Contacts of the helix formed by residues 307 - 320 (chain H) in PDB entry 2R9R
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 307 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303H LEU* 3.0 15.6 + - - -
304H SER 3.4 1.8 + - - +
305H ARG 3.6 1.6 - - - -
306H HIS* 1.3 78.2 - - - +
308H LYS* 1.3 63.3 + - - +
309H GLY* 3.6 3.3 + - - -
310H LEU* 3.0 34.5 + - - +
311H GLN* 3.1 27.9 + - - +
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Residues in contact with LYS 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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306H HIS 4.1 1.8 + - - -
307H SER* 1.3 72.5 + - - +
309H GLY* 1.3 58.4 - - - +
311H GLN* 3.0 29.2 + - - +
312H ILE* 2.8 44.6 + - + +
416H GLU* 4.2 23.6 - - + -
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Residues in contact with GLY 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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307H SER* 3.3 3.7 + - - -
308H LYS* 1.3 79.9 - - - +
310H LEU* 1.3 54.8 + - - +
312H ILE* 3.1 15.6 + - - +
313H LEU* 2.8 29.6 + - - +
409H PHE* 4.8 5.4 - - - -
413H TYR* 6.0 3.4 - - - -
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Residues in contact with LEU 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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300H ILE 5.1 4.0 - - - +
301H PHE* 5.2 16.6 - - + -
303H LEU* 4.0 12.6 - - + -
304H SER* 3.5 38.8 - - - +
307H SER* 3.0 24.7 + - - +
309H GLY* 1.3 75.8 - - - +
311H GLN* 1.3 57.4 + - - +
313H LEU* 3.4 25.2 + - + +
314H GLY* 2.9 24.3 + - - -
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Residues in contact with GLN 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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255H MET* 4.1 15.5 - - + +
304H SER* 3.0 27.5 + - - +
305H ARG 3.9 14.3 + - - -
306H HIS 4.7 0.4 - - - -
307H SER 3.1 19.7 + - - +
308H LYS* 3.0 37.7 + - + +
310H LEU* 1.3 72.6 - - - +
312H ILE* 1.3 62.4 + - + +
314H GLY* 3.2 3.0 + - - +
315H GLN* 2.9 36.9 + - + +
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Residues in contact with ILE 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 LYS* 2.8 31.1 + - + +
309H GLY* 3.1 14.1 + - - +
311H GLN* 1.3 75.0 - - + +
313H LEU* 1.3 55.2 + - - +
315H GLN* 3.0 14.7 + - - +
316H THR* 2.8 37.4 + - - -
409H PHE* 3.7 22.9 - - + -
412H PHE* 3.9 16.8 - - + +
413H TYR* 3.6 56.5 - - + +
416H GLU* 4.4 11.9 - - + -
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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 GLY 2.8 16.3 + - - +
310H LEU* 3.5 28.9 - - + +
312H ILE* 1.3 72.7 - - - +
314H GLY* 1.3 57.7 + - - +
316H THR* 3.2 11.2 + - + -
317H LEU* 2.9 63.7 + - + +
409H PHE* 4.4 15.0 - - + -
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Residues in contact with GLY 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 LEU 2.9 14.5 + - - -
311H GLN* 3.2 4.9 + - - -
312H ILE 3.1 0.4 - - - -
313H LEU* 1.3 78.7 - - - +
315H GLN* 1.3 61.7 + - - +
317H LEU* 3.4 8.1 + - - +
318H LYS* 3.1 23.8 + - - +
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Residues in contact with GLN 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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311H GLN* 2.9 22.3 + - + +
312H ILE* 3.0 19.0 + - - +
314H GLY* 1.3 74.4 - - - +
316H THR* 1.3 64.1 + - - +
318H LYS* 3.3 10.2 + - - +
319H ALA* 3.0 24.6 + - - +
412H PHE* 3.5 39.7 - - + +
415H ARG* 3.8 18.0 + - - +
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Residues in contact with THR 316 (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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312H ILE* 2.8 22.7 + - - +
313H LEU* 3.4 14.1 - - + -
314H GLY 3.2 0.2 - - - -
315H GLN* 1.3 76.7 - - - +
317H LEU* 1.3 62.9 + - + +
319H ALA* 3.2 3.5 + - - +
320H SER* 2.7 35.9 + - - +
405H ILE* 3.7 17.3 - - + +
408H ASN* 4.1 1.6 - - + -
409H PHE* 3.3 54.1 - - + +
412H PHE* 4.1 12.2 - - - -
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Residues in contact with LEU 317 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313H LEU* 2.9 47.4 + - + +
314H GLY* 3.9 6.7 - - - +
316H THR* 1.3 78.2 - - + +
318H LYS* 1.3 63.8 + - - +
320H SER* 3.0 14.3 + - - +
321H MET* 3.2 20.5 + - - +
324H LEU* 4.1 28.2 - - + +
405H ILE* 5.2 7.2 - - + -
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Residues in contact with LYS 318 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314H GLY 3.1 16.8 + - - +
315H GLN* 3.6 8.7 - - - +
317H LEU* 1.3 76.6 - - - +
319H ALA* 1.3 60.4 + - - +
321H MET* 3.4 23.5 + - + +
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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
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315H GLN 3.0 16.2 + - - +
316H THR 3.8 4.0 - - - +
317H LEU 3.2 0.2 - - - -
318H LYS* 1.3 77.8 - - - +
320H SER* 1.3 59.5 + - - +
321H MET 3.5 0.8 + - - -
322H ARG 5.3 0.2 + - - -
323H GLU* 3.6 7.6 - - - +
408H ASN* 3.6 14.9 + - - +
412H PHE* 3.8 24.5 - - + -
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Residues in contact with SER 320 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316H THR 2.7 22.3 + - - -
317H LEU* 3.0 8.3 + - - -
319H ALA* 1.3 78.4 - - - +
321H MET* 1.3 64.5 + - - +
322H ARG 3.1 3.4 + - - -
323H GLU* 3.1 20.5 + - - -
324H LEU* 2.8 26.0 + - - +
405H ILE* 3.9 23.7 - - - +
408H ASN* 2.8 23.1 + - - +
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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