Contacts of the helix formed by residues 204 - 215 (chain A) in PDB entry 4GDF
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 ARG 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A SER 5.4 1.1 - - - +
153A ASN* 3.0 44.6 + - - +
154A ARG 3.4 22.7 - - - +
155A THR* 4.1 6.3 - - + +
159A PHE* 4.4 1.3 - - - -
203A HIS* 1.3 72.6 - - - +
205A VAL* 1.3 56.8 + - - +
206A SER* 2.4 51.4 + - - +
207A ALA* 2.6 16.5 + - - +
208A ILE 3.4 5.7 + - - -
25C C 4.7 0.2 - - - +
7D G 3.2 32.1 + - - -
8D G 2.7 65.2 + - + +
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Residues in contact with VAL 205 (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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147A SER* 6.1 1.1 - - - -
154A ARG 4.8 1.0 + - - -
156A LEU* 4.7 9.6 - - + +
159A PHE* 3.8 25.0 - - + -
204A ARG* 1.3 70.1 - - - +
206A SER* 1.3 52.6 + - - +
207A ALA 3.3 0.2 - - - -
208A ILE* 3.7 4.4 - - - +
209A ASN* 2.7 36.6 + - + +
223A CYS* 3.8 28.7 - - - +
224A LYS* 4.4 3.8 - - + -
225A GLY* 3.6 27.6 - - - +
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Residues in contact with SER 206 (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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152A SER 4.8 5.5 + - - -
204A ARG* 2.4 49.9 + - - +
205A VAL* 1.3 74.0 - - - +
207A ALA* 1.3 57.8 + - - -
209A ASN* 3.5 4.6 + - - +
210A ASN* 2.8 37.7 + - - +
7D G 4.1 7.9 - - - -
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Residues in contact with ALA 207 (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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179A TYR* 4.1 6.7 + - + +
203A HIS* 5.2 2.5 - - + -
204A ARG* 2.6 9.2 + - - +
206A SER* 1.3 73.0 - - - +
208A ILE* 1.3 66.2 + - - +
210A ASN* 3.3 1.6 + - - +
211A TYR* 3.0 25.3 + - - +
7D G 3.4 53.0 + - + +
8D G 3.5 15.0 - - - +
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Residues in contact with ILE 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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159A PHE* 3.7 39.3 - - + -
161A ILE* 4.3 10.8 - - + -
175A ILE* 5.7 1.1 - - + -
179A TYR* 3.5 42.2 - - + -
197A PHE* 4.0 30.7 - - + -
199A THR* 5.2 0.2 - - + -
203A HIS* 4.4 10.1 - - + -
204A ARG 3.4 2.4 + - - +
205A VAL* 3.2 9.7 + - - +
207A ALA* 1.3 76.7 - - - +
209A ASN* 1.3 62.0 + - - +
211A TYR* 3.5 3.7 + - + +
212A ALA* 3.2 21.5 + - - +
223A CYS* 4.2 13.5 - - - -
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Residues in contact with ASN 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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205A VAL* 2.7 26.0 + - + +
206A SER* 3.5 5.3 + - - +
208A ILE* 1.3 70.6 - - - +
210A ASN* 1.3 71.6 + - - +
211A TYR 3.0 5.9 + - - -
212A ALA* 3.2 3.6 + - - +
213A GLN* 3.0 40.5 + - - +
221A LEU* 3.6 16.6 - - - +
223A CYS* 3.3 28.9 + - - +
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Residues in contact with ASN 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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206A SER* 2.8 25.2 + - - +
207A ALA 3.9 1.3 - - - +
209A ASN* 1.3 81.0 + - - +
211A TYR* 1.3 56.0 + - - +
213A GLN* 3.7 9.9 - - - +
214A LYS* 3.1 36.3 + - - +
6D C 4.2 24.0 + - - +
7D G 3.0 29.0 + - - +
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Residues in contact with TYR 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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171A LEU* 4.6 3.1 - - + -
174A LYS* 3.4 38.9 + - + +
175A ILE* 4.3 20.4 - - + -
178A LYS* 3.4 41.3 - - + +
179A TYR* 3.7 20.4 - + - +
207A ALA 3.0 17.0 + - - +
208A ILE* 3.6 5.2 - - + +
209A ASN 3.0 0.6 - - - -
210A ASN* 1.3 76.0 - - - +
212A ALA* 1.3 72.4 + - + +
213A GLN 3.0 2.4 + - - -
214A LYS* 3.2 11.5 + - + +
215A LEU* 2.9 42.2 - - + +
7D G 5.7 0.2 + - - -
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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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161A ILE* 4.2 11.9 - - + -
171A LEU* 3.9 21.4 - - + +
175A ILE* 5.5 0.2 - - + -
208A ILE 3.2 12.6 + - - +
209A ASN* 3.2 4.4 + - - +
211A TYR* 1.3 86.7 - - + +
213A GLN* 1.3 63.9 + - - +
215A LEU* 3.3 9.1 + - - +
216A CYS* 3.4 19.1 - - - -
221A LEU* 3.4 28.3 - - + -
223A CYS* 5.3 0.2 - - - -
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Residues in contact with GLN 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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209A ASN* 3.0 40.1 + - - +
210A ASN* 3.7 12.6 - - - +
211A TYR 3.0 0.2 - - - -
212A ALA* 1.3 76.9 - - - +
214A LYS* 1.3 55.7 + - + +
216A CYS* 2.8 28.2 + - - +
217A THR* 3.2 12.5 + - - -
221A LEU* 3.3 44.1 + - - +
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Residues in contact with LYS 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 ASN* 3.1 25.1 - - - +
211A TYR* 3.2 11.0 + - + +
213A GLN* 1.3 77.2 - - + +
215A LEU* 1.3 68.5 + - + +
216A CYS 3.6 0.3 + - - -
217A THR* 4.1 10.9 + - - -
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Residues in contact with LEU 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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167A LYS* 3.7 10.4 + - - -
170A LEU* 4.0 19.1 - - + +
171A LEU* 4.0 20.9 - - + -
174A LYS* 4.0 30.7 - - + +
211A TYR* 2.9 53.8 - - + +
212A ALA 3.8 6.5 - - - +
213A GLN 2.8 1.8 + - - -
214A LYS* 1.3 85.3 - - + +
216A CYS* 1.3 62.8 + - - +
217A THR* 5.1 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