Contacts of the helix formed by residues 304 - 318 (chain H) in PDB entry 5N9G
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 SER 304 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302H PRO 3.5 5.0 + - - -
303H TRP* 1.3 71.2 - - - +
305H ASN* 1.3 57.5 + - - +
306H LYS* 3.3 14.4 + - - +
307H GLU* 2.9 24.9 + - - -
308H THR* 2.8 34.4 + - - -
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Residues in contact with ASN 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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303H TRP 3.8 2.2 + - - +
304H SER* 1.3 70.7 + - - +
306H LYS* 1.3 62.0 + - + +
308H THR* 3.5 8.3 - - - -
309H ASP* 2.9 30.6 + - - +
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Residues in contact with LYS 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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304H SER* 3.1 8.4 + - - +
305H ASN* 1.3 79.1 - - + +
307H GLU* 1.4 60.6 + - - +
308H THR 3.2 0.4 - - - -
309H ASP* 3.2 19.3 + - + +
310H MET* 2.9 30.5 + - + +
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Residues in contact with GLU 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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302H PRO 4.2 1.2 - - - +
303H TRP* 3.5 13.8 - - + -
304H SER* 2.9 33.8 + - - +
306H LYS* 1.4 73.4 - - - +
308H THR* 1.4 55.1 - - - +
310H MET* 3.2 10.2 + - + +
311H PHE 2.8 27.0 + - - -
329H PHE* 3.7 25.9 - - + -
332H ARG* 3.1 44.3 + - - +
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Residues in contact with THR 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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303H TRP* 3.4 12.5 + - - +
304H SER 2.8 17.2 + - - -
305H ASN* 3.5 9.6 - - - +
307H GLU* 1.4 73.2 - - - +
309H ASP* 1.4 63.5 + - - +
311H PHE* 3.1 8.3 + - - +
312H PHE* 3.1 47.2 + - + -
340H LYS* 3.0 33.4 + - - +
344H GLU* 4.2 6.3 - - - +
351H ARG* 4.4 9.0 - - - -
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Residues in contact with ASP 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 ASN 2.9 20.8 + - - +
306H LYS* 3.2 23.6 + - + +
308H THR* 1.4 74.2 - - - +
310H MET* 1.4 57.5 + - + +
312H PHE* 3.3 6.0 + - - +
313H LEU* 3.1 25.2 + - - +
351H ARG* 3.9 22.1 - - - -
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Residues in contact with MET 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 LYS 2.9 17.6 + - - +
307H GLU* 3.2 14.1 + - + +
309H ASP* 1.4 72.4 - - - +
311H PHE* 1.3 65.0 + - - +
313H LEU* 3.3 32.8 + - + +
314H ALA* 3.2 17.3 + - - +
329H PHE* 3.8 18.5 - - + -
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Residues in contact with PHE 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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303H TRP* 3.5 28.5 - + + -
307H GLU 2.8 7.2 + - - +
308H THR* 3.1 9.4 + - - +
310H MET* 1.3 75.1 - - - +
312H PHE* 1.4 77.6 + + - +
314H ALA* 3.0 24.1 + - - +
315H ILE* 3.3 35.5 + - + +
322H PHE* 6.0 0.2 - + - -
325H ILE* 4.9 6.5 - - + -
329H PHE* 3.6 8.3 - + - -
337H ILE* 3.6 35.0 - - + -
340H LYS* 3.8 24.7 - - + -
341H PHE* 3.5 29.4 - + + -
344H GLU* 4.1 14.4 - - + -
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Residues in contact with PHE 312 (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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308H THR* 3.1 29.5 + - + -
309H ASP* 3.3 8.0 + - - +
311H PHE* 1.4 82.0 - + - +
313H LEU* 1.3 55.6 + - - +
314H ALA 3.3 0.2 - - - -
315H ILE* 3.5 21.8 + - + +
316H SER* 2.8 33.0 + - - -
344H GLU* 3.3 49.1 - - + -
348H ASN 4.9 1.1 - - - -
351H ARG* 3.4 74.7 - - + +
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Residues in contact with LEU 313 (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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309H ASP 3.1 13.4 + - - +
310H MET* 3.4 42.4 - - + +
311H PHE 3.2 0.4 - - - -
312H PHE* 1.3 75.6 - - - +
314H ALA* 1.4 57.8 + - - +
316H SER* 3.2 12.6 - - - -
317H MET* 2.9 55.9 + - + +
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Residues in contact with ALA 314 (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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310H MET 3.2 9.8 + - - +
311H PHE 3.0 13.8 + - - +
313H LEU* 1.4 74.7 - - - +
315H ILE* 1.4 54.5 + - - +
317H MET* 4.5 5.4 - - - +
318H VAL* 2.8 37.9 + - - +
319H GLY 3.5 0.2 + - - -
325H ILE* 3.4 35.4 - - + -
328H LEU* 4.2 15.3 - - + -
329H PHE* 4.3 4.9 - - + -
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Residues in contact with ILE 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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188G ARG* 3.4 8.5 + - - +
311H PHE* 3.3 39.0 + - + +
312H PHE* 3.5 22.9 + - + +
313H LEU 3.4 0.2 - - - -
314H ALA* 1.4 73.1 - - - +
316H SER* 1.4 62.6 + - - +
319H GLY* 3.2 40.1 + - - +
320H THR* 5.0 7.0 - - + -
325H ILE* 4.5 8.1 - - + -
341H PHE* 3.7 27.6 - - + -
351H ARG 6.1 0.7 - - - +
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Residues in contact with SER 316 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188G ARG* 2.8 23.6 + - - +
312H PHE 2.8 19.5 + - - -
313H LEU* 3.2 19.1 - - - +
315H ILE* 1.4 76.2 - - - +
317H MET* 1.4 54.1 + - - +
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Residues in contact with MET 317 (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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398F GLU* 5.4 1.0 - - - +
188G ARG* 3.0 12.6 + - - -
313H LEU* 2.9 43.6 + - + +
314H ALA* 4.1 4.3 - - - +
316H SER* 1.4 73.5 - - - +
318H VAL* 1.3 67.5 + - + +
328H LEU* 5.6 7.0 - - + -
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Residues in contact with VAL 318 (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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394F ARG* 3.1 23.2 + - - +
402F PHE* 4.5 11.2 - - + -
188G ARG* 3.2 15.0 + - - +
314H ALA 2.8 19.8 + - - +
317H MET* 1.3 74.1 - - + +
319H GLY* 1.3 56.1 + - - +
321H ASP* 3.8 34.8 - - + +
324H MET* 3.8 24.5 - - + -
325H ILE* 3.9 8.5 - - + -
328H LEU* 3.6 29.8 - - + -
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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