Contacts of the strand formed by residues 247 - 254 (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 GLY 247 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246M PHE* 1.3 83.7 - - - +
248M MLY 1.3 67.5 + - - +
267M THR* 3.6 1.4 - - - -
268M TYR* 3.0 36.8 + - - -
269M LEU* 4.4 0.6 + - - +
463M ASP* 3.3 10.8 - - - -
464M ILE* 4.2 16.6 - - - -
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Residues in contact with MLY 248 (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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186M THR* 3.3 33.0 - - - -
189M THR* 4.8 13.5 - - - -
190M MLY 4.8 9.6 - - - -
193M ILE* 5.6 1.8 - - - -
226M ASN* 2.8 42.1 - - - -
229M LEU* 5.4 9.7 - - + +
230M GLU* 5.0 5.6 - - - -
234M ASN* 5.9 0.2 - - - -
244M SER* 4.6 7.2 - - - -
246M PHE* 4.0 25.2 - - + -
247M GLY* 1.3 78.2 - - - +
249M PHE* 1.3 64.4 + - - +
250M ILE* 3.8 32.8 - - + -
265M ILE* 4.5 14.4 - - + -
266M GLU 3.3 11.7 - - - +
267M THR* 4.9 0.4 - - - -
268M TYR* 4.1 6.6 - - - -
461M VAL 3.7 1.0 - - - +
462M LEU* 3.5 3.3 - - - +
463M ASP* 2.4 64.9 + - + +
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Residues in contact with PHE 249 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174M SER* 5.5 2.0 - - - -
248M MLY 1.3 77.8 - - - +
250M ILE* 1.3 60.5 + - - +
251M ARG* 4.0 26.5 - - + -
264M ASP 3.0 12.6 - - - +
265M ILE* 3.5 0.3 - - - -
266M GLU* 3.1 24.6 + - + +
268M TYR* 3.8 23.8 - - + +
458M PHE* 4.7 5.4 - + - -
460M GLY* 3.9 28.7 - - - -
461M VAL 3.5 6.5 - - - -
462M LEU* 3.6 28.0 - - + -
660M LEU* 3.9 18.8 - - + -
663M ASN* 4.2 21.1 - - + -
664M LEU* 4.0 24.0 - - + -
667M THR* 6.0 0.4 - - - -
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Residues in contact with ILE 250 (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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189M THR* 5.0 3.6 - - + -
193M ILE* 3.1 34.5 - - + -
222M ILE* 6.0 0.9 - - + -
226M ASN* 5.4 0.7 - - - +
248M MLY 3.8 39.7 - - + -
249M PHE* 1.3 75.6 - - - +
251M ARG* 1.3 71.2 + - - +
252M ILE* 4.3 14.3 - - + +
263M ALA* 4.3 6.1 - - + -
264M ASP 3.2 17.9 - - - +
265M ILE* 4.3 16.4 - - + -
459M ILE 3.5 2.4 - - - +
460M GLY* 3.3 4.7 - - - -
461M VAL* 3.1 38.3 + - + +
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Residues in contact with ARG 251 (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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249M PHE* 4.0 21.3 - - + -
250M ILE* 1.3 79.0 - - - +
252M ILE* 1.3 62.4 + - - +
253M HIS* 3.1 45.8 + - + -
263M ALA* 3.0 22.5 - - - -
264M ASP* 3.0 42.1 + - + -
458M PHE* 3.7 35.3 - - + -
459M ILE 4.0 2.2 - - - -
663M ASN* 3.6 34.5 + - - +
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Residues in contact with ILE 252 (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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193M ILE* 3.9 32.8 - - + -
196M PHE* 4.6 20.2 - - + -
222M ILE* 5.0 6.7 - - + -
250M ILE* 4.3 12.3 - - + -
251M ARG* 1.3 71.4 - - - +
253M HIS* 1.3 61.4 + - - +
254M PHE* 3.3 24.1 - - + -
260M LEU* 3.2 35.0 - - + -
262M SER 3.4 5.8 - - - +
263M ALA* 4.6 7.0 - - + -
458M PHE* 3.0 3.1 - - - -
459M ILE 2.7 44.5 + - - +
461M VAL* 4.6 10.3 - - + -
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Residues in contact with HIS 253 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251M ARG* 3.1 66.5 + - + -
252M ILE* 1.3 71.6 - - - +
254M PHE* 1.3 64.0 + - - +
260M LEU* 4.4 0.3 - - - -
261M ALA* 2.9 24.6 + - - +
262M SER* 2.4 39.2 + - - +
263M ALA 4.3 0.4 + - - -
264M ASP* 3.6 10.3 + - - -
455M ARG* 4.2 33.3 + - + -
457M TYR 3.5 5.8 - - - +
458M PHE* 3.6 20.0 - + + +
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Residues in contact with PHE 254 (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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163M TYR* 4.1 11.7 - + - -
166M MET* 3.0 40.4 - - + -
196M PHE* 3.6 31.9 - + + -
200M ALA* 4.3 7.6 - - + -
252M ILE* 3.3 36.8 - - + -
253M HIS* 1.3 76.0 - - - +
255M GLY* 1.3 66.6 + - - +
258M GLY* 3.9 20.4 - - - +
259M LYS 4.2 1.1 - - - -
260M LEU* 3.7 30.1 - - + -
261M ALA* 4.2 0.4 - - - -
455M ARG* 3.8 3.5 - - - -
456M GLN 3.4 11.8 + - - -
457M TYR* 2.7 18.7 + - + +
459M ILE* 3.3 25.4 - - + -
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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