Contacts of the helix formed by residues 271 - 276 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245M ARG* 2.6 52.5 + - + +
269M LEU 3.9 0.4 + - - -
270M LEU* 1.3 69.3 - - - +
272M MLY 1.3 63.4 + - - +
273M SER* 3.2 18.6 + - - +
274M ARG* 2.5 48.8 + - + -
285M TYR* 2.5 29.0 + - - +
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Residues in contact with MLY 272 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270M LEU* 2.8 24.0 + - + +
271M GLU* 1.3 69.8 - - - +
273M SER* 1.3 65.6 + - - +
274M ARG 3.2 0.9 + - - -
275M VAL* 3.3 26.5 + - - +
431M MLY 3.4 42.6 - - + +
432M ALA* 5.2 1.5 - - - +
434M TYR* 6.3 0.4 - - - -
435M GLU* 2.8 49.1 - - + +
436M MLY 4.2 5.3 - - - -
598M MLY 4.8 14.8 - - - -
601M ASP* 3.5 39.4 + - - -
649M VAL* 4.8 15.7 - - - -
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Residues in contact with SER 273 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271M GLU* 3.2 16.5 + - - +
272M MLY 1.3 81.3 + - - +
274M ARG* 1.3 51.3 + - - +
276M THR* 2.9 3.8 + - - -
277M PHE* 2.7 48.4 + - - +
431M MLY 4.6 20.7 - - - -
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Residues in contact with ARG 274 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235M ALA* 3.7 19.2 - - - +
236M MLY 4.2 3.6 + - - -
237M THR* 4.5 5.2 + - - +
245M ARG* 3.4 19.2 - - - +
271M GLU* 2.5 56.5 + - - +
272M MLY 3.2 0.2 + - - -
273M SER* 1.3 75.5 - - - +
275M VAL* 1.3 54.9 - - - +
276M THR 2.8 8.7 + - - -
277M PHE 2.5 25.4 + - - +
278M GLN* 3.3 7.1 + - - +
279M LEU 5.1 1.6 - - - +
282M GLU* 2.2 56.1 + - - +
283M ARG 3.0 22.9 + - - -
284M SER* 3.2 15.6 + - - +
285M TYR* 3.2 25.6 - - + -
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Residues in contact with VAL 275 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272M MLY 3.3 21.3 - - - +
274M ARG* 1.3 77.2 - - - +
276M THR* 1.3 58.4 + - - +
284M SER* 4.1 7.2 - - - -
285M TYR* 3.9 15.2 - - + -
288M PHE* 4.9 6.6 - - + -
314M TYR* 3.7 21.2 - - - +
315M VAL* 4.7 4.3 - - - +
358M VAL* 3.9 26.7 - - + +
430M ALA* 4.4 13.9 - - + +
431M MLY 4.4 10.3 - - + +
434M TYR* 3.9 35.9 - - + -
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Residues in contact with THR 276 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273M SER* 2.9 6.8 + - - -
274M ARG 2.9 0.4 - - - -
275M VAL* 1.3 79.4 + - - +
277M PHE* 1.3 60.7 + - + +
313M HIS* 5.6 0.3 + - - -
314M TYR* 3.8 41.1 - - + +
317M GLU* 2.6 22.1 - - - +
427M GLY* 4.2 8.3 + - - -
430M ALA* 4.8 0.7 - - - +
431M MLY 3.6 38.3 - - + +
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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