Contacts of the helix formed by residues 309 - 320 (chain H) in PDB entry 4MNE
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 ALA 309 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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612G GLN* 4.9 10.3 - - - +
613G LEU* 5.7 4.0 - - + -
625G ILE 5.3 0.9 - - - +
626G ARG 4.4 5.8 - - - +
627G MET* 3.8 35.9 - - + +
307H PRO 3.6 4.0 + - - -
308H MET* 1.3 77.7 - - - +
310H ILE* 1.3 66.3 + - - +
311H PHE 3.2 4.5 - - - +
312H GLU* 3.2 21.2 + - + +
313H LEU* 3.3 9.0 + - - +
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Residues in contact with ILE 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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612G GLN* 5.2 3.4 - - - +
613G LEU* 5.3 6.6 - - + +
625G ILE 5.5 0.7 - - - +
663G ASP* 4.3 17.3 - - - +
666G ILE* 4.1 16.8 - - + -
224H VAL* 3.6 25.8 - - + -
225H GLY* 3.2 31.9 - - - +
226H THR 3.5 15.8 + - - +
227H ARG* 3.3 28.0 - - - +
228H SER* 4.4 3.6 - - - -
308H MET 3.6 1.0 + - - -
309H ALA* 1.3 73.1 - - - +
311H PHE* 1.3 61.9 + - + +
313H LEU* 3.1 6.6 + - + +
314H LEU* 2.7 37.0 + - + +
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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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625G ILE* 3.2 41.0 + - + +
626G ARG* 3.8 29.8 - - + +
628G GLN* 4.2 17.5 - - - -
666G ILE* 4.0 7.2 - - + -
667G PHE* 3.5 31.4 - + - -
670G GLY* 3.5 18.8 - - - -
671G ARG* 3.4 29.2 - - - -
309H ALA* 3.2 2.0 - - - +
310H ILE* 1.3 83.2 - - - +
312H GLU* 1.3 62.2 + - - +
314H LEU* 3.2 8.4 + - - +
315H ASP* 2.9 35.0 + - + +
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Residues in contact with GLU 312 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626G ARG 5.2 2.2 + - - +
627G MET 5.4 0.8 - - - +
628G GLN* 2.8 46.2 + - + +
308H MET* 3.3 43.3 - - + +
309H ALA* 3.2 11.5 + - + +
311H PHE* 1.3 78.3 - - + +
313H LEU* 1.3 67.8 + - - +
315H ASP* 3.6 7.5 - - + +
316H TYR* 2.9 20.3 + - - +
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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
----------------------------------------------------------
226H THR* 3.8 22.9 - - + +
227H ARG* 4.0 8.7 - - + -
228H SER 5.5 0.7 - - - +
261H TYR* 3.8 27.8 - - + +
263H ILE* 3.2 38.2 - - + +
264H PRO* 4.1 0.4 - - + -
308H MET* 3.9 35.9 - - + +
309H ALA 3.3 10.4 + - - +
310H ILE* 3.1 10.6 + - + +
312H GLU* 1.3 76.9 - - - +
314H LEU* 1.3 66.6 + - + +
315H ASP 3.2 0.5 + - - -
316H TYR* 3.4 2.1 + - - +
317H ILE* 3.4 26.2 + - + +
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Residues in contact with LEU 314 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663G ASP* 3.2 37.7 - - + +
666G ILE* 3.8 25.1 - - + -
667G PHE* 3.7 17.0 - - + +
228H SER* 3.5 35.7 - - - +
235H LEU* 3.4 23.2 - - + +
310H ILE* 2.7 24.6 + - + +
311H PHE* 3.2 8.0 + - - +
313H LEU* 1.3 78.7 - - - +
315H ASP* 1.3 58.6 + - - +
317H ILE* 3.8 2.2 + - + -
318H VAL* 3.3 27.0 + - - +
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Residues in contact with ASP 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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628G GLN* 5.7 1.2 + - - -
667G PHE* 3.3 12.0 - - + -
671G ARG* 3.2 30.1 + - - -
311H PHE* 2.9 23.7 + - + +
312H GLU* 3.6 11.3 - - + +
313H LEU 3.1 0.2 - - - -
314H LEU* 1.3 75.3 - - - +
316H TYR* 1.3 66.6 + - - +
317H ILE 3.1 1.6 - - - -
318H VAL 3.1 1.6 + - - -
319H ASN* 2.7 54.1 + - - +
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Residues in contact with TYR 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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263H ILE* 4.1 25.1 - - + -
264H PRO* 4.0 14.4 - - + -
265H PRO* 3.0 41.3 - - + +
308H MET* 4.6 7.0 - - + -
312H GLU 2.9 16.7 + - - +
313H LEU 3.9 4.7 - - - +
315H ASP* 1.3 78.0 - - - +
317H ILE* 1.3 63.2 + - - +
320H GLU* 3.1 51.8 + - + +
321H PRO* 3.6 27.0 + - - +
323H PRO* 4.9 8.1 - - + -
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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
----------------------------------------------------------
228H SER* 4.7 20.9 - - - +
230H MET 3.9 15.3 - - - +
232H PRO* 3.7 32.1 - - + +
235H LEU* 3.6 22.4 - - + -
247H TRP* 4.0 13.6 - - + +
251H LEU* 5.1 2.0 - - + -
261H TYR* 4.9 2.0 - - - +
263H ILE* 3.4 30.7 - - + -
313H LEU 3.4 14.5 + - - +
314H LEU* 3.8 8.3 - - + +
315H ASP 3.1 0.8 - - - -
316H TYR* 1.3 79.8 - - - +
318H VAL* 1.3 63.8 + - - +
320H GLU 5.1 0.2 - - - -
344H LYS* 3.2 20.1 + - - +
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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
----------------------------------------------------------
667G PHE* 3.5 32.1 - - + -
232H PRO* 4.5 6.7 - - - +
235H LEU* 3.8 26.0 - - + -
236H GLN* 3.1 34.7 + - - +
314H LEU 3.3 17.9 - - - +
315H ASP 3.1 4.7 + - - +
317H ILE* 1.3 77.4 - - + +
319H ASN* 1.3 69.6 + - - +
344H LYS* 3.3 16.1 - - - +
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Residues in contact with ASN 319 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667G PHE* 4.4 4.2 - - - -
671G ARG* 4.3 13.4 - - - +
673G TYR* 5.5 2.4 + - - -
315H ASP* 2.7 39.4 + - - +
318H VAL* 1.3 94.6 - - - +
320H GLU* 1.3 77.9 + - + +
344H LYS* 4.6 2.0 - - - +
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Residues in contact with GLU 320 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316H TYR* 3.1 56.6 + - + +
317H ILE* 3.9 0.5 - - - +
319H ASN* 1.3 93.7 - - + +
321H PRO* 1.3 75.9 - - + +
322H PRO* 4.5 0.2 - - - +
344H LYS* 1.9 34.3 + - - +
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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