Contacts of the strand formed by residues 401 - 407 (chain M) in PDB entry 2VGL
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 VAL 401 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365B VAL* 3.6 38.9 - - + +
366B ASP* 3.4 21.5 - - - +
367B VAL 4.6 1.2 + - - -
175M LEU* 3.9 24.7 - - + -
177M VAL* 4.1 22.7 - - + -
200M VAL* 5.6 0.9 - - + -
214M PHE* 4.0 22.0 - - + -
215M GLY 4.0 3.4 - - - -
216M MET* 4.6 2.2 - - + +
399M LEU* 5.8 2.9 - - + -
400M LYS* 1.3 72.0 - - - +
402M ARG* 1.3 61.2 + - - +
403M TYR 4.2 1.3 - - - +
422M VAL* 4.3 5.6 - - + -
424M TYR* 2.7 19.3 + - + +
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Residues in contact with ARG 402 (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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328B TYR 5.9 0.4 - - - +
330B ASP 6.1 1.3 - - - +
332B ILE* 3.2 49.8 - - - +
335B LYS* 4.1 14.6 + - - +
364B GLU* 6.0 1.2 - - - +
365B VAL* 4.3 1.9 - - - +
366B ASP* 2.8 61.0 + - - +
368B ASP* 3.9 7.3 + - - -
215M GLY 2.9 17.7 + - - +
216M MET 4.1 13.5 - - - +
217M ASN* 4.1 10.5 - - - +
400M LYS* 3.5 38.5 + - - +
401M VAL* 1.3 76.3 + - - +
403M TYR* 1.3 69.9 + - + +
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Residues in contact with TYR 403 (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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328B TYR* 3.6 54.5 - + + +
329B ASN* 4.3 14.9 - - + +
335B LYS* 5.5 0.2 - - - +
365B VAL* 3.4 11.2 - - - -
213M LYS* 3.4 30.7 + - + -
214M PHE* 3.3 14.5 - - - -
215M GLY* 2.7 54.5 + - - -
261M ARG 5.0 1.2 + - - -
262M SER* 3.4 23.4 - - - -
401M VAL* 3.9 1.0 - - - -
402M ARG* 1.3 88.4 - - + +
404M LEU* 1.3 63.3 + - - +
405M LYS* 4.3 4.0 - - + -
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Residues in contact with LEU 404 (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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364B GLU* 6.3 0.2 - - - -
365B VAL* 3.2 20.0 - - + +
173M LEU* 3.4 41.1 - - + -
175M LEU* 3.8 22.0 - - + -
202M MET* 4.3 10.3 - - + -
212M CYS* 4.7 7.2 - - + -
213M LYS 3.3 4.7 - - - +
214M PHE* 3.4 40.4 - - + -
265M PHE* 4.1 14.8 - - + -
403M TYR* 1.3 72.9 - - - +
405M LYS* 1.3 58.3 + - - +
406M VAL* 4.3 1.1 - - + +
420M LYS* 2.6 35.0 + - - +
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Residues in contact with LYS 405 (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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328B TYR* 3.5 64.3 - - + +
360B GLU* 5.8 5.5 + - - +
364B GLU* 2.9 21.9 + - - +
211M GLU 3.7 1.0 - - - +
212M CYS* 3.1 5.4 - - - +
213M LYS* 2.6 52.7 + - + +
403M TYR* 4.5 3.1 - - + -
404M LEU* 1.3 72.6 - - - +
406M VAL* 1.3 62.0 + - - +
407M PHE* 6.5 0.2 - - + -
415M ASP* 2.5 34.9 + - + +
416M HIS 5.5 0.8 - - - +
420M LYS* 4.6 0.9 - - - +
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Residues in contact with VAL 406 (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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173M LEU* 4.0 27.6 - - + -
206M LEU* 4.1 15.0 - - + -
210M PRO* 3.4 28.0 - - + -
211M GLU 3.7 3.6 - - - +
212M CYS* 4.4 7.6 - - - +
404M LEU 4.3 2.0 - - - +
405M LYS* 1.3 77.4 - - - +
407M PHE* 1.3 67.6 + - - +
413M TYR* 4.3 14.8 - - + -
414M SER* 5.2 0.3 - - - -
415M ASP* 3.2 44.0 + - - +
418M VAL* 4.0 15.3 - - + -
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Residues in contact with PHE 407 (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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210M PRO* 4.1 1.6 - - - -
211M GLU* 2.8 45.7 + - + +
406M VAL* 1.3 76.6 - - - +
408M GLU* 1.3 70.3 + - - +
409M PRO* 3.8 32.1 - - + +
413M TYR 5.8 0.4 - - - -
414M SER* 6.4 0.4 - - - +
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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