Contacts of the strand formed by residues 363 - 371 (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 GLU 363 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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426A LEU* 3.9 21.4 - - - +
456A TYR 3.9 10.6 - - - +
458A SER* 3.7 43.6 + - - +
459A GLU* 5.5 0.9 - - - +
306M VAL* 3.8 23.6 - - + +
307M ILE 3.6 6.3 - - - -
308M LYS* 3.6 23.7 - - + +
358M MET* 4.0 2.2 - - - +
362M LYS* 1.3 80.2 - - - +
364M SER* 1.3 74.3 + - - +
365M GLN* 5.4 3.1 - - - +
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Residues in contact with SER 364 (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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306M VAL* 3.3 6.4 - - - +
307M ILE* 3.0 39.9 + - - -
339M LYS* 3.7 25.4 + - - +
353M TRP* 3.9 20.8 - - - -
355M ILE* 4.6 2.9 - - - +
358M MET* 4.3 12.7 - - - +
363M GLU* 1.3 81.9 + - - +
365M GLN* 1.3 62.2 + - - +
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Residues in contact with GLN 365 (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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426A LEU* 5.2 0.9 - - - +
430A ILE* 4.1 20.7 - - - +
433A GLU* 4.3 15.0 + - - -
460A GLU* 4.7 17.2 + - - +
304M LYS* 5.0 15.6 - - - +
305M VAL 3.5 4.3 - - - -
306M VAL* 3.7 23.7 - - + +
336M ILE 4.4 0.4 - - - +
337M CYS* 3.8 18.5 - - - +
338M MET 4.2 4.9 + - - -
339M LYS* 5.3 0.7 + - - +
353M TRP* 3.7 6.4 - - - -
363M GLU* 5.4 4.3 - - + +
364M SER* 1.3 78.8 - - - +
366M ILE* 1.3 73.2 + - - +
367M SER* 4.7 5.2 + - - +
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Residues in contact with ILE 366 (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 5.7 1.1 - - - +
304M LYS* 3.6 2.6 - - - +
305M VAL* 2.9 41.3 + - + +
324M ILE* 3.6 27.8 - - + -
335M VAL* 3.7 15.0 - - + -
336M ILE 3.6 10.5 - - - +
337M CYS* 4.1 3.4 - - + -
342M ALA* 3.6 31.2 - - + -
351M ILE* 4.2 13.0 - - + -
353M TRP* 3.6 36.0 - - + -
365M GLN* 1.3 82.3 - - - +
367M SER* 1.3 68.6 + - - +
368M ALA* 5.5 0.9 - - + -
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Residues in contact with SER 367 (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 3.8 4.9 - - - -
304M LYS* 3.5 33.0 - - - -
335M VAL* 3.5 2.8 - - - +
336M ILE* 2.7 66.2 + - - +
365M GLN* 5.2 6.9 + - - +
366M ILE* 1.3 77.0 - - - +
368M ALA* 1.3 59.6 + - - +
369M GLU* 6.5 0.2 - - - -
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Residues in contact with ALA 368 (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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302M GLU* 4.3 2.3 - - - +
303M VAL* 2.8 37.7 + - + +
304M LYS* 5.4 0.9 + - - +
324M ILE* 6.5 0.7 - - + -
333M VAL* 4.0 4.3 - - + -
334M GLN 3.4 5.8 - - - -
335M VAL* 3.4 26.0 - - + -
351M ILE* 3.8 17.9 - - + -
366M ILE* 5.5 2.0 - - + +
367M SER* 1.3 76.2 - - - +
369M GLU* 1.3 68.0 + - - +
370M ILE* 4.2 5.8 - - + -
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Residues in contact with GLU 369 (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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434A LYS* 5.5 7.7 - - - -
301M LEU 4.1 3.1 - - - -
302M GLU* 4.8 16.4 - - + +
304M LYS* 5.2 7.7 + - - +
332M GLY 4.2 0.2 - - - +
333M VAL* 3.6 3.2 - - - -
334M GLN* 2.9 47.5 + - + +
367M SER* 6.5 0.2 - - - -
368M ALA* 1.3 78.1 - - - +
370M ILE* 1.3 63.5 + - - +
371M GLU* 5.3 1.0 - - - +
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Residues in contact with ILE 370 (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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300M LYS* 3.7 7.1 - - - +
301M LEU* 3.0 47.1 + - + +
303M VAL* 3.4 34.3 - - + -
324M ILE* 6.1 0.4 - - + -
325M PRO 5.2 1.3 - - - +
326M THR* 3.8 22.2 - - + -
327M PRO* 4.7 2.9 - - + -
330M THR* 3.4 27.8 - - + +
332M GLY 3.8 3.8 - - - +
333M VAL* 4.3 17.0 - - + -
351M ILE* 4.8 4.9 - - + -
368M ALA* 4.6 3.6 - - + -
369M GLU* 1.3 78.2 - - - +
371M GLU* 1.3 66.7 + - - +
372M LEU* 3.8 16.6 - - + -
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Residues in contact with GLU 371 (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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299M THR* 4.0 4.0 - - - +
300M LYS* 3.5 39.8 + - - +
330M THR* 3.1 8.0 - - - +
331M SER* 2.7 45.4 + - - +
332M GLY 3.2 19.1 + - - +
369M GLU 5.3 0.7 - - - +
370M ILE* 1.3 78.7 - - - +
372M LEU* 1.3 60.5 + - - +
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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