Contacts of the helix formed by residues 251 - 262 (chain G) in PDB entry 3Q3G
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 251 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212G ALA* 3.9 3.1 - - - -
245G LYS* 4.4 6.3 - - - -
249G PRO 4.3 0.2 + - - -
250G LEU* 1.3 74.7 - - - +
252G TYR* 1.4 65.3 + - - -
253G GLU* 3.1 17.0 - - - -
254G ASP* 2.6 28.2 + - - -
255G VAL* 3.4 15.9 - - - +
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Residues in contact with TYR 252 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211G THR* 3.4 17.5 - - + -
212G ALA* 3.9 19.7 - - + +
215G ILE* 3.8 20.0 - - + -
245G LYS* 3.6 21.6 - - + +
251G GLY* 1.4 71.3 - - - -
253G GLU* 1.4 59.5 + - - +
255G VAL* 3.1 3.5 + - + +
256G ILE* 2.8 46.5 + - + +
283G GLU* 2.6 42.9 + - + -
286G THR* 3.6 30.1 - - + -
287G ILE* 3.5 28.3 - - + +
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Residues in contact with GLU 253 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251G GLY* 3.5 13.8 - - - -
252G TYR* 1.4 85.0 + - - +
254G ASP* 1.3 71.4 + - - +
255G VAL 3.3 0.2 - - - -
256G ILE* 5.4 0.2 - - - -
257G PRO* 3.2 28.5 - - + +
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Residues in contact with ASP 254 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216G ARG* 2.8 35.2 + - - +
249G PRO 4.7 1.7 - - - +
250G LEU* 3.6 14.3 - - + +
251G GLY* 2.6 33.7 + - - +
253G GLU* 1.3 92.5 - - - +
255G VAL* 1.3 57.8 + - + +
257G PRO* 4.6 1.3 - - - -
258G GLU* 4.5 7.6 - - - +
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Residues in contact with VAL 255 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212G ALA* 3.3 35.9 - - + +
215G ILE* 3.5 20.4 - - + -
216G ARG* 3.4 24.0 - - + +
219G VAL* 5.5 1.1 - - + +
250G LEU* 3.8 23.3 - - + -
251G GLY 3.4 13.5 - - - +
252G TYR* 3.1 5.8 + - + +
254G ASP* 1.3 85.0 - - - +
256G ILE* 1.4 65.6 + - + +
257G PRO* 3.6 2.0 - - - -
258G GLU* 3.5 11.1 + - - +
259G ALA* 3.3 18.5 + - - +
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Residues in contact with ILE 256 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215G ILE* 4.5 18.4 - - + -
252G TYR* 2.8 38.3 + - + +
253G GLU* 5.4 0.2 - - - -
255G VAL* 1.4 69.6 - - + +
257G PRO* 1.4 68.5 - - + +
259G ALA* 3.0 6.4 + - - +
260G ASP* 3.0 30.0 + - - +
266G ARG* 3.8 28.5 - - - +
286G THR* 3.4 29.2 - - + +
287G ILE* 3.7 20.2 - - - +
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Residues in contact with PRO 257 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253G GLU* 3.2 30.1 - - - +
254G ASP 4.6 0.7 - - - -
255G VAL 3.7 3.1 - - - +
256G ILE* 1.4 92.1 - - + +
258G GLU* 1.4 54.3 + - - +
260G ASP* 3.2 11.0 + - + +
261G ARG* 2.9 51.0 + - - +
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Residues in contact with GLU 258 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216G ARG* 3.8 17.2 + - - +
219G VAL* 4.3 13.2 - - + +
220G ARG* 2.8 54.0 + - - +
254G ASP 4.5 7.0 - - - +
255G VAL 3.5 11.7 + - - +
256G ILE 3.3 0.4 - - - -
257G PRO* 1.4 78.7 - - - +
259G ALA* 1.4 56.7 + - - +
261G ARG* 3.4 28.3 + - - +
262G GLU* 3.1 35.3 + - + +
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Residues in contact with ALA 259 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215G ILE* 4.8 4.3 - - + -
219G VAL* 3.9 26.6 - - + +
255G VAL 3.3 9.4 + - - +
256G ILE* 3.0 11.5 + - - +
258G GLU* 1.4 75.6 - - - +
260G ASP* 1.4 60.2 + - - +
262G GLU 3.5 0.3 + - - -
263G GLY 3.3 3.6 + - - -
264G VAL* 2.8 36.8 + - + +
266G ARG* 3.8 28.0 - - - +
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Residues in contact with ASP 260 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256G ILE* 3.0 25.2 + - - +
257G PRO* 3.5 11.0 - - + +
259G ALA* 1.4 74.4 - - - +
261G ARG* 1.3 57.3 + - + +
263G GLY* 2.9 20.4 + - - -
266G ARG* 2.9 28.9 + - - +
290G LYS* 5.0 13.9 + - - -
907G CL 3.3 16.1 - - - +
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Residues in contact with ARG 261 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257G PRO* 2.9 27.1 + - - +
258G GLU* 3.4 44.1 - - - +
260G ASP* 1.3 75.0 - - + +
262G GLU* 1.3 65.4 + - + +
263G GLY 3.2 0.7 + - - -
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Residues in contact with GLU 262 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219G VAL* 4.2 17.5 - - + +
223G PHE* 5.2 3.7 - - + +
235G LYS* 3.3 39.5 + - - +
258G GLU* 3.1 26.1 + - + +
259G ALA 3.5 4.0 + - - +
260G ASP 3.3 0.2 - - - -
261G ARG* 1.3 81.3 - - + +
263G GLY* 1.3 61.7 + - - +
264G VAL* 3.5 11.4 - - + -
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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