Contacts of the helix formed by residues 301 - 311 (chain K) in PDB entry 3E20
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 GLY 301 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300K PHE* 1.3 75.6 + - - -
302K VAL* 1.3 55.1 + - - -
303K VAL* 3.6 2.1 - - - +
304K ASP* 4.2 7.0 + - - +
305K THR* 2.2 45.1 + - - -
405K PHE 4.2 5.2 - - - -
406K GLY* 5.9 0.4 - - - -
408K ILE* 3.0 21.5 - - - -
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Residues in contact with VAL 302 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301K GLY* 1.3 70.5 - - - +
303K VAL* 1.3 77.2 + - + +
305K THR* 4.1 1.2 - - - -
306K MET* 3.2 32.0 + - - +
323K LEU* 5.5 0.4 - - + -
325K MET* 3.8 41.5 - - + -
341K TYR* 5.6 6.7 - - + -
373K LEU* 4.8 6.5 - - + -
406K GLY* 5.5 2.0 - - - +
408K ILE* 3.5 25.2 - - + +
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Residues in contact with VAL 303 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301K GLY 5.2 1.6 - - - +
302K VAL* 1.3 86.8 - - + +
304K ASP* 1.3 76.2 + - - +
306K MET* 3.7 4.1 + - - +
307K ASN* 3.2 36.6 + - - +
341K TYR* 5.5 8.3 - - + -
420K MET* 4.5 10.3 - - + +
421K LEU 5.3 3.1 - - - +
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Residues in contact with ASP 304 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299K CYS* 4.1 18.5 - - + +
300K PHE 4.1 12.4 - - - +
301K GLY 3.7 3.8 + - - +
302K VAL 3.3 0.4 - - - -
303K VAL* 1.3 93.5 - - - +
305K THR* 1.3 54.7 + - - +
307K ASN* 3.1 10.7 + - - +
308K ALA* 2.7 35.5 + - - +
418K LEU* 3.8 34.3 - - + +
420K MET 5.5 0.3 - - - +
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Residues in contact with THR 305 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299K CYS* 3.7 3.9 - - - +
300K PHE 3.5 5.9 + - - -
301K GLY 2.2 37.0 + - - -
302K VAL 4.1 1.8 - - - -
304K ASP* 1.3 73.2 - - - +
306K MET* 1.3 61.0 + - + +
308K ALA* 3.1 7.8 + - - +
309K LEU* 2.9 28.4 + - - +
314K VAL* 4.6 0.4 - - + +
317K LEU* 3.5 31.6 - - + -
408K ILE* 3.2 21.7 + - + -
409K GLY* 3.4 20.2 - - - -
410K ALA* 4.2 7.0 - - + +
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Residues in contact with MET 306 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302K VAL 3.2 18.8 + - - +
303K VAL 4.0 3.4 - - - +
305K THR* 1.3 88.6 - - + +
307K ASN* 1.3 55.8 + - - +
309K LEU* 3.8 16.2 - - + +
310K GLN* 2.7 35.1 + - - +
317K LEU* 5.2 1.1 - - + -
327K ARG* 5.8 0.7 - - - -
341K TYR* 3.3 40.6 - - + +
373K LEU* 4.1 23.6 - - + -
376K TRP* 4.9 10.3 - - - -
377K LEU* 3.5 31.4 - - + -
408K ILE* 4.6 4.7 - - + -
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Residues in contact with ASN 307 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303K VAL* 3.2 23.1 + - - +
304K ASP* 3.1 14.8 + - - +
306K MET* 1.3 77.4 - - - +
308K ALA* 1.3 55.6 + - - +
310K GLN* 3.3 10.8 - - - +
311K GLU* 2.7 43.2 + - + +
418K LEU* 5.6 6.0 - - + +
419K SER 3.5 12.0 + - - +
420K MET* 2.8 50.4 + - - +
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Residues in contact with ALA 308 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299K CYS* 4.0 6.5 - - - -
304K ASP 2.7 15.4 + - - +
305K THR* 3.3 10.1 - - - +
307K ASN* 1.3 72.9 - - - +
309K LEU* 1.3 53.1 + - - +
311K GLU* 2.4 30.0 - - - +
313K ALA 4.0 5.7 + - - +
314K VAL* 3.5 19.0 - - + +
412K MET* 3.1 35.7 - - + -
416K LEU* 5.9 4.1 - - - +
418K LEU* 5.5 2.2 - - - +
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Residues in contact with LEU 309 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305K THR* 2.9 15.9 + - + +
306K MET* 3.8 21.3 - - + +
308K ALA* 1.3 72.5 - - - +
310K GLN* 1.3 69.1 + - - +
311K GLU 3.3 5.2 - - - +
312K GLY 4.0 4.5 - - - +
313K ALA* 4.8 0.9 - - - -
314K VAL* 3.5 32.0 - - + +
317K LEU* 3.9 22.7 - - + -
376K TRP* 5.0 3.1 - - + -
377K LEU* 4.0 9.4 - - + -
381K TYR* 5.2 4.9 - - - +
384K TYR* 3.3 66.4 - - + +
386K ALA* 4.5 8.1 - - + -
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Residues in contact with GLN 310 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306K MET 2.7 23.4 + - - +
307K ASN* 3.3 15.3 - - - +
309K LEU* 1.3 77.4 - - - +
311K GLU* 1.3 79.4 + - + +
312K GLY 4.3 1.9 - - - +
339K ILE* 5.9 4.8 - - - +
384K TYR* 4.6 19.8 + - - -
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Residues in contact with GLU 311 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307K ASN* 2.7 27.0 + - + +
308K ALA* 2.4 26.5 - - - +
309K LEU 3.3 0.9 - - - +
310K GLN* 1.3 99.2 - - + +
312K GLY* 1.3 69.0 + - - +
313K ALA 3.6 0.2 - - - -
416K LEU* 4.7 15.7 - - + -
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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