Contacts of the helix formed by residues 308 - 316 (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 ASN 308 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292M MET* 3.4 1.3 - - - -
306M THR* 3.6 3.9 + - - +
307M THR* 1.3 76.7 + - - +
309M PRO* 1.3 63.6 - - - +
310M TYR* 2.8 37.7 + - - +
311M ASP* 3.1 42.0 + - - +
312M TYR* 3.7 1.7 - - - -
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Residues in contact with PRO 309 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289M TYR* 4.7 11.0 - - + -
292M MET* 3.0 30.5 - - + -
307M THR 3.1 7.4 - - - +
308M ASN* 1.3 85.7 - - - +
310M TYR* 1.3 58.1 + - + +
311M ASP 2.8 12.4 + - - -
312M TYR* 2.9 16.9 + - + +
315M VAL* 4.8 2.5 - - + -
316M SER* 3.3 17.5 - - - -
320M ILE* 3.5 44.9 - - + -
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Residues in contact with TYR 310 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308M ASN* 2.8 29.2 + - - +
309M PRO* 1.3 80.7 - - + +
311M ASP* 1.3 59.1 + - - +
312M TYR 3.3 3.1 - - - -
313M HIS* 5.0 1.8 + - - -
316M SER* 3.8 27.3 + - - -
318M GLY 5.3 4.8 + - - -
319M GLU* 6.0 0.2 - - - -
320M ILE* 2.8 37.4 - - + +
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Residues in contact with ASP 311 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306M THR* 2.5 30.7 + - - +
308M ASN* 3.1 19.2 + - - +
309M PRO 2.8 0.8 + - - -
310M TYR* 1.3 78.8 - - - +
312M TYR* 1.3 77.0 + - + +
313M HIS 3.8 1.6 - - - -
363M ASN* 2.6 35.0 + - - +
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Residues in contact with TYR 312 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292M MET* 4.4 11.9 - - + -
304M LEU 4.3 1.0 + - - -
305M ILE* 2.9 31.4 - - + -
306M THR* 2.7 37.1 + - - +
308M ASN 3.7 6.7 - - - -
309M PRO* 2.9 18.3 + - + +
310M TYR 4.8 0.2 - - - -
311M ASP* 1.3 106.2 - - + +
313M HIS* 1.3 57.0 + - - +
314M TYR* 3.2 2.7 - - + +
315M VAL* 2.8 38.1 + - + +
316M SER 3.4 4.2 + - - -
359M MET* 3.6 37.0 - - + +
360M HIS* 4.2 12.5 + + - -
363M ASN* 3.8 16.6 - - - -
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Residues in contact with HIS 313 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276M THR 5.6 0.4 + - - -
310M TYR 5.0 2.5 + - - -
311M ASP 3.8 2.4 - - - -
312M TYR* 1.3 71.6 - - - +
314M TYR* 1.3 80.1 + + - +
315M VAL 3.0 1.2 + - - -
316M SER* 3.4 11.4 + - - -
317M GLU* 3.2 45.2 + - + +
362M GLY 4.1 19.3 - - - +
363M ASN* 4.0 4.9 + - - +
365M LYS* 5.4 7.2 - - - +
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Residues in contact with TYR 314 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275M VAL 3.7 20.5 - - - +
276M THR* 3.8 35.5 - - + +
278M GLN* 3.1 20.4 + - - +
312M TYR 3.2 1.3 - - - +
313M HIS* 1.3 93.2 - + - +
315M VAL* 1.3 66.3 + - + +
317M GLU* 4.4 0.4 - - - -
358M VAL* 3.4 23.8 - - + -
359M MET* 4.5 7.2 - - - +
361M TYR 4.1 0.9 - - - -
362M GLY* 3.1 38.3 - - - -
423M HIS 4.6 3.1 + - - -
426M VAL* 3.8 8.3 - - - +
427M GLY* 3.3 30.1 + - - -
430M ALA* 3.8 20.0 - - + -
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Residues in contact with VAL 315 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275M VAL 4.7 3.4 - - - +
278M GLN* 2.8 9.4 - - - +
284M SER* 4.6 4.5 - - - -
288M PHE* 4.0 42.8 - - + -
289M TYR* 2.3 49.8 + - + +
292M MET* 4.8 4.0 - - - -
309M PRO* 4.5 9.6 - - + +
312M TYR* 2.8 27.7 + - + +
314M TYR* 1.3 89.6 - - + +
316M SER* 1.3 55.3 + - - -
319M GLU 4.4 0.2 - - - +
359M MET* 4.7 10.3 - - + -
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Residues in contact with SER 316 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278M GLN* 2.8 0.6 + - - -
289M TYR* 4.5 0.2 - - - -
309M PRO* 3.3 34.5 + - - -
310M TYR* 3.8 32.3 - - - -
312M TYR 3.4 5.0 + - - -
313M HIS* 3.4 9.5 + - - -
315M VAL* 1.3 79.6 - - - +
317M GLU* 1.3 63.9 + - - +
318M GLY 3.2 6.7 - - - +
319M GLU 5.0 2.0 - - - -
320M ILE* 4.5 8.3 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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