
318C PHE* 1.3 73.2 - - + +
320C GLU* 1.3 61.0 + - - +
322C SER* 3.6 5.7 - - - -
323C VAL* 2.8 34.1 + - + +
368C LEU* 3.5 33.9 - - + -
407C ILE* 3.8 23.8 - - + -
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Residues in contact with GLU 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C ASP* 3.0 19.7 + - - +
317C GLU* 3.6 11.3 - - + +
319C VAL* 1.3 76.5 - - - +
321C ARG* 1.3 63.7 + - + +
323C VAL* 3.5 6.0 + - - +
324C ALA* 3.2 23.0 + - - +
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Residues in contact with ARG 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C MET* 3.6 27.0 - - - +
284C ASP* 2.7 40.1 + - - +
287C VAL* 3.7 24.7 - - + +
317C GLU* 3.0 35.9 + - + +
318C PHE 3.6 3.6 - - - +
320C GLU* 1.3 77.7 - - + +
322C SER* 1.3 59.4 + - - +
324C ALA* 3.4 6.5 + - - +
325C ARG* 3.0 28.9 + - - +
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Residues in contact with SER 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C VAL* 4.1 13.3 + - - +
291C HIS* 5.0 3.3 + - - -
318C PHE* 2.8 50.0 + - - -
319C VAL 3.6 4.0 - - - -
321C ARG* 1.3 72.3 - - - +
323C VAL* 1.3 58.0 + - - +
325C ARG* 3.3 4.8 + - - +
326C ALA* 2.9 31.3 + - - +
385C VAL* 4.7 2.6 - - - +
405C MET* 4.4 14.6 - - - +
407C ILE* 4.1 19.5 - - - -
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Residues in contact with VAL 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C VAL* 2.8 26.1 + - + +
320C GLU* 3.8 6.1 - - - +
322C SER* 1.3 71.7 - - - +
324C ALA* 1.3 58.4 + - - +
326C ALA* 3.2 7.3 + - - +
327C LYS* 2.9 55.6 + - + +
368C LEU* 3.6 48.0 - - + +
369C CYS* 4.2 3.1 - - + -
385C VAL* 4.5 10.5 - - + -
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Residues in contact with ALA 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320C GLU 3.2 14.6 + - - +
321C ARG* 3.8 6.3 - - - +
322C SER 3.3 0.2 - - - -
323C VAL* 1.3 80.5 - - - +
325C ARG* 1.3 63.7 + - - +
327C LYS* 3.3 8.7 + - - +
328C SER* 3.1 23.7 + - - -
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Residues in contact with ARG 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C VAL* 4.6 9.6 - - + -
288C GLU* 2.8 40.0 + - - +
291C HIS* 3.6 40.3 + - + +
321C ARG 3.0 18.4 + - - +
322C SER* 3.7 7.0 - - - +
323C VAL 3.2 0.2 - - - -
324C ALA* 1.3 77.6 - - - +
326C ALA* 1.3 60.4 + - - +
328C SER* 3.0 28.8 + - - -
329C ARG* 3.2 11.4 + - - +
340C GLU* 3.0 36.4 + - - -
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Residues in contact with ALA 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C HIS* 3.8 12.0 - - + -
295C PHE* 4.3 15.5 - - + -
322C SER 2.9 17.0 + - - +
323C VAL 3.6 3.6 - - - +
325C ARG* 1.3 75.8 - - - +
327C LYS* 1.3 62.6 + - - +
329C ARG* 3.3 16.6 + - - +
369C CYS* 3.9 7.6 - - - -
383C PRO* 3.5 17.4 - - + +
385C VAL* 3.6 27.1 - - + -
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Residues in contact with LYS 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323C VAL* 2.9 33.2 + - + +
324C ALA* 3.8 6.7 - - - +
326C ALA* 1.3 75.5 - - - +
328C SER* 1.3 60.0 + - - +
329C ARG 3.3 3.7 + - - +
368C LEU 4.3 4.5 + - - -
369C CYS* 3.6 31.2 - - + +
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Residues in contact with SER 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C ALA 3.1 13.1 + - - -
325C ARG* 3.0 27.5 + - - -
326C ALA 3.3 0.2 - - - -
327C LYS* 1.3 75.7 - - - +
329C ARG* 1.3 64.1 + - - +
330C VAL* 3.1 12.6 + - - +
340C GLU* 3.6 5.0 - - - +
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Residues in contact with ARG 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C HIS* 2.9 41.0 + - + +
292C PHE* 5.8 1.4 - - - +
295C PHE* 3.3 37.3 + - - +
296C PHE* 4.4 4.0 - - - +
297C ASN 4.9 2.2 - - - +
298C GLN 5.1 1.2 - - - +
325C ARG* 3.2 13.6 + - - +
326C ALA 3.3 17.1 + - - +
327C LYS 3.3 3.3 - - - +
328C SER* 1.3 76.5 - - - +
330C VAL* 1.3 62.6 + - - +
331C VAL* 3.4 10.6 + - - +
340C GLU* 3.3 50.1 + - + +
341C GLN* 3.2 33.1 + - + +
383C PRO* 3.9 12.7 - - + +
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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