Contacts of the helix formed by residues 314 - 327 (chain H) in PDB entry 5TJ4
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 ASP 314 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310H GLU 4.6 0.2 + - - -
311H LEU* 2.9 16.6 + - + +
312H ALA 3.6 6.9 - - - +
313H LYS* 1.3 77.5 - - - +
315H PRO* 1.4 72.8 - - - +
316H ARG* 2.7 68.4 + - - +
317H ILE* 3.4 13.6 + - + +
318H ALA* 3.4 16.1 + - - +
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Residues in contact with PRO 315 (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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244H VAL 4.8 2.2 - - - +
313H LYS 3.5 7.2 - - - +
314H ASP* 1.4 91.6 - - - +
316H ARG* 1.3 60.2 + - + +
318H ALA* 3.4 9.3 + - + +
319H ALA* 3.0 26.2 + - - +
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Residues in contact with ARG 316 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232H TRP* 3.5 52.1 - - + +
236H ASP* 3.6 13.5 + - - -
242H TYR* 2.7 46.8 + - + -
244H VAL* 3.7 23.3 - - + +
298H PRO* 5.3 4.9 - - - +
314H ASP* 2.7 37.2 + - - +
315H PRO* 1.3 72.7 - - + +
317H ILE* 1.3 58.9 + - - +
319H ALA* 3.4 4.0 + - - +
320H THR* 3.0 29.1 + - - -
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Residues in contact with ILE 317 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232H TRP* 4.0 21.1 - - + -
294H ASN* 5.9 1.1 - - - +
298H PRO* 6.0 0.9 - - + -
300H GLY* 3.5 29.6 - - - +
301H ALA* 3.9 25.1 - - + +
308H GLU* 4.2 11.7 - - - +
311H LEU* 3.5 33.4 - - + +
312H ALA* 4.5 5.4 - - - -
314H ASP* 3.4 18.8 + - + +
315H PRO 3.4 0.4 - - - -
316H ARG* 1.3 73.6 - - - +
318H ALA* 1.3 59.8 + - - +
320H THR* 3.1 7.6 + - - +
321H MET* 2.9 31.5 + - + +
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Residues in contact with ALA 318 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312H ALA* 4.9 7.5 + - - +
314H ASP 3.4 10.5 + - - +
315H PRO* 3.5 13.2 - - + +
316H ARG 3.3 0.2 - - - -
317H ILE* 1.3 79.8 - - - +
319H ALA* 1.3 55.1 + - - +
321H MET* 3.3 6.4 + - - +
322H GLU* 3.0 29.3 + - - +
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Residues in contact with ALA 319 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H SER* 4.4 0.2 - - - -
244H VAL* 3.3 38.8 - - + +
245H THR* 4.0 9.9 - - - +
246H VAL* 4.9 2.1 - - - +
315H PRO 3.0 11.7 + - - +
316H ARG 3.5 9.0 - - - +
318H ALA* 1.3 72.1 - - - +
320H THR* 1.3 64.7 + - - +
322H GLU* 3.4 7.2 + - - +
323H ASN* 2.9 31.1 + - - -
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Residues in contact with THR 320 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110H VAL 4.6 4.0 - - - +
112H ALA* 3.8 28.9 + - + +
114H SER* 3.3 19.5 + - - -
229H PRO* 4.2 11.4 - - + +
232H TRP* 3.6 16.9 - - - -
301H ALA* 5.0 3.6 - - + +
316H ARG 3.0 13.6 + - - -
317H ILE* 3.4 11.9 - - - -
319H ALA* 1.3 76.0 - - - +
321H MET* 1.3 76.6 + - + +
323H ASN* 3.2 5.2 + - - +
324H ALA* 2.8 25.5 + - - +
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Residues in contact with MET 321 (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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92H PHE* 5.8 4.9 - - - -
110H VAL* 3.8 28.7 - - + +
301H ALA* 3.5 33.2 - - + -
308H GLU* 5.1 3.6 - - - +
317H ILE* 2.9 22.2 + - + +
318H ALA* 3.9 7.0 - - - +
320H THR* 1.3 94.5 - - + +
322H GLU* 1.3 56.2 + - - +
324H ALA* 3.6 12.4 - - + +
325H GLN* 2.8 44.0 + - + +
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Residues in contact with GLU 322 (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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246H VAL* 3.9 22.6 - - + +
318H ALA 3.0 17.3 + - - +
319H ALA* 3.7 7.6 - - - +
321H MET* 1.3 75.0 - - - +
323H ASN* 1.3 57.1 + - - +
325H GLN* 3.5 10.7 + - - +
326H LYS* 3.1 26.2 + - - +
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Residues in contact with ASN 323 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112H ALA* 4.9 1.1 - - + -
113H LEU 3.3 21.1 - - - +
114H SER* 3.4 17.1 + - - +
245H THR 3.3 22.2 + - - -
246H VAL* 3.4 7.6 - - - +
247H LEU* 2.9 32.3 + - - +
255H SER 5.4 0.9 - - - +
257H PRO* 3.6 14.7 - - + +
319H ALA 2.9 22.2 + - - -
320H THR 3.5 6.1 - - - +
322H GLU* 1.3 73.7 - - - +
324H ALA* 1.3 65.2 + - - +
326H LYS* 3.1 9.1 + - - +
327H GLY 2.9 19.9 + - - -
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Residues in contact with ALA 324 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110H VAL* 4.9 1.6 - - + -
112H ALA* 4.0 14.9 - - + +
257H PRO* 5.1 0.2 - - - -
259H VAL* 3.7 27.4 - - + +
320H THR 2.8 19.2 + - - +
321H MET* 3.6 25.1 - - + +
323H ASN* 1.3 72.4 - - - +
325H GLN* 1.3 63.3 + - + +
327H GLY 3.3 19.1 + - - +
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Residues in contact with GLN 325 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321H MET* 2.8 30.7 + - + +
322H GLU* 3.6 9.6 + - - +
323H ASN 3.2 0.2 - - - -
324H ALA* 1.3 77.1 - - + +
326H LYS* 1.3 61.9 + - - +
327H GLY 3.3 8.1 - - - +
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Residues in contact with LYS 326 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254H PRO* 4.2 21.7 - - + +
255H SER 3.9 16.8 - - - +
256H LYS* 3.6 18.7 - - - +
322H GLU 3.1 13.1 + - - +
323H ASN* 3.1 12.3 + - - +
325H GLN* 1.3 76.6 - - - +
327H GLY* 1.3 59.5 + - - +
328H GLU* 5.6 0.3 - - - +
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Residues in contact with GLY 327 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256H LYS* 3.7 15.0 - - - -
257H PRO* 3.4 18.6 - - - +
259H VAL* 4.5 0.2 - - - -
323H ASN 2.9 11.2 + - - -
324H ALA 3.3 14.2 - - - +
325H GLN 3.2 6.7 - - - +
326H LYS* 1.3 80.8 - - - +
328H GLU* 1.3 67.7 + - - +
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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