Contacts of the strand formed by residues 316 - 325 (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 LEU 316 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440B ASP* 4.0 25.1 - - + +
441B GLU* 5.5 0.4 - - - -
442B PRO* 5.3 12.3 - - + -
475B ASP 5.7 2.7 - - - +
311M PHE* 4.6 0.4 - - - -
314M SER 4.4 1.8 + - - +
315M LEU* 1.3 73.4 - - - +
317M ALA* 1.3 62.1 + - - +
318M GLN* 3.9 7.3 + - + +
357M ARG* 3.5 54.3 - - + +
358M MET 3.9 1.1 - - - -
359M ALA* 3.8 27.8 - - + +
391M GLU 4.3 0.7 - - - +
393M PRO* 3.4 25.2 - - - +
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Residues in contact with ALA 317 (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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287M PHE* 3.8 18.2 - - + -
311M PHE* 3.3 27.8 - - + -
316M LEU* 1.3 74.1 - - - +
318M GLN* 1.3 61.4 + - - +
320M ILE* 4.0 4.6 - - + +
357M ARG* 3.4 4.9 - - - -
358M MET 2.9 34.1 + - - +
391M GLU 3.2 11.9 - - - +
392M VAL* 3.7 11.9 - - + -
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Residues in contact with GLN 318 (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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316M LEU* 4.2 9.6 - - + +
317M ALA* 1.3 77.1 - - - +
319M LYS* 1.3 77.8 + - + +
320M ILE* 3.1 7.3 - - - +
356M LYS 3.3 10.8 - - - +
357M ARG* 2.9 42.1 + - - +
391M GLU* 2.8 50.5 + - + +
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Residues in contact with LYS 319 (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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318M GLN* 1.3 88.3 - - + +
320M ILE* 1.3 65.5 + - - +
321M GLU* 3.4 7.7 + - - +
355M ILE 4.4 1.8 - - - -
356M LYS* 3.4 9.0 + - - +
389M ASN* 3.6 15.1 - - - +
390M PHE* 3.9 1.5 - - - -
391M GLU* 3.1 34.6 + - + +
427M ARG* 5.8 4.2 - - - +
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Residues in contact with ILE 320 (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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287M PHE* 3.7 18.4 - - + -
307M ILE* 4.3 15.0 - - + -
317M ALA* 4.0 6.5 - - + +
318M GLN* 3.2 29.2 - - - +
319M LYS* 1.3 76.9 - - - +
321M GLU* 1.3 68.0 + - - +
322M VAL* 4.6 1.1 - - + -
353M TRP 5.4 0.4 - - - +
354M LYS* 3.4 5.2 - - - +
355M ILE* 3.0 58.1 + - + +
358M MET* 4.9 4.5 - - + +
388M MET* 3.9 22.9 - - + -
389M ASN 3.3 2.7 - - - -
390M PHE* 3.3 23.6 - - + -
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Residues in contact with GLU 321 (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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319M LYS 3.4 7.5 + - - +
320M ILE* 1.3 79.6 - - - +
322M VAL* 1.3 67.2 + - - +
323M ARG* 4.0 19.2 + - + +
352M VAL* 4.1 7.4 - - + +
353M TRP 3.2 7.0 - - - +
354M LYS* 3.5 33.3 - - + +
388M MET* 3.3 10.3 - - - +
389M ASN* 3.1 54.6 + - + +
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Residues in contact with VAL 322 (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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289M VAL* 5.1 0.7 - - + -
305M VAL* 4.5 8.3 - - + -
307M ILE* 3.9 28.9 - - + -
320M ILE* 4.6 2.7 - - + -
321M GLU* 1.3 79.7 - - - +
323M ARG* 1.3 61.6 + - - +
324M ILE* 3.9 13.3 + - + +
351M ILE 3.7 0.9 - - - +
352M VAL* 3.5 5.1 - - - +
353M TRP* 2.7 65.3 + - + +
355M ILE* 5.7 0.2 - - + -
386M ILE* 3.6 24.9 - - + -
387M SER 3.7 3.6 - - - +
388M MET* 4.0 13.5 - - + -
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Residues in contact with ARG 323 (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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321M GLU* 4.0 18.2 + - + +
322M VAL* 1.3 72.2 - - - +
324M ILE* 1.3 58.8 + - - +
325M PRO* 3.6 5.2 - - + +
345M LYS* 5.1 2.6 - - - +
348M GLU* 3.3 37.0 + - - +
350M ALA* 4.3 18.1 - - + +
351M ILE 3.4 4.5 - - - +
352M VAL* 3.5 29.4 - - - +
385M PRO 4.3 0.7 - - - +
386M ILE* 3.5 6.9 - - - -
387M SER* 2.9 49.1 + - - +
389M ASN* 5.9 0.8 - - - +
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Residues in contact with ILE 324 (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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303M VAL* 3.9 25.6 - - + +
305M VAL* 3.5 34.1 - - + -
322M VAL* 4.1 16.6 - - + +
323M ARG* 1.3 71.9 - - - +
325M PRO* 1.3 72.6 - - + +
326M THR* 5.5 0.4 - - + -
350M ALA* 4.3 1.1 - - - -
351M ILE* 2.6 59.0 + - + +
353M TRP* 5.2 1.8 - - + -
366M ILE* 3.6 25.8 - - + -
370M ILE* 6.1 0.2 - - + -
386M ILE* 4.3 14.1 - - + -
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Residues in contact with PRO 325 (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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303M VAL* 5.9 0.9 - - - +
323M ARG* 3.6 10.9 - - + +
324M ILE* 1.3 97.3 - - + +
326M THR* 1.3 68.4 + - - +
349M ASN 3.4 11.0 - - - +
350M ALA* 3.9 6.7 - - + -
370M ILE* 5.2 1.7 - - - +
381M TRP* 4.3 10.8 - - + -
384M PRO* 3.4 48.0 - - + +
385M PRO 3.9 11.2 - - - +
386M ILE* 4.1 8.7 - - + -
435M CYS* 5.5 3.4 - - - -
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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