Contacts of the helix formed by residues 271 - 276 (chain G) in PDB entry 1MVW
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 271 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245G ARG* 2.6 52.5 + - + +
269G LEU 3.9 0.2 + - - -
270G LEU* 1.3 70.3 - - - +
272G MLY 1.3 63.6 + - - +
273G SER* 3.2 19.1 + - - +
274G ARG* 2.5 49.6 + - + +
285G TYR* 2.5 27.9 + - - +
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Residues in contact with MLY 272 (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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270G LEU* 2.8 23.4 + - + +
271G GLU* 1.3 71.4 - - - +
273G SER* 1.3 65.0 + - - +
274G ARG 3.2 0.7 + - - -
275G VAL* 3.3 27.4 + - - +
431G MLY 3.4 42.8 - - + +
432G ALA* 5.2 1.3 - - - +
434G TYR* 6.3 0.2 - - - -
435G GLU* 2.8 48.9 - - + +
436G MLY 4.2 5.8 - - - -
598G MLY 4.8 14.4 - - - -
601G ASP* 3.5 39.4 + - - -
649G VAL* 4.8 16.4 - - - -
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Residues in contact with SER 273 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271G GLU* 3.2 16.5 + - - +
272G MLY 1.3 79.7 + - - +
274G ARG* 1.3 49.9 + - - +
276G THR* 2.9 4.0 + - - +
277G PHE* 2.7 47.8 + - - +
431G MLY 4.6 21.1 - - - -
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Residues in contact with ARG 274 (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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235G ALA* 3.7 19.2 - - - +
236G MLY 4.2 3.6 + - - -
237G THR* 4.5 5.4 + - - +
245G ARG* 3.4 19.0 - - - +
271G GLU* 2.5 54.5 + - - +
272G MLY 3.2 1.6 + - - -
273G SER* 1.3 75.7 - - - +
275G VAL* 1.3 59.1 - - - +
276G THR 2.8 5.2 + - - -
277G PHE* 2.5 25.8 + - - +
278G GLN* 3.3 7.7 + - - +
279G LEU 5.1 1.8 - - - +
282G GLU* 2.2 55.1 + - - +
283G ARG 3.0 22.6 + - - -
284G SER* 3.2 15.7 + - - +
285G TYR* 3.2 25.1 - - + -
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Residues in contact with VAL 275 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270G LEU* 6.2 0.2 - - + -
272G MLY 3.3 20.9 - - - +
274G ARG* 1.3 76.4 - - - +
276G THR* 1.3 58.1 + - - +
284G SER* 4.1 6.5 - - - -
285G TYR* 3.9 16.3 - - + -
288G PHE* 4.9 6.8 - - + -
314G TYR* 3.7 21.2 - - - +
315G VAL* 4.7 4.2 - - - +
358G VAL* 3.9 26.1 - - + +
430G ALA* 4.4 13.9 - - + +
431G MLY 4.4 9.0 - - + -
434G TYR* 3.9 36.3 - - + -
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Residues in contact with THR 276 (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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273G SER* 2.9 6.6 + - - -
274G ARG 2.9 0.4 - - - -
275G VAL* 1.3 78.8 + - - +
277G PHE* 1.3 60.0 + - + +
313G HIS* 5.6 0.5 + - - -
314G TYR* 3.8 39.5 - - + +
317G GLU* 2.6 22.7 - - - +
427G GLY* 4.2 8.7 + - - -
430G ALA* 4.8 0.3 - - - +
431G MLY 3.6 38.7 - - + +
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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