Contacts of the helix formed by residues 207 - 218 (chain A) in PDB entry 3RLG
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 LEU 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A GLY* 1.4 76.1 - - - -
208A SER* 1.3 66.2 + - - +
209A ARG 3.3 2.5 - - - -
210A VAL* 3.2 15.3 + - + -
211A ASN* 2.8 38.3 + - - +
229A TYR* 3.7 39.0 - - + +
240A ASP* 3.8 34.5 - - + +
241A ALA* 4.6 11.9 - - - +
244A ALA* 4.3 9.0 - - + -
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Residues in contact with SER 208 (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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205A GLY 3.4 3.8 - - - -
207A LEU* 1.3 78.3 - - - +
209A ARG* 1.3 63.0 + - - +
211A ASN* 3.3 10.0 + - - +
212A ALA* 3.2 19.8 + - - +
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Residues in contact with ARG 209 (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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165A PHE 4.7 0.6 + - - -
173A ASN* 3.3 26.0 + - - +
174A ASP 2.9 38.3 + - - +
175A ASP* 4.9 1.7 - - - +
176A ILE* 3.9 20.4 - - + +
179A VAL* 4.2 4.2 - - - +
194A GLN* 3.4 27.7 - - - +
195A SER 2.9 21.4 + - - -
196A ASP* 2.7 43.4 + - - +
204A ARG* 3.8 15.5 - - - +
205A GLY 5.1 0.8 + - - -
207A LEU 3.3 0.4 - - - -
208A SER* 1.3 76.2 - - - +
210A VAL* 1.3 54.8 + - - +
212A ALA* 3.1 5.9 + - + +
213A ALA* 2.8 33.8 + - - +
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Residues in contact with VAL 210 (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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196A ASP* 3.4 30.3 + - + +
207A LEU* 3.2 17.6 + - + +
209A ARG* 1.3 76.9 - - - +
211A ASN* 1.3 59.2 + - - +
213A ALA* 3.1 5.8 + - - +
214A VAL* 2.8 39.2 + - + +
227A VAL* 4.7 4.4 - - + +
229A TYR* 3.4 32.3 - - + -
244A ALA* 4.0 20.0 - - + -
246A VAL* 3.6 26.9 - - + -
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Residues in contact with ASN 211 (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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207A LEU* 2.8 33.9 + - - +
208A SER* 3.6 8.4 - - - +
209A ARG 3.1 0.2 - - - -
210A VAL* 1.3 79.0 - - - +
212A ALA* 1.3 56.4 + - - +
214A VAL* 3.4 6.2 + - - +
215A ALA* 2.8 29.5 + - - +
244A ALA* 3.7 27.5 - - - +
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Residues in contact with ALA 212 (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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176A ILE* 4.4 15.7 - - + +
208A SER 3.2 12.4 + - - +
209A ARG* 3.1 12.4 + - + +
211A ASN* 1.3 74.4 - - - +
213A ALA* 1.3 64.1 + - - +
215A ALA* 3.2 7.6 + - - +
216A ASN* 3.0 23.6 + - - +
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Residues in contact with ALA 213 (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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176A ILE* 4.0 14.1 - - + +
194A GLN* 4.1 9.2 - - + -
196A ASP* 5.8 1.6 - - + -
209A ARG* 2.8 19.1 + - + +
210A VAL* 3.6 6.1 - - - +
212A ALA* 1.3 78.5 - - - +
214A VAL* 1.3 57.3 + - - +
216A ASN* 3.2 4.0 + - - +
217A ARG* 2.9 28.6 + - - +
224A ILE* 3.6 21.5 - - + +
227A VAL* 3.9 21.5 - - + -
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Residues in contact with VAL 214 (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 VAL* 2.8 31.9 + - + +
211A ASN* 3.7 5.8 - - - +
213A ALA* 1.3 74.5 - - - +
215A ALA* 1.3 66.5 + - - +
217A ARG* 3.3 35.8 + - - +
218A ASP* 2.9 28.8 + - + +
227A VAL* 4.2 16.4 - - + -
244A ALA 3.7 24.7 - - - +
245A GLY* 4.4 4.3 - - - +
246A VAL 4.7 0.2 - - - +
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Residues in contact with ALA 215 (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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211A ASN 2.8 20.7 + - - +
212A ALA* 3.5 8.7 - - - +
214A VAL* 1.3 74.4 - - - +
216A ASN* 1.3 61.7 + - - +
218A ASP* 3.4 3.4 + - - -
219A SER* 3.2 25.1 + - - -
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Residues in contact with ASN 216 (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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176A ILE* 4.0 12.0 - - + +
212A ALA 3.0 12.9 + - - +
213A ALA 3.5 7.2 - - - +
215A ALA* 1.3 73.5 - - - +
217A ARG* 1.3 65.3 + - - +
219A SER* 2.7 24.7 + - - -
222A GLY* 3.3 16.0 - - - -
223A PHE* 2.9 51.1 + - - -
224A ILE* 3.2 18.9 + - + +
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Residues in contact with ARG 217 (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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5A ARG* 3.4 21.8 - - - +
213A ALA 2.9 14.0 + - - +
214A VAL* 3.3 23.5 + - - +
216A ASN* 1.3 79.0 + - - +
218A ASP* 1.3 89.9 + - - +
219A SER 3.4 5.7 + - - +
222A GLY* 5.4 1.4 - - - -
224A ILE* 3.3 34.4 - - + +
225A ASN 3.4 23.3 - - - +
226A LYS* 4.2 1.8 - - - +
227A VAL* 4.1 9.8 - - + +
245A GLY* 2.8 30.9 + - - -
246A VAL* 4.1 2.2 - - - +
247A ASP* 2.7 36.9 + - - +
282A THR* 3.6 21.7 + - + +
283A PHE 5.6 0.4 - - - +
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Residues in contact with ASP 218 (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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5A ARG* 4.6 4.8 + - - -
214A VAL* 2.9 24.4 + - + +
215A ALA* 3.8 4.0 - - - +
216A ASN 3.2 0.2 - - - -
217A ARG* 1.3 117.3 + - - +
219A SER* 1.3 61.5 + - - +
220A ALA 4.0 0.3 + - - -
282A THR* 4.2 7.2 - - - +
283A PHE 4.6 6.2 - - - +
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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