Contacts of the helix formed by residues 210 - 219 (chain F) in PDB entry 4LQL
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 PRO 210 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C GLN 5.0 4.3 - - - +
281C ASP* 3.2 44.0 - - + +
181F PHE* 5.7 0.2 - - - -
182F GLY* 6.0 0.7 - - - -
209F TYR* 1.3 81.7 - - - +
211F THR* 1.3 63.3 + - - +
212F ASN* 4.1 12.6 - - + +
213F GLU* 3.8 18.3 + - + +
214F LEU* 4.5 2.3 + - - +
281F ASP* 5.4 0.9 - - - +
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Residues in contact with THR 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181F PHE* 4.2 20.1 + - - +
209F TYR 3.7 0.4 + - - -
210F PRO* 1.3 72.3 - - - +
212F ASN* 1.3 65.7 + - - +
214F LEU* 3.2 12.6 + - - +
215F VAL* 3.2 30.5 + - - +
281F ASP* 3.3 45.9 + - - -
282F LEU* 5.5 2.9 - - - -
283F GLU 5.7 2.2 - - - -
285F LEU* 5.9 3.0 - - - +
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Residues in contact with ASN 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C ASP* 5.0 0.4 - - - +
283C GLU* 3.5 39.3 - - + -
210F PRO* 3.3 10.7 - - + +
211F THR* 1.3 75.8 - - - +
213F GLU* 1.3 64.3 + - + +
215F VAL* 3.8 6.0 - - - +
216F ALA* 3.0 27.7 + - - +
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Residues in contact with GLU 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C GLN 6.1 0.9 - - - +
209F TYR* 5.1 10.1 - - + -
210F PRO* 3.8 18.9 + - + +
211F THR 3.3 0.2 - - - -
212F ASN* 1.3 79.0 - - + +
214F LEU* 1.3 57.9 + - - +
216F ALA* 3.9 2.2 - - - +
217F VAL* 3.1 34.1 + - + +
266F PHE* 4.7 17.5 - - + -
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Residues in contact with LEU 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181F PHE* 5.0 17.3 - - + -
210F PRO 4.5 1.9 + - - +
211F THR* 3.2 15.3 + - - +
213F GLU* 1.3 77.2 - - - +
215F VAL* 1.3 58.6 + - + +
217F VAL* 3.4 10.1 - - + +
218F VAL* 3.2 30.7 + - + +
262F GLY 3.8 23.3 - - - +
263F ILE* 4.3 22.4 - - + -
266F PHE* 3.9 31.6 - - + -
285F LEU* 4.9 16.6 - - + -
289F PRO* 6.3 2.7 - - + -
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Residues in contact with VAL 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211F THR* 3.2 22.8 + - - +
212F ASN* 3.8 6.1 - - - +
213F GLU 3.2 0.8 - - - -
214F LEU* 1.3 78.9 - - + +
216F ALA* 1.3 55.1 + - + +
217F VAL 2.9 4.0 - - - -
218F VAL* 2.9 10.9 + - + +
219F ASN* 2.7 32.5 + - + +
282F LEU* 6.0 1.6 - - - -
283F GLU 5.3 4.0 - - - +
284F GLY* 3.6 26.7 - - - +
285F LEU* 3.7 36.3 - - + +
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Residues in contact with ALA 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212F ASN 3.0 15.4 + - - +
213F GLU* 3.9 2.9 - - - +
215F VAL* 1.3 77.0 - - + +
217F VAL* 1.3 59.7 + - - +
219F ASN* 3.5 25.1 - - + +
220F GLY* 4.4 0.9 + - - -
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Residues in contact with VAL 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213F GLU 3.1 25.3 + - - +
214F LEU* 3.4 13.9 - - + +
215F VAL 2.9 0.6 - - - -
216F ALA* 1.3 76.2 - - - +
218F VAL* 1.3 67.5 + - + +
219F ASN 3.1 0.9 - - - -
220F GLY* 3.2 15.4 + - - -
221F ILE* 3.9 7.5 - - + +
262F GLY* 4.5 20.9 - - - +
265F LYS* 5.6 4.5 - - + +
266F PHE* 4.4 20.2 - - + -
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Residues in contact with VAL 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214F LEU* 3.2 24.4 + - + +
215F VAL* 2.9 13.5 + - + +
217F VAL* 1.3 72.3 - - + +
219F ASN* 1.3 52.4 + - - +
220F GLY 2.6 17.2 + - - -
221F ILE* 3.3 24.9 + - + +
258F ARG* 3.1 43.3 - - + +
259F GLU* 4.6 14.4 - - + -
262F GLY* 5.2 4.9 - - - -
285F LEU* 5.5 7.0 - - + -
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Residues in contact with ASN 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215F VAL* 2.7 15.6 + - + +
216F ALA* 3.5 21.4 - - + +
217F VAL 3.1 1.3 - - - -
218F VAL* 1.3 74.3 - - - +
220F GLY* 1.3 54.0 + - - +
221F ILE 4.0 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