Contacts of the helix formed by residues 295 - 300 (chain G) in PDB entry 6MZL
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 295 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291G MET 4.0 7.6 - - - +
292G LYS* 3.8 18.4 - - - +
293G GLY 3.3 3.6 + - - +
294G ASN* 1.3 67.7 - - - +
296G THR* 1.3 59.2 + - - +
297G MET 3.1 1.3 - - - -
298G LEU* 3.3 6.6 + - + +
299G ASP* 2.9 41.6 + - - +
607G ARG* 4.4 14.4 + - - +
627G LEU* 4.9 11.5 + - + +
85M SER* 4.6 6.5 - - - -
86M PRO 2.9 29.1 - - - +
87M PRO* 3.3 12.1 - - - +
88M PRO* 3.3 23.2 - - - +
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Residues in contact with THR 296 (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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278G ASP* 4.3 16.6 - - - +
281G VAL* 6.4 2.0 - - + -
294G ASN* 4.2 19.7 + - - -
295G GLU* 1.3 76.7 + - - +
297G MET* 1.3 54.7 + - - -
300G PHE* 2.8 36.4 + - + +
301G ARG* 2.7 29.1 + - - +
627G LEU* 3.3 36.9 + - + +
628G ALA* 4.9 4.7 - - - +
648G ASP* 5.9 1.1 - - + -
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Residues in contact with MET 297 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249G LEU* 3.2 30.1 - - + +
252G VAL* 4.9 7.6 - - + -
281G VAL* 5.1 4.3 - - + -
285G LEU* 3.6 44.6 - - + -
290G HIS* 3.2 31.0 - - + +
291G MET* 3.7 31.0 - - + +
294G ASN* 3.2 24.0 - - + +
295G GLU 3.1 0.6 - - - -
296G THR* 1.3 75.8 - - + +
298G LEU* 1.3 58.0 + - - +
301G ARG* 3.2 32.9 - - - +
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Residues in contact with LEU 298 (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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249G LEU* 4.0 13.0 - - + -
253G TYR* 5.8 1.8 - - + -
291G MET* 3.7 40.4 - - + +
294G ASN 4.6 0.2 + - - -
295G GLU* 3.3 6.8 + - - +
296G THR 3.2 0.2 - - - -
297G MET* 1.3 86.2 - - + +
299G ASP* 1.3 61.1 + - - +
300G PHE 3.3 1.8 - - - -
301G ARG* 2.8 17.7 + - + +
302G THR* 2.3 27.3 + - - +
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Residues in contact with ASP 299 (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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295G GLU* 2.9 24.2 + - - +
298G LEU* 1.3 78.3 - - - +
300G PHE* 1.3 62.7 + - - +
301G ARG 3.1 1.7 + - - -
302G THR* 3.6 16.6 + - - +
304G LYS* 4.9 4.9 - - - +
627G LEU* 3.6 28.0 - - + +
88M PRO* 3.4 29.4 - - - +
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Residues in contact with PHE 300 (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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241G TYR* 4.6 17.5 - + - -
242G PRO* 5.6 7.9 - - + -
245G VAL* 4.3 16.4 - - + -
278G ASP* 4.3 18.8 - - - -
296G THR* 2.8 33.2 + - + +
299G ASP* 1.3 77.3 - - - +
301G ARG* 1.3 82.4 + - + +
302G THR 3.5 1.8 - - - -
304G LYS* 3.3 71.6 + - + +
305G PHE* 6.1 0.2 - - - -
627G LEU* 3.8 11.1 - - + +
648G ASP* 6.2 2.7 - - + -
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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
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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