Contacts of the helix formed by residues 300 - 309 (chain B) 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 MET 300 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296B ILE 4.4 2.0 - - - +
297B GLN* 3.5 15.0 - - - +
298B LYS 3.1 0.8 - - - -
299B LYS* 1.3 80.2 - - - +
301B PHE* 1.3 63.5 + - - +
302B PRO* 3.5 2.2 - - - -
303B GLN* 3.1 38.7 + - - +
304B TYR* 3.1 47.6 + - + +
399F PHE* 4.3 8.1 - - - -
402F LEU* 3.8 44.6 - - + +
404F SER* 3.6 36.3 - - - +
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Residues in contact with PHE 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B PHE* 4.9 6.7 - + - -
297B GLN 3.8 4.5 - - - -
298B LYS* 3.4 39.5 - - + +
299B LYS 3.4 0.6 - - - -
300B MET* 1.3 76.6 - - - +
302B PRO* 1.3 67.1 - - + +
304B TYR* 3.3 14.2 + + - +
305B TRP* 3.1 17.8 + - - +
325B PHE* 3.4 39.7 - + - -
328B GLU* 4.9 6.7 - - + -
329B PHE* 3.5 44.4 - + + -
333B TYR* 3.5 47.6 - + + -
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Residues in contact with PRO 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B LYS 4.7 1.6 - - - +
299B LYS* 4.0 14.4 - - - +
300B MET 3.8 1.3 - - - -
301B PHE* 1.3 91.4 - - + +
303B GLN* 1.3 56.7 + - - +
305B TRP* 4.4 4.7 - - + -
306B PHE* 3.1 24.1 + - - +
333B TYR* 3.4 24.7 - - + +
40C PRO* 3.4 34.1 - - + +
42C VAL* 3.8 22.9 - - + -
330C PHE* 4.4 3.1 - - + -
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Residues in contact with GLN 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B LYS 5.4 0.9 - - - +
300B MET* 3.1 42.3 + - + +
302B PRO* 1.3 79.4 - - + +
304B TYR* 1.3 64.4 + - - +
306B PHE* 3.9 3.7 + - - +
307B GLU* 2.9 39.9 + - - +
478B HIS* 3.7 17.0 + - - -
323C TYR* 4.0 1.0 + - - -
330C PHE* 3.7 33.4 - - + -
403F GLY 3.8 5.0 + - - -
404F SER* 4.2 0.9 - - - +
405F MET* 3.3 38.2 - - + +
406F LEU* 5.9 0.2 - - + -
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Residues in contact with TYR 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B GLN 4.6 0.7 + - - -
300B MET* 3.1 49.6 + - + +
301B PHE* 3.3 22.6 + + - +
302B PRO 3.3 0.2 - - - -
303B GLN* 1.3 81.8 - - - +
305B TRP* 1.3 60.3 + - - +
306B PHE 3.2 0.7 - - - -
307B GLU* 3.0 21.5 + - - +
308B LEU* 3.1 12.8 + - - +
314B LEU* 3.6 13.2 - - + +
316B PHE* 3.5 30.6 - + - -
325B PHE* 4.0 8.2 - + - -
329B PHE* 3.8 20.0 - + + -
478B HIS* 3.4 49.1 - + - +
480B ILE* 4.1 14.6 - - - +
402F LEU* 4.8 2.9 + - - +
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Residues in contact with TRP 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B PHE 3.1 16.5 + - - +
302B PRO* 4.0 2.2 - - + +
303B GLN 3.5 0.2 - - - -
304B TYR* 1.3 73.4 - - - +
306B PHE* 1.3 63.8 + - - +
308B LEU* 3.5 3.5 + - + +
309B THR* 3.3 34.3 + - + +
329B PHE* 4.7 0.6 - - + -
333B TYR* 4.0 21.1 - + + -
334B LEU* 3.7 33.4 - - + -
337B LYS* 3.2 54.7 - - + -
338B ILE* 3.5 18.8 - - + +
341B SER* 4.0 12.9 + - - -
38C HIS* 3.8 24.2 - - - -
39C ILE 3.7 7.4 - - - -
40C PRO* 3.6 38.4 - - + -
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Residues in contact with PHE 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B PRO 3.1 17.8 + - - +
303B GLN 4.1 4.7 - - - +
304B TYR 3.2 0.4 - - - -
305B TRP* 1.3 77.5 - - - +
307B GLU* 1.3 58.9 + - - +
309B THR* 2.9 19.6 + - - -
310B GLN* 3.3 15.3 - - + +
40C PRO* 3.7 12.9 - - + +
41C PHE* 3.5 29.4 - + - -
58C TRP* 3.7 22.0 - + - -
61C TYR* 3.6 42.8 - + - -
326C MET* 3.5 42.4 - - + -
330C PHE* 4.2 6.5 - + + -
405F MET* 3.7 19.7 - - + -
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Residues in contact with GLU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B GLN* 2.9 35.0 - - - +
304B TYR* 3.0 8.0 + - - +
306B PHE* 1.3 77.0 - - - +
308B LEU* 1.3 63.7 + - - +
309B THR 3.2 0.7 - - - -
310B GLN* 3.2 10.7 + - - +
312B PHE* 3.3 23.9 + - + +
314B LEU* 3.3 16.7 - - + +
476B VAL* 3.4 16.9 - - + +
478B HIS* 3.0 27.2 - - - -
323C TYR* 3.2 25.7 + - + -
326C MET* 3.7 22.2 - - + -
405F MET* 5.0 2.5 - - + -
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Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B TYR 3.1 17.0 + - - +
305B TRP* 3.5 6.5 + - + +
307B GLU* 1.3 76.8 - - - +
309B THR* 1.3 60.5 + - + +
310B GLN 3.2 1.6 + - - -
311B GLY* 3.8 8.7 + - - -
312B PHE 3.3 20.8 + - - +
314B LEU* 4.0 13.0 - - + -
329B PHE* 4.3 8.3 - - + -
334B LEU* 3.7 39.3 - - + -
338B ILE* 5.7 2.9 - - + -
418B ILE* 4.2 17.7 - - + +
448B ARG* 5.5 0.5 - - - +
451B ALA* 3.9 23.2 - - + +
452B ILE 3.5 22.4 - - - +
453B VAL* 3.8 12.1 - - + -
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Residues in contact with THR 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B TRP* 3.3 36.9 + - + +
306B PHE* 2.9 23.6 + - - -
308B LEU* 1.3 77.8 - - - +
310B GLN* 1.3 71.4 + - - +
311B GLY 3.5 0.7 - - - -
338B ILE* 5.5 3.8 - - + -
341B SER* 6.0 1.1 - - - +
418B ILE* 5.5 11.2 - - + -
448B ARG* 3.6 11.2 + - - -
40C PRO* 4.8 3.3 - - + +
58C TRP* 4.8 9.1 - - + -
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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