Contacts of the helix formed by residues 286 - 297 (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 GLN 286 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285B PHE* 1.3 93.2 - - + +
287B LYS* 1.3 63.9 + - - +
288B ARG 3.4 1.3 - - - -
289B PRO* 3.7 20.2 - - + +
290B ARG* 2.8 40.6 + - + +
494C TRP* 4.7 7.3 - - - -
498C LEU* 3.3 25.1 - - - +
514C ASP* 3.3 35.1 + - - +
517C MET 3.7 20.6 + - - -
519C PRO* 3.7 22.2 - - - +
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Residues in contact with LYS 287 (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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282B ASN 4.2 5.3 + - - +
283B GLU* 3.2 36.5 - - - +
284B ASN* 4.0 6.7 + - - +
285B PHE 3.7 2.2 + - - -
286B GLN* 1.3 75.8 - - - +
288B ARG* 1.3 55.2 + - - +
290B ARG* 2.9 27.4 + - + +
291B GLN* 2.5 71.6 + - - +
484B GLU* 5.5 4.6 + - - -
508C THR* 6.0 1.6 - - - +
510C SER* 5.2 0.4 + - - -
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Residues in contact with ARG 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B GLN* 4.4 0.2 - - - +
287B LYS* 1.3 78.2 - - - +
289B PRO* 1.3 66.7 - - + +
291B GLN* 4.1 23.4 + - - +
292B LYS* 3.4 31.6 + - - +
501C LEU* 3.5 23.7 - - + +
503C LYS* 5.4 1.2 - - - +
504C GLU* 3.4 43.2 + - + +
505C ASN* 4.4 7.6 - - - +
508C THR* 4.6 19.5 - - + +
514C ASP* 5.5 0.9 - - - +
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Residues in contact with PRO 289 (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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286B GLN* 3.7 34.8 - - + +
288B ARG* 1.3 92.7 - - + +
290B ARG* 1.3 58.7 + - - +
292B LYS 3.4 0.5 + - - -
293B LEU* 2.9 23.6 + - - +
498C LEU* 4.4 15.7 - - + -
499C PRO* 3.3 41.1 - - + +
501C LEU* 4.3 7.6 - - + -
505C ASN* 4.7 6.7 - - - +
514C ASP* 4.1 13.7 - - + +
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Residues in contact with ARG 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B PHE 4.4 3.6 + - - -
282B ASN* 3.3 25.8 + - - +
286B GLN* 2.8 32.6 + - + +
287B LYS* 2.9 41.3 + - + +
289B PRO* 1.3 70.1 - - - +
291B GLN* 1.3 61.6 + - + +
293B LEU* 3.9 7.2 - - - +
294B PHE* 3.1 27.2 + - - +
482B ASN* 3.3 26.2 - - + +
483B PHE* 3.8 12.7 + - - -
484B GLU* 3.4 29.3 + - - +
485B PRO* 3.4 31.3 - - - +
498C LEU* 3.9 13.5 - - + -
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Residues in contact with GLN 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B LYS* 2.5 59.5 + - - +
288B ARG* 4.1 25.6 + - - +
290B ARG* 1.3 75.0 - - - +
292B LYS* 1.3 60.1 + - - +
294B PHE* 3.3 7.6 + - - +
295B GLU* 3.1 32.1 + - + +
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Residues in contact with LYS 292 (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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288B ARG* 3.4 29.2 + - - +
289B PRO 3.9 2.9 - - - +
290B ARG 3.4 0.2 - - - -
291B GLN* 1.3 74.7 - - - +
293B LEU* 1.3 64.4 - - - +
295B GLU* 3.3 14.4 + - + +
296B ILE* 3.2 46.3 + - - +
499C PRO* 4.3 14.8 - - + -
501C LEU* 4.1 15.7 - - + -
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Residues in contact with LEU 293 (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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289B PRO 2.9 19.1 + - - +
290B ARG* 3.9 5.2 - - - +
292B LYS* 1.3 78.2 - - - +
294B PHE* 1.3 59.7 + - - +
296B ILE* 3.1 16.2 + - + +
297B GLN* 3.2 26.9 + - + +
481B SER 3.3 26.5 - - - +
482B ASN* 3.8 13.2 - - + +
497C VAL* 3.4 22.9 - - + +
498C LEU* 3.7 24.0 - - + -
499C PRO* 3.7 9.1 - - + +
394F TYR* 4.0 7.4 - - - +
398F ILE* 4.0 19.5 - - + -
402F LEU* 6.0 0.9 - - + -
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Residues in contact with PHE 294 (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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290B ARG 3.1 18.6 + - - +
291B GLN* 3.3 6.7 + - - +
293B LEU* 1.3 79.1 - - - +
295B GLU* 1.3 63.3 + - - +
297B GLN* 3.9 11.9 - - - +
298B LYS* 3.1 55.7 + - - +
301B PHE* 4.9 7.4 - + - -
324B ASN 4.9 0.7 - - - -
325B PHE* 3.5 44.9 - + + -
328B GLU* 3.2 38.8 - - + -
482B ASN* 5.8 2.2 - - + -
484B GLU* 6.1 0.7 - - - +
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Residues in contact with GLU 295 (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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291B GLN* 3.1 19.9 + - + +
292B LYS* 3.7 19.5 - - + +
293B LEU 3.2 0.2 - - - -
294B PHE* 1.3 81.0 - - - +
296B ILE* 1.3 64.6 + - - +
298B LYS* 3.6 38.2 + - - +
299B LYS* 3.9 15.6 - - - +
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Residues in contact with ILE 296 (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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292B LYS* 3.2 36.7 + - + +
293B LEU* 3.1 11.8 + - + +
295B GLU* 1.3 77.0 - - - +
297B GLN* 1.3 58.2 + - + +
298B LYS 3.2 0.4 - - - -
299B LYS* 3.2 36.1 + - - +
300B MET 4.3 0.7 + - - -
499C PRO* 4.2 19.7 - - + -
394F TYR* 4.3 18.6 - - + +
395F ASP* 5.5 3.6 - - - +
398F ILE* 4.2 16.4 - - + -
399F PHE* 3.6 35.4 - - + -
402F LEU* 4.3 7.9 - - + -
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Residues in contact with GLN 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B LEU* 3.4 21.3 + - + +
294B PHE* 3.9 21.4 - - - +
296B ILE* 1.3 74.7 - - + +
298B LYS* 1.3 61.6 + - - +
299B LYS 3.3 1.3 - - - -
300B MET* 3.5 23.8 - - + +
301B PHE* 3.8 12.5 - - - -
304B TYR* 5.2 0.2 - - - +
325B PHE* 3.8 31.8 - - + -
480B ILE* 3.4 25.3 - - + +
481B SER 4.6 4.7 - - - +
482B ASN* 4.1 26.3 - - - +
402F LEU* 3.5 27.5 - - + +
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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