Contacts of the helix formed by residues 312 - 322 (chain M) in PDB entry 2QJK
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 312 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307M ALA 3.7 24.0 - - - +
308M PHE* 4.0 17.0 - - + -
309M THR* 3.0 23.6 + - - +
310M ALA 3.4 0.2 - - - -
311M ASP* 1.3 80.2 - - - +
313M TRP* 1.3 71.2 + - - +
314M VAL* 3.8 21.8 - - + +
315M VAL* 3.1 27.8 - - + +
316M GLN* 3.1 9.7 + - - +
394M LEU* 3.9 25.4 - - + -
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Residues in contact with TRP 313 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313J TRP* 3.5 80.2 - + + +
316J GLN* 3.6 27.3 + - + -
317J ILE* 4.2 24.2 - - + -
311M ASP 4.3 6.8 + - - -
312M VAL* 1.3 73.7 - - + +
314M VAL* 1.3 61.6 + - + +
316M GLN* 2.6 38.2 + - - +
317M ILE* 2.9 13.6 + - + +
391M TRP* 6.5 0.9 - + - -
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Residues in contact with VAL 314 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308M PHE* 5.5 5.2 - - + -
312M VAL* 4.1 12.6 - - + -
313M TRP* 1.3 78.2 - - + +
315M VAL* 1.3 63.1 + - - +
317M ILE* 3.4 20.3 - - + +
318M ALA* 3.2 20.8 + - - +
331M PHE* 3.9 21.7 - - + -
394M LEU* 6.6 0.2 - - + -
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Residues in contact with VAL 315 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308M PHE* 3.8 16.6 - - + -
309M THR 3.9 17.5 - - - +
310M ALA* 4.4 6.7 - - - -
312M VAL* 3.1 21.0 + - + +
313M TRP 2.9 0.2 + - - -
314M VAL* 1.3 80.3 - - - +
316M GLN* 1.3 55.7 + - + +
318M ALA* 3.0 7.1 + - - +
319M ASN* 2.7 34.8 + - + +
326M ILE 4.4 1.2 - - - +
327M ASP 4.9 2.2 - - - -
328M ALA* 4.2 22.4 - - + +
331M PHE* 3.4 43.7 - - + -
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Residues in contact with GLN 316 (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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313J TRP* 4.2 15.8 + - + +
310M ALA 4.1 18.4 + - - +
311M ASP* 3.8 9.6 - - - +
312M VAL 3.4 21.3 - - - +
313M TRP* 2.6 26.9 + - - +
315M VAL* 1.3 72.6 - - + +
317M ILE* 1.3 68.4 + - - +
319M ASN* 3.2 9.7 + - + +
320M PHE* 3.0 20.3 + - - +
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Residues in contact with ILE 317 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313J TRP* 4.1 21.3 - - + -
313M TRP* 2.9 12.7 + - + +
314M VAL* 3.4 28.0 - - + +
316M GLN* 1.3 74.9 - - - +
318M ALA* 1.3 55.1 + - - +
320M PHE* 2.8 28.2 + - + +
321M ILE* 2.9 39.9 + - + +
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Residues in contact with ALA 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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314M VAL 3.2 9.4 + - - +
315M VAL 3.0 12.1 - - - +
317M ILE* 1.3 76.6 - - - +
319M ASN* 1.3 62.1 + - - +
320M PHE 3.0 2.3 + - - -
321M ILE* 3.5 10.7 + - - +
322M SER* 2.8 29.7 + - - -
326M ILE* 4.1 16.5 - - + +
331M PHE* 4.0 23.6 - - + -
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Residues in contact with ASN 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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315M VAL* 2.7 18.6 + - + +
316M GLN* 3.2 13.0 + - + +
318M ALA* 1.3 73.0 - - - +
320M PHE* 1.3 59.7 + - - +
322M SER* 3.4 3.9 + - - -
324M GLY* 2.9 53.7 + - - +
326M ILE 3.5 14.5 + - - +
327M ASP* 4.4 10.5 - - - +
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Residues in contact with PHE 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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391J TRP* 6.5 1.3 - + - -
316M GLN 3.0 10.8 + - - +
317M ILE* 2.8 17.0 + - + +
319M ASN* 1.3 75.2 - - - +
321M ILE* 1.3 68.6 + - + -
322M SER 2.9 6.2 + - - -
323M PHE* 3.0 16.6 + - - -
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Residues in contact with ILE 321 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317M ILE* 2.9 42.6 + - + +
318M ALA* 4.2 7.6 - - - +
320M PHE* 1.3 81.7 - - + +
322M SER* 1.3 56.7 + - - +
323M PHE* 3.4 19.7 - - - -
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Residues in contact with SER 322 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318M ALA 2.8 20.8 + - - -
319M ASN 3.4 6.9 + - - -
320M PHE 2.9 1.2 + - - -
321M ILE* 1.3 76.6 - - - +
323M PHE* 1.3 73.8 + - - +
325M ILE* 3.2 23.2 + - - +
326M ILE* 2.9 46.4 + - - +
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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