Contacts of the strand formed by residues 308 - 315 (chain H) in PDB entry 3GHG
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 THR 308 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302H LEU* 4.0 7.9 + - + +
303H THR* 3.5 22.3 - - + -
305H MET* 5.9 0.9 - - - +
306H GLY 3.3 12.9 + - - -
307H PRO* 1.3 73.0 - - - +
309H GLU* 1.3 64.2 + - - +
327H GLY 4.3 3.3 + - - -
328H GLY* 3.5 1.5 - - - -
329H PHE* 2.9 43.4 + - + +
330H THR* 5.6 2.2 - - - +
454H ILE* 3.4 42.6 - - + -
455H ARG 3.6 8.5 - - - +
456H PRO* 4.4 7.0 - - - +
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Residues in contact with GLU 309 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249H TRP* 3.6 17.6 - - + -
307H PRO 4.0 1.6 + - - -
308H THR* 1.3 75.1 - - - +
310H LEU* 1.3 59.5 - - - +
325H HIS* 3.8 20.8 + - - -
326H TYR 3.3 11.9 - - - +
327H GLY* 3.9 15.8 + - - +
454H ILE* 3.2 3.3 - - - -
455H ARG* 2.7 78.2 + - - +
457H PHE* 4.0 27.5 - - + +
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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
----------------------------------------------------------
249H TRP* 4.5 2.0 - - - -
308H THR 3.9 0.4 + - - -
309H GLU* 1.3 74.0 - - - +
311H LEU* 1.3 91.3 + - - +
312H ILE* 3.7 19.1 - - + -
324H ALA 3.6 0.3 - - - +
325H HIS* 3.6 4.9 + - - -
326H TYR* 2.8 45.1 + - + +
329H PHE* 3.5 45.1 - - + -
340H ILE* 5.7 1.3 - - + -
342H VAL* 5.0 0.7 - - + -
353H LEU* 4.9 11.7 - - + -
452H MET* 3.9 23.8 - - + -
453H LYS 3.1 23.8 - - - +
454H ILE* 4.0 4.9 - - + -
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Residues in contact with LEU 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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244H THR* 4.7 4.0 - - - +
245H GLU* 4.2 15.0 - - + +
249H TRP* 3.7 35.9 - - + +
310H LEU* 1.3 84.0 - - - +
312H ILE* 1.3 65.7 + - - +
313H GLU* 4.3 23.8 - - + +
323H LYS* 3.6 24.2 - - + -
324H ALA 3.5 5.4 - - - +
325H HIS* 3.4 37.2 - - + +
452H MET* 3.7 0.2 - - - -
453H LYS* 2.8 37.3 + - + +
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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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310H LEU* 3.7 22.4 - - + -
311H LEU* 1.3 78.7 - - - +
313H GLU* 1.3 61.4 + - - +
314H MET* 4.3 10.0 - - + +
322H VAL 3.8 0.7 - - - +
323H LYS* 3.3 4.0 - - - -
324H ALA* 2.9 44.6 + - + +
326H TYR* 4.6 0.4 - - + -
349H ALA* 5.6 0.2 - - - +
353H LEU* 4.3 15.3 - - + -
402H TRP* 5.9 1.3 - - + -
412H PRO* 5.6 1.1 - - + -
437H TRP* 4.1 24.7 - - + -
450H MET* 4.0 22.4 - - - -
451H SER 2.8 20.4 - - - +
452H MET* 3.9 26.5 - - + -
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Residues in contact with GLU 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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241H ASP* 3.7 0.9 - - - +
244H THR* 3.4 26.2 + - - +
311H LEU* 4.0 18.3 - - + +
312H ILE* 1.3 75.4 - - - +
314H MET* 1.3 65.0 + - - +
321H LYS* 6.6 0.2 - - + -
322H VAL 3.7 5.4 - - - +
323H LYS* 4.5 4.5 - - + +
449H LYS* 5.2 0.4 - - - -
450H MET* 3.6 2.1 - - - +
451H SER* 2.9 46.3 + - - +
453H LYS* 2.9 36.6 + - + +
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Residues in contact with MET 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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312H ILE* 4.3 9.2 - - + +
313H GLU* 1.3 74.2 - - - +
315H GLU* 1.3 60.5 + - - +
320H ASP 3.7 0.3 - - - +
321H LYS* 3.3 3.9 - - - +
322H VAL* 3.0 67.4 + - + +
349H ALA* 4.2 3.8 - - + -
437H TRP* 3.4 50.7 - - + -
440H TRP* 4.1 10.9 - - + -
447H MET* 4.6 7.2 - - + -
449H LYS* 3.1 16.8 - - - +
450H MET* 3.2 38.6 - - + -
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Residues in contact with GLU 315 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314H MET* 1.3 74.5 - - - +
316H ASP* 1.3 70.3 + - - +
319H GLY* 3.6 17.7 - - - -
320H ASP 2.9 12.8 - - - +
321H LYS* 4.0 24.9 - - + +
440H TRP* 4.2 4.9 - - - -
447H MET* 3.8 3.5 - - - +
448H ARG* 3.1 37.0 + - - +
449H LYS* 3.0 61.9 + - + +
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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