Contacts of the helix formed by residues 301 - 311 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300H PHE* 1.3 82.2 - - - +
302H VAL* 1.3 59.8 + - - -
303H VAL* 3.5 5.6 - - - -
304H ASP* 4.4 7.2 - - - -
305H THR* 2.0 43.5 + - - -
405H PHE 4.3 3.9 + - - -
408H ILE 3.1 10.8 + - - +
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Residues in contact with VAL 302 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301H GLY* 1.3 68.5 - - - +
303H VAL* 1.3 79.8 + - + +
305H THR* 4.1 1.2 - - - -
306H MET* 3.2 31.4 + - - +
323H LEU* 5.4 0.2 - - + -
325H MET* 3.8 41.5 - - + -
341H TYR* 5.6 6.7 - - + -
373H LEU* 4.7 7.2 - - + -
406H GLY* 5.5 2.2 - - - +
408H ILE* 3.6 26.2 - - + +
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Residues in contact with VAL 303 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301H GLY* 5.0 2.5 - - - -
302H VAL* 1.3 87.4 - - + +
304H ASP* 1.3 76.9 + - + +
306H MET* 3.6 4.3 + - - +
307H ASN* 3.2 41.6 + - - +
341H TYR* 5.5 9.0 - - + -
420H MET* 4.5 9.9 - - + +
421H LEU 5.3 3.1 - - - +
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Residues in contact with ASP 304 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299H CYS* 4.2 10.0 - - + +
300H PHE 4.1 20.7 - - - +
301H GLY* 3.9 2.5 + - - -
302H VAL 3.3 0.4 - - - -
303H VAL* 1.3 94.4 - - - +
305H THR* 1.3 54.4 + - - +
307H ASN* 3.1 10.3 + - - +
308H ALA* 2.7 34.7 + - - +
418H LEU* 3.8 35.1 - - + +
420H MET 5.5 0.3 - - - +
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Residues in contact with THR 305 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299H CYS* 4.0 5.2 - - - +
300H PHE 3.8 2.3 + - - -
301H GLY 2.0 32.3 + - - -
302H VAL 4.1 1.6 - - - -
304H ASP* 1.3 76.8 - - - +
306H MET* 1.3 62.7 + - + +
308H ALA* 3.2 6.8 + - + +
309H LEU* 2.9 28.1 + - - +
314H VAL* 4.6 0.8 - - + +
317H LEU* 3.6 31.9 - - + -
408H ILE* 3.2 22.3 + - + -
409H GLY* 3.4 20.1 - - - -
410H ALA* 4.2 6.5 - - + +
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Residues in contact with MET 306 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302H VAL 3.2 17.7 + - - +
303H VAL 3.9 3.6 - - - +
305H THR* 1.3 89.4 - - + +
307H ASN* 1.3 56.4 + - - +
309H LEU* 3.8 16.5 - - + +
310H GLN* 2.7 35.4 + - - +
317H LEU* 5.2 1.3 - - + -
327H ARG* 5.8 0.4 - - - -
341H TYR* 3.3 40.4 - - + +
373H LEU* 4.1 23.8 - - + -
376H TRP* 4.9 9.9 - - - -
377H LEU* 3.5 31.6 - - + -
408H ILE* 4.6 4.5 - - + -
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Residues in contact with ASN 307 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303H VAL* 3.2 24.3 + - - +
304H ASP* 3.1 14.1 + - - +
306H MET* 1.3 75.7 - - - +
308H ALA* 1.3 56.3 + - - +
310H GLN* 3.2 11.1 - - - +
311H GLU* 2.6 44.3 + - + +
418H LEU* 5.6 6.0 - - + +
419H SER 3.6 11.2 + - - +
420H MET* 2.9 52.4 + - - +
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Residues in contact with ALA 308 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299H CYS* 4.1 6.3 - - - -
304H ASP 2.7 15.0 + - - +
305H THR* 3.2 9.8 + - - +
307H ASN* 1.3 74.2 - - - +
309H LEU* 1.3 53.8 + - - +
311H GLU* 2.4 29.7 - - - +
313H ALA 4.0 5.5 + - - +
314H VAL* 3.5 19.2 - - + +
412H MET* 3.2 35.9 - - + -
416H LEU* 5.9 3.3 - - - +
418H LEU* 5.6 1.9 - - - +
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Residues in contact with LEU 309 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305H THR* 2.9 17.2 + - + +
306H MET* 3.8 22.0 - - + +
308H ALA* 1.3 73.2 - - - +
310H GLN* 1.3 68.1 + - - +
311H GLU 3.3 5.0 - - - +
312H GLY 4.0 5.0 - - - +
313H ALA* 4.9 0.3 - - - -
314H VAL* 3.5 32.0 - - + +
317H LEU* 3.9 22.9 - - + -
376H TRP* 5.0 3.6 - - + -
377H LEU* 4.0 8.7 - - + -
381H TYR* 5.2 5.2 - - - +
384H TYR* 3.3 66.4 - - + +
386H ALA* 4.6 8.5 - - + -
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Residues in contact with GLN 310 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306H MET 2.7 20.4 + - - +
307H ASN* 3.2 14.6 - - - +
309H LEU* 1.3 79.7 - - - +
311H GLU* 1.3 80.4 + - + +
312H GLY 4.0 2.1 + - - +
339H ILE* 5.9 4.9 - - - +
384H TYR* 4.6 20.1 + - - -
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Residues in contact with GLU 311 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307H ASN* 2.6 26.4 + - + +
308H ALA* 2.4 29.6 - - - +
309H LEU 3.3 0.9 - - - +
310H GLN* 1.3 100.4 - - + +
312H GLY* 1.3 67.8 + - - +
416H LEU* 4.8 15.0 - - + -
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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