Contacts of the helix formed by residues 274 - 293 (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 ASN 274 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275H VAL* 1.3 72.4 + - - +
276H LYS 3.1 2.9 - - - -
277H TYR* 2.8 35.3 + - + +
278H VAL* 2.7 46.2 + - + +
281H LYS* 5.8 6.7 - - - +
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Residues in contact with VAL 275 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274H ASN* 1.3 76.6 - - - +
276H LYS* 1.3 81.7 + - + +
278H VAL* 3.0 22.6 - - - +
279H GLN* 4.3 6.8 + - - +
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Residues in contact with LYS 276 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H ARG* 5.6 7.1 - - - +
137H LEU 5.7 6.9 - - - -
274H ASN 2.9 1.0 + - - -
275H VAL* 1.3 100.5 - - + +
277H TYR* 1.3 81.3 + - + +
278H VAL 3.5 0.2 - - - -
279H GLN* 4.1 3.4 + - - +
280H GLU* 3.6 18.5 + - - +
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Residues in contact with TYR 277 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274H ASN* 2.8 40.9 + - + +
276H LYS* 1.3 90.3 - - + +
278H VAL* 1.3 60.3 + - - +
279H GLN 3.2 2.2 - - - -
280H GLU* 3.2 18.1 + - - +
281H LYS* 2.9 37.4 + - + +
392H SER* 5.7 1.6 - - - -
394H ARG* 3.6 40.6 - - + +
395H SER* 4.8 8.7 - - - -
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Residues in contact with VAL 278 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274H ASN* 2.7 38.3 + - + +
275H VAL* 3.0 27.4 - - - +
277H TYR* 1.3 72.8 - - - +
279H GLN* 1.3 63.9 + - + +
281H LYS* 3.7 8.2 + - + +
282H LYS* 2.9 29.7 + - - +
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Residues in contact with GLN 279 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H ALA* 4.4 14.1 + - - +
275H VAL 4.7 4.7 - - - +
276H LYS 4.1 6.6 + - - +
277H TYR 3.2 0.2 - - - -
278H VAL* 1.3 85.8 - - + +
280H GLU* 1.3 59.4 + - - +
282H LYS* 3.5 17.4 - - + +
283H LEU* 2.7 39.2 + - + +
389H GLU* 4.3 15.2 - - - +
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Residues in contact with GLU 280 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276H LYS 3.6 13.9 + - - +
277H TYR* 3.3 18.6 - - - +
279H GLN* 1.3 79.4 - - - +
281H LYS* 1.3 61.1 + - - +
283H LEU* 4.0 3.1 - - - +
284H ILE* 3.2 30.2 + - + +
390H PHE 4.6 1.5 - - - +
391H VAL* 3.3 25.7 - - + +
392H SER* 2.5 52.0 + - - +
395H SER* 2.7 35.4 + - - +
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Residues in contact with LYS 281 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274H ASN* 5.8 7.1 - - - +
277H TYR* 2.9 22.1 + - + +
278H VAL* 3.8 6.7 - - + +
280H GLU* 1.3 73.0 - - - +
282H LYS* 1.3 67.7 + - - +
284H ILE* 2.8 14.6 + - - +
285H GLN* 2.9 15.1 + - + +
395H SER* 3.3 30.5 - - - -
396H GLN* 5.2 3.3 - - - +
397H GLU* 3.2 43.3 - - - +
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Residues in contact with LYS 282 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278H VAL 2.9 23.1 + - - +
279H GLN* 3.1 19.4 + - + +
281H LYS* 1.3 73.6 - - - +
283H LEU* 1.3 62.4 + - - +
285H GLN* 3.3 10.1 + - - +
286H ARG* 3.3 17.7 + - - +
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Residues in contact with LEU 283 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279H GLN* 2.7 22.5 + - + +
280H GLU* 4.0 3.6 - - - +
282H LYS* 1.3 71.2 - - - +
284H ILE* 1.3 64.1 + - + +
286H ARG* 3.0 56.2 - - - +
287H PHE* 3.2 6.6 + - - +
316H THR* 3.8 15.0 - - + -
318H LEU* 3.3 30.3 - - + -
389H GLU* 3.3 39.0 - - + +
391H VAL* 5.1 6.1 - - + -
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Residues in contact with ILE 284 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280H GLU* 3.2 15.7 + - + +
281H LYS 2.8 7.2 + - - +
283H LEU* 1.3 76.6 - - - +
285H GLN* 1.3 51.1 + - - +
287H PHE* 3.2 7.5 + - + +
288H PHE* 2.7 61.3 + - + -
318H LEU* 3.9 20.2 - - + -
391H VAL* 4.3 16.2 - - + -
397H GLU* 3.8 9.0 - - + -
398H GLY* 3.7 23.1 - - - +
401H PHE* 3.6 35.2 - - + -
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Residues in contact with GLN 285 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570E PRO 5.1 1.0 + - - -
571E SER* 3.6 31.2 + - - -
572E ILE* 5.1 1.9 + - - +
281H LYS 2.9 10.4 + - - +
282H LYS* 3.4 12.8 - - - +
283H LEU 3.1 0.2 - - - -
284H ILE* 1.3 74.2 - - - +
286H ARG* 1.3 59.6 + - - +
288H PHE* 3.0 25.8 + - - +
289H ASP* 2.8 45.7 + - - +
397H GLU* 3.6 26.9 - - + +
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Residues in contact with ARG 286 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282H LYS 3.3 6.8 + - - +
283H LEU* 3.0 41.4 + - - +
285H GLN* 1.3 79.5 - - - +
287H PHE* 1.3 58.2 + - - +
289H ASP* 3.5 16.2 + - - +
290H GLU* 3.6 16.6 + - + +
315H GLU* 2.8 27.8 + - - -
316H THR* 3.6 9.9 + - - +
411H VAL* 3.7 31.1 - - + +
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Residues in contact with PHE 287 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283H LEU 3.2 2.7 + - - +
284H ILE* 3.2 10.7 + - + +
286H ARG* 1.3 76.2 - - - +
288H PHE* 1.3 77.9 + + - +
290H GLU* 3.1 18.2 + - - +
291H ILE* 3.6 29.7 - - + +
298H TYR* 3.9 13.2 - + + -
299H CYS 3.9 21.1 - - - -
300H PHE* 4.0 24.2 - - + -
318H LEU* 3.8 24.5 - - + -
401H PHE* 4.1 20.6 - + - -
405H PHE* 4.0 20.0 - + - -
410H ALA 4.1 10.1 - - - -
411H VAL* 3.4 27.8 - - + +
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Residues in contact with PHE 288 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571E SER* 5.4 0.2 - - - +
572E ILE* 3.4 28.2 - - + +
574E THR* 4.4 1.8 - - - -
284H ILE* 2.7 39.4 + - + +
285H GLN* 3.0 31.8 + - - +
287H PHE* 1.3 89.8 - + - +
289H ASP* 1.3 52.4 + - - +
291H ILE* 2.7 31.9 + - + +
292H SER* 2.8 15.1 + - - -
397H GLU* 4.0 13.9 - - + -
400H GLN* 3.7 42.0 - - + -
401H PHE* 4.5 1.8 - - - -
405H PHE* 3.5 28.9 - + - -
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Residues in contact with ASP 289 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571E SER* 4.3 9.5 + - - -
285H GLN* 2.8 39.3 + - - +
286H ARG* 3.7 11.3 - - - +
287H PHE 3.3 0.4 - - - -
288H PHE* 1.3 73.9 - - - +
290H GLU* 1.3 62.0 + - - +
291H ILE 3.0 0.2 - - - -
292H SER* 4.0 8.7 - - - -
293H LEU* 2.8 39.4 + - + +
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Residues in contact with GLU 290 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286H ARG* 3.6 15.1 - - + +
287H PHE* 3.1 9.8 + - - +
288H PHE 3.0 1.2 - - - -
289H ASP* 1.3 80.3 - - - +
291H ILE* 1.3 59.5 + - - +
293H LEU* 5.3 4.0 - - - +
294H ASP* 4.3 4.1 - - - +
295H SER* 2.2 45.0 + - - +
297H LYS* 2.8 40.2 - - + +
298H TYR* 3.5 23.3 - - + -
411H VAL* 4.6 11.9 - - + -
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Residues in contact with ILE 291 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572E ILE* 4.0 8.7 - - + -
611E MET* 4.9 9.2 - - + -
612E PHE* 3.3 38.8 - - + -
287H PHE* 3.6 31.6 - - + +
288H PHE* 2.7 17.1 + - + +
290H GLU* 1.3 77.8 - - - +
292H SER* 1.3 66.4 + - - +
293H LEU 3.4 1.6 - - - -
294H ASP* 3.4 12.9 + - - +
298H TYR* 3.3 42.4 - - + +
405H PHE* 3.7 23.8 - - + -
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Residues in contact with SER 292 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571E SER* 3.1 24.7 + - - -
572E ILE* 3.5 18.4 - - - +
612E PHE* 4.1 19.1 - - - -
614E THR* 5.7 1.7 + - - -
288H PHE 2.8 12.5 + - - -
289H ASP* 3.8 11.7 - - - -
291H ILE* 1.3 79.6 - - - +
293H LEU* 1.3 63.7 + - - +
294H ASP* 4.9 0.9 - - - +
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Residues in contact with LEU 293 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289H ASP* 2.8 22.4 + - + +
290H GLU* 5.3 4.0 - - - +
292H SER* 1.3 77.7 - - - +
294H ASP* 1.3 74.1 + - - +
295H SER* 4.8 9.0 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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