Contacts of the helix formed by residues 287 - 294 (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 LYS 287 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252G VAL* 4.3 11.3 - - - +
255G GLN* 4.3 34.5 + - + +
286G THR* 1.3 98.5 - - + +
288G LYS* 1.3 63.1 + - - +
289G GLU* 3.2 7.0 - - + +
290G HIS* 3.1 31.3 + - + +
291G MET* 3.7 5.5 + - - +
72M ARG* 3.1 44.6 - - - +
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Residues in contact with LYS 288 (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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252G VAL 5.7 1.1 - - - +
253G TYR* 4.0 36.0 + - + -
255G GLN* 3.4 28.7 - - + +
287G LYS* 1.3 74.4 - - - +
289G GLU* 1.3 59.3 + - - +
290G HIS 3.2 1.6 - - - -
291G MET* 3.2 27.4 + - + +
292G LYS* 2.9 36.3 + - + +
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Residues in contact with GLU 289 (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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287G LYS* 3.2 4.5 - - + +
288G LYS* 1.3 77.5 - - - +
290G HIS* 1.3 67.2 + - + +
292G LYS* 3.2 17.1 + - + +
293G GLY 2.9 22.3 + - - -
42I GLU* 5.9 0.7 - - - +
46I ARG* 4.8 3.8 + - - -
75M ILE* 3.1 47.4 - - - +
76M GLN* 2.9 30.1 + - - +
79M ALA* 3.9 22.2 - - + +
83M PHE* 3.2 17.3 - - + -
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Residues in contact with HIS 290 (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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284G SER 3.3 14.4 + - - -
285G LEU* 3.9 19.0 - - + +
286G THR* 3.2 19.1 + - - -
287G LYS* 3.1 36.0 + - + +
289G GLU* 1.3 85.8 + - + +
291G MET* 1.3 55.7 + - - +
293G GLY* 3.0 2.3 + - - +
294G ASN* 2.8 32.2 + - - +
297G MET* 3.2 11.8 - - + +
42I GLU* 6.3 0.2 - - - +
45I TYR* 3.4 44.8 - + + -
49I GLU* 3.6 18.3 + - - +
83M PHE* 4.9 1.3 - + - -
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Residues in contact with MET 291 (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* 4.2 11.2 - - + -
252G VAL* 5.4 3.6 - - + -
253G TYR* 3.6 38.8 - - + -
287G LYS 4.2 3.6 - - - +
288G LYS* 3.2 39.2 + - + +
290G HIS* 1.3 75.6 - - - +
292G LYS* 1.3 61.8 + - + +
294G ASN 3.2 18.3 - - - +
295G GLU* 3.9 8.5 + - - +
297G MET* 3.7 23.7 - - + +
298G LEU* 3.7 42.8 - - + +
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Residues in contact with LYS 292 (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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288G LYS* 2.9 23.0 + - + +
289G GLU* 3.3 19.3 - - + +
290G HIS 3.2 0.2 - - - -
291G MET* 1.3 79.2 - - - +
293G GLY* 1.3 64.7 + - - +
295G GLU* 3.8 14.8 - - - +
76M GLN* 4.0 22.4 + - - +
79M ALA* 6.0 4.9 - - + +
80M ASP* 4.5 13.3 + - - +
83M PHE* 4.7 7.4 - - + +
85M SER* 4.0 11.0 - - - -
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Residues in contact with GLY 293 (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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289G GLU 2.9 11.1 + - - -
290G HIS 3.0 2.4 + - - -
292G LYS* 1.3 80.4 - - - +
294G ASN* 1.3 60.7 + - - +
295G GLU* 3.3 5.2 + - - +
607G ARG* 5.0 6.1 + - - -
49I GLU* 5.7 0.2 - - - -
83M PHE* 3.6 28.4 - - - -
84M THR 5.7 1.1 - - - -
85M SER* 4.2 16.9 - - - -
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Residues in contact with ASN 294 (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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281G VAL* 3.4 35.0 - - + +
284G SER* 5.6 0.6 + - - -
285G LEU* 5.3 1.6 - - - +
290G HIS* 2.8 10.7 + - - +
291G MET 3.2 12.7 - - - +
293G GLY* 1.3 70.4 - - - +
295G GLU* 1.3 58.9 + - - +
296G THR* 3.1 19.8 + - - +
297G MET* 3.1 40.1 + - + +
49I GLU* 5.2 14.6 + - - +
52I GLN* 5.4 1.6 + - - -
56I LYS* 5.7 2.9 + - - -
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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