Contacts of the strand formed by residues 419 - 433 (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 ILE 419 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363B THR* 5.6 1.8 - - - -
401B THR* 5.1 15.3 - - + +
403B VAL* 5.0 9.6 - - + -
170M ARG* 2.8 51.6 - - + +
171M ASN 3.0 10.7 + - - +
172M GLU* 3.4 6.8 - - + +
173M LEU 2.7 33.5 + - - +
417M ASP 4.2 8.5 - - - +
418M VAL* 1.3 75.4 - - - +
420M LYS* 1.3 57.7 + - - +
421M TRP* 4.0 22.6 - - + +
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Residues in contact with LYS 420 (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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363B THR* 3.7 17.9 + - - +
364B GLU* 2.8 34.9 + - - +
365B VAL* 3.7 27.0 - - + +
403B VAL* 4.5 8.9 - - - +
405B TYR* 3.9 9.0 + - - -
173M LEU* 3.4 17.0 - - + -
404M LEU* 2.6 25.0 + - - +
405M LYS* 4.6 0.6 - - - +
415M ASP* 2.6 37.4 + - - -
418M VAL* 3.6 26.4 + - + +
419M ILE* 1.3 83.8 - - - +
421M TRP* 1.3 60.7 + - - +
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Residues in contact with TRP 421 (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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401B THR 4.1 13.5 - - - -
402B LYS* 3.9 27.4 - - + -
403B VAL* 3.8 31.6 - - + -
404B ASN* 4.2 7.2 - - + -
405B TYR* 4.0 4.9 - + + -
170M ARG* 5.1 3.8 - - - +
172M GLU* 4.3 6.2 + - + -
173M LEU* 3.1 11.7 + - - +
174M PHE* 3.3 49.7 - + + +
175M LEU 3.0 24.1 + - - +
419M ILE* 4.0 20.5 - - + +
420M LYS* 1.3 75.3 - - - +
422M VAL* 1.3 66.6 + - - +
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Residues in contact with VAL 422 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B VAL* 3.6 33.9 - - + +
367B VAL* 4.3 6.9 - - + +
405B TYR* 3.1 33.3 + - - +
175M LEU* 3.4 35.0 - - + +
177M VAL* 5.2 1.1 - - + -
401M VAL* 4.3 7.9 - - + -
421M TRP* 1.3 77.2 - - - +
423M ARG* 1.3 72.1 + - - +
424M TYR* 3.7 33.0 - - + +
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Residues in contact with ARG 423 (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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175M LEU 2.9 11.4 + - - +
176M ASP* 3.2 31.6 + - - +
177M VAL* 3.0 25.4 + - - +
422M VAL* 1.3 80.2 - - - +
424M TYR* 1.3 87.2 + - - +
425M ILE* 4.1 23.0 - - + +
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Residues in contact with TYR 424 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B VAL* 4.3 17.1 - - + +
177M VAL* 3.6 35.0 - - + -
393M PRO* 3.3 26.6 - - - +
394M PHE* 3.6 21.5 - - + -
395M ALA 4.0 13.5 - - - -
399M LEU 3.4 20.6 - - - -
400M LYS* 3.2 22.6 + - + +
401M VAL* 2.7 35.9 + - - +
422M VAL* 3.7 20.2 - - + -
423M ARG* 1.3 82.8 - - - +
425M ILE* 1.3 63.5 + - - +
426M GLY 4.0 0.4 - - - -
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Residues in contact with ILE 425 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176M ASP* 4.8 1.1 - - - +
177M VAL 2.9 13.3 + - - +
178M LEU* 3.3 29.1 - - + +
179M GLU* 2.8 26.0 + - - +
391M GLU* 3.9 36.3 - - + +
392M VAL 3.9 0.9 - - - -
394M PHE 4.2 1.8 - - - -
423M ARG* 4.1 34.5 - - + +
424M TYR* 1.3 76.7 - - - +
426M GLY* 1.3 60.1 + - - +
427M ARG* 3.9 15.6 - - + +
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Residues in contact with GLY 426 (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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179M GLU* 3.4 6.5 - - - -
391M GLU* 3.5 1.2 - - - +
392M VAL* 2.8 46.6 + - - +
394M PHE 3.4 17.5 + - - -
396M PRO* 3.8 10.8 - - - -
425M ILE* 1.3 74.9 - - - +
427M ARG* 1.3 63.2 + - - +
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Residues in contact with ARG 427 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179M GLU 2.7 15.7 + - - +
180M SER* 3.2 11.8 + - - +
181M VAL* 2.7 32.1 + - - +
319M LYS* 5.8 4.2 - - - +
390M PHE* 3.6 7.2 - - - +
391M GLU* 4.0 15.3 - - + -
396M PRO* 4.9 1.8 - - - +
425M ILE* 3.9 18.2 - - + +
426M GLY* 1.3 79.6 - - - +
428M SER* 1.3 71.4 + - - +
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Residues in contact with SER 428 (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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180M SER* 3.8 6.3 + - - -
181M VAL 3.9 4.3 - - - -
388M MET 3.6 20.0 - - - -
389M ASN* 3.1 11.5 + - - +
390M PHE* 2.7 56.7 + - - -
427M ARG* 1.3 85.4 + - - +
429M GLY* 1.3 60.6 + - - +
431M TYR* 4.4 3.6 - - - -
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Residues in contact with GLY 429 (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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180M SER* 3.9 12.5 + - - -
181M VAL 2.9 13.1 + - - -
182M ASN* 3.3 12.1 - - - -
388M MET 4.5 3.6 - - - +
389M ASN* 5.0 3.3 - - - +
427M ARG 3.6 0.8 + - - -
428M SER* 1.3 76.4 - - - +
430M ILE* 1.3 63.5 + - - +
431M TYR* 3.4 4.6 + - - +
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Residues in contact with ILE 430 (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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182M ASN* 2.7 20.7 + - + +
183M LEU 2.9 25.3 + - - +
429M GLY* 1.3 71.4 - - - -
431M TYR* 1.3 55.4 + - - +
432M GLU* 3.1 40.6 - - + +
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Residues in contact with TYR 431 (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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181M VAL* 3.8 26.7 - - + +
183M LEU* 3.4 35.4 - - + -
285M LEU* 3.5 7.6 - - + +
286M PRO* 3.5 14.2 - - + -
287M PHE* 2.5 39.5 + - + -
289M VAL* 5.1 5.2 - - + -
386M ILE 3.8 0.9 - - - +
387M SER* 3.3 5.6 - - - -
388M MET* 3.1 56.5 + - + +
390M PHE* 3.4 38.8 - + - -
428M SER* 4.4 5.4 - - - -
429M GLY 3.4 2.8 + - - -
430M ILE* 1.3 71.6 - - - +
432M GLU* 1.3 60.0 + - - +
433M THR* 5.6 1.8 - - - -
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Residues in contact with GLU 432 (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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183M LEU* 2.5 16.8 + - - +
184M LEU* 3.1 23.9 - - + +
185M MET* 2.9 25.3 + - - +
385M PRO* 3.9 26.6 - - + +
386M ILE 3.3 2.5 - - - -
387M SER* 4.2 15.2 - - - -
430M ILE* 3.1 33.3 - - + +
431M TYR* 1.3 75.9 - - - +
433M THR* 1.3 64.6 + - - +
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Residues in contact with THR 433 (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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183M LEU* 5.0 4.9 - - - +
185M MET* 3.4 21.5 - - + +
186M SER 3.7 12.1 - - - +
289M VAL* 3.6 46.0 + - - +
291M PRO* 4.4 7.4 - - + -
385M PRO* 3.8 2.7 - - - -
386M ILE* 2.6 47.9 + - - +
431M TYR* 5.4 2.4 + - - -
432M GLU* 1.3 77.3 + - - +
434M ARG* 1.3 76.1 + - - +
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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