Contacts of the helix formed by residues 295 - 306 (chain C) in PDB entry 5ZR1
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 SER 295 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294C LEU* 1.3 76.1 - - - +
296C ASP* 1.3 67.4 + - - +
297C ARG* 3.2 11.3 + - - +
298C PHE* 3.0 16.3 + - - +
299C VAL* 3.0 13.0 + - - +
432C LEU* 4.1 0.4 - - - -
467C THR* 3.8 8.6 + - - -
468C LEU 3.0 13.7 + - - -
469C ASP* 3.4 37.7 + - - -
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Residues in contact with ASP 296 (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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294C LEU 3.7 1.8 + - - -
295C SER* 1.3 76.0 + - - +
297C ARG* 1.3 76.9 + - - +
298C PHE 3.2 0.2 - - - -
299C VAL 3.7 1.6 - - - +
300C GLU* 3.1 28.8 + - - +
429C HIS* 3.6 19.1 - - + +
432C LEU* 3.8 30.9 - - + +
433C ILE* 3.8 19.7 - - + +
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Residues in contact with ARG 297 (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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295C SER* 3.2 4.2 - - - +
296C ASP* 1.3 92.5 + - - +
298C PHE* 1.3 59.1 + - - +
300C GLU* 4.0 19.6 + - - +
301C PHE* 3.6 15.8 + - - +
469C ASP* 3.3 20.2 - - - +
470C ASN* 3.0 24.7 + - - +
471C ARG* 4.6 26.5 - - + +
409E ARG* 5.3 12.7 - - - +
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Residues in contact with PHE 298 (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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281C PHE* 5.8 0.2 - + - -
294C LEU* 4.1 33.0 - - + -
295C SER 3.0 8.7 + - - +
297C ARG* 1.3 79.4 - - - +
299C VAL* 1.3 61.1 + - + +
301C PHE* 3.2 5.2 + + - +
302C ILE* 3.0 64.2 + - + +
320C MET 4.4 0.7 - - - -
321C LEU* 4.1 12.1 - - + -
324C SER* 3.4 36.1 - - - -
468C LEU* 3.4 34.1 - - + +
469C ASP* 3.9 10.7 + - - -
470C ASN* 3.5 16.3 + - + -
475C LEU* 3.9 15.3 - - + -
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Residues in contact with VAL 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C PHE* 4.6 4.5 - - + -
294C LEU* 3.9 29.8 - - + -
295C SER 3.0 14.9 + - - +
296C ASP* 3.4 7.5 + - - +
298C PHE* 1.3 77.2 - - + +
300C GLU* 1.3 57.8 + - - +
302C ILE* 3.2 10.7 + - - +
303C LEU* 2.8 25.3 + - - +
425C ILE* 3.7 32.2 - - + +
428C TYR* 4.0 7.9 - - + -
429C HIS* 3.7 18.8 - - + +
432C LEU* 3.9 16.2 - - + -
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Residues in contact with GLU 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C ASP 3.1 18.8 + - - +
297C ARG* 4.0 26.7 + - - +
299C VAL* 1.3 74.7 - - - +
301C PHE* 1.3 62.0 + - - +
303C LEU* 3.6 12.3 - - + +
304C SER* 2.9 36.3 + - - +
429C HIS* 3.3 32.6 + - + +
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Residues in contact with PHE 301 (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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297C ARG 3.6 6.6 + - - +
298C PHE* 3.2 10.0 + + - +
300C GLU* 1.3 80.2 - - - +
302C ILE* 1.3 70.2 + - + +
304C SER* 4.0 3.8 - - - -
305C LYS* 3.1 64.0 + - + +
320C MET* 4.4 8.7 - - - -
470C ASN* 3.2 29.6 - - - +
475C LEU* 3.6 33.0 - - + -
476C THR* 3.7 36.1 - - + -
480C PHE* 4.1 6.1 - + - -
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Residues in contact with ILE 302 (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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281C PHE* 5.0 9.4 - - + -
298C PHE* 3.0 52.8 + - + +
299C VAL* 3.3 11.2 - - + +
301C PHE* 1.3 78.3 - - + +
303C LEU* 1.3 61.2 + - - +
306C MET* 3.2 27.7 + - - +
317C LEU* 3.6 30.3 - - + -
320C MET* 3.6 39.6 - - + +
321C LEU* 4.6 5.8 - - + -
425C ILE* 4.5 13.5 - - + -
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Residues in contact with LEU 303 (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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299C VAL 2.8 16.4 + - - +
300C GLU* 3.7 11.2 - - + +
301C PHE 3.2 0.4 - - - -
302C ILE* 1.3 76.3 - - - +
304C SER* 1.3 62.3 + - - +
306C MET* 4.4 11.0 - - + +
307C ALA* 3.7 18.2 + - - +
423C ASN* 4.2 16.4 - - - +
425C ILE* 3.8 23.3 - - + -
426C GLU* 3.7 40.2 - - + +
429C HIS* 4.6 17.5 - - + -
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Residues in contact with SER 304 (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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300C GLU* 2.9 23.5 + - - +
301C PHE* 4.1 5.4 - - - -
302C ILE 3.3 0.2 - - - -
303C LEU* 1.3 78.1 - - - +
305C LYS* 1.3 68.7 + - - +
306C MET 3.2 0.2 - - - -
307C ALA* 3.3 15.6 + - - +
308C ASN* 3.4 19.2 + - - -
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Residues in contact with LYS 305 (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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301C PHE* 3.1 54.6 + - + +
304C SER* 1.3 78.9 - - - +
306C MET* 1.3 60.4 + - - +
307C ALA 3.3 0.2 - - - -
308C ASN* 3.5 15.8 + - - +
309C ASN* 4.0 5.7 + - - +
316C LEU* 3.8 10.6 - - - +
320C MET* 3.9 16.8 - - - -
476C THR* 4.5 7.0 + - - -
480C PHE* 3.9 23.3 - - + +
417E ASN* 3.5 26.7 - - - +
419E GLU* 3.3 32.3 + - - +
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Residues in contact with MET 306 (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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271C ASN* 5.5 3.4 + - - +
274C PHE* 5.5 6.3 - - + -
277C GLY* 5.9 5.6 - - - -
302C ILE 3.2 18.9 + - - +
303C LEU* 4.4 12.6 - - + +
304C SER 3.2 0.4 - - - -
305C LYS* 1.3 76.6 - - - +
307C ALA* 1.3 59.0 + - - +
308C ASN 3.4 0.2 - - - -
309C ASN 3.1 6.1 - - - +
310C THR* 4.9 1.2 - - - +
313C ASN* 2.5 57.5 + - + +
314C LEU* 6.1 0.9 - - - -
316C LEU* 4.5 6.7 - - + -
317C LEU* 3.9 34.3 - - + +
320C MET* 4.6 5.4 - - + +
423C ASN* 4.4 15.3 - - - +
425C ILE* 3.7 23.1 - - + -
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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