Contacts of the helix formed by residues 228 - 240 (chain A) in PDB entry 6GHM
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 GLY 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A ASP 3.6 8.1 - - - -
213A VAL* 3.3 23.5 - - - +
215A GLY 3.0 17.3 + - - -
227A PHE* 1.3 76.5 - - - +
229A ALA* 1.3 66.2 + - - -
230A GLU 3.2 2.9 - - - -
231A VAL* 3.2 14.3 + - - +
232A VAL* 3.4 13.2 + - - +
258A PHE* 3.9 3.8 - - - -
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Residues in contact with ALA 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ASP 4.7 0.4 + - - -
211A LYS* 5.9 1.9 - - - +
213A VAL 4.5 1.6 + - - -
228A GLY* 1.3 72.9 - - - -
230A GLU* 1.3 60.9 + - - +
232A VAL* 3.3 4.7 + - - +
233A ALA* 3.1 21.8 + - - +
258A PHE* 3.7 19.2 - - + -
259A ALA* 3.7 26.3 - - + +
262A GLN* 4.8 0.3 - - - +
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Residues in contact with GLU 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A GLN* 6.4 0.9 - - - -
215A GLY 5.6 6.3 - - - +
228A GLY 3.2 0.8 - - - -
229A ALA* 1.3 76.5 - - - +
231A VAL* 1.3 61.8 + - + +
233A ALA* 3.3 7.0 + - - +
234A LYS* 2.9 46.1 + - - +
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Residues in contact with VAL 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LEU* 3.8 18.2 - - + -
215A GLY* 3.7 37.9 - - - +
216A TRP* 3.6 38.6 - - + +
227A PHE* 4.0 7.2 - - + -
228A GLY 3.2 10.2 + - - +
230A GLU* 1.3 78.4 - - + +
232A VAL* 1.3 62.9 + - - +
234A LYS* 3.4 9.2 + - + +
235A PHE* 2.9 23.0 + - - +
403A EDO 4.5 7.6 - - - +
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Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LEU* 4.0 7.2 - - + -
227A PHE* 3.7 31.6 - - + -
228A GLY 3.4 5.6 + - - +
229A ALA 3.3 9.1 + - - +
230A GLU 3.2 0.6 - - - -
231A VAL* 1.3 76.2 - - - +
233A ALA* 1.3 63.7 + - - +
235A PHE* 3.1 3.3 + - - +
236A LEU* 3.0 27.6 + - + +
244A ILE* 4.0 15.5 - - + -
258A PHE* 4.0 14.6 - - + -
259A ALA* 4.2 7.9 - - + -
262A GLN* 3.6 34.1 - - + +
263A LEU* 4.1 9.9 - - + -
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Residues in contact with ALA 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ALA 3.1 10.9 + - - +
230A GLU* 3.3 10.1 + - - +
232A VAL* 1.3 78.7 - - - +
234A LYS* 1.3 63.9 + - + +
236A LEU* 3.5 1.7 + - - +
237A HIS* 3.0 25.8 + - - +
262A GLN* 3.8 30.2 + - - +
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Residues in contact with LYS 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLU* 2.9 31.4 + - + +
231A VAL* 3.8 8.3 - - + +
233A ALA* 1.3 77.2 - - + +
235A PHE* 1.3 62.7 + - - +
237A HIS* 3.9 4.5 - - - +
238A LYS* 3.0 26.9 + - - +
403A EDO 4.4 9.4 + - - +
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Residues in contact with PHE 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A PHE* 4.0 17.5 - + + -
176A LEU* 3.8 32.5 - - + -
180A LEU* 3.6 28.5 - - + -
183A MET* 3.6 22.4 - - + -
231A VAL 2.9 17.2 + - - +
232A VAL 3.1 2.7 + - - +
234A LYS* 1.3 76.9 - - - +
236A LEU* 1.3 68.2 + - + +
239A HIS* 3.1 53.1 + + - +
241A LEU* 3.6 18.4 - - + -
244A ILE* 3.9 12.8 - - + -
403A EDO 3.6 27.1 - - - -
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Residues in contact with LEU 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A VAL* 3.0 19.9 + - + +
233A ALA 4.0 3.1 - - - +
235A PHE* 1.3 79.7 - - + +
237A HIS* 1.3 57.4 + - - +
240A ASP* 2.9 9.7 + - - -
241A LEU* 2.8 59.4 + - + +
242A ASP 3.5 20.9 - - - +
243A LEU 3.8 10.8 - - - +
244A ILE* 3.8 26.5 - - + -
262A GLN* 3.5 44.4 - - + +
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Residues in contact with HIS 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ALA 3.0 18.1 + - - +
234A LYS* 3.9 5.8 - - - +
236A LEU* 1.3 78.1 - - - +
238A LYS* 1.3 66.3 + - + +
239A HIS 3.4 0.5 + - - -
240A ASP* 3.4 11.0 + - - +
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Residues in contact with LYS 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU 4.8 0.2 + - - -
181A GLN* 2.9 50.7 + - - +
234A LYS 3.0 18.1 + - - +
235A PHE 3.9 3.8 - - - +
237A HIS* 1.3 83.7 - - + +
239A HIS* 1.3 75.0 + - + +
240A ASP 3.7 0.5 + - - -
403A EDO 4.0 15.5 + - - +
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Residues in contact with HIS 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLU 5.0 0.9 - - - +
180A LEU* 4.9 2.2 + - + -
181A GLN 3.5 28.8 + - - -
182A SER* 4.3 8.1 - - - -
183A MET* 3.8 22.0 - - + +
235A PHE* 3.1 57.5 + + - +
238A LYS* 1.3 98.5 + - + +
240A ASP* 1.3 69.8 + - - +
241A LEU* 3.2 24.9 + - + +
403A EDO 4.7 1.2 + - - -
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Residues in contact with ASP 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLU 3.6 9.0 - - - +
168A LYS* 2.8 45.1 + - - -
236A LEU 2.9 7.6 + - - -
237A HIS 3.4 9.7 + - - +
238A LYS 3.4 1.2 - - - +
239A HIS* 1.3 79.4 - - - +
241A LEU* 1.3 59.4 + - - +
242A ASP* 5.0 0.2 - - - -
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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