Contacts of the helix formed by residues 204 - 214 (chain A) in PDB entry 4KM9
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 CYS 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A ARG* 3.9 30.5 - - + +
174A ILE* 3.9 7.0 - - - -
176A HIS* 4.0 1.1 - - - -
203A VAL* 1.3 77.0 - - - +
205A THR* 1.3 66.1 + - - +
206A GLU* 3.4 16.2 - - + +
207A GLU* 3.0 30.8 + - + +
208A LEU* 2.9 21.8 + - - +
240A ARG* 3.7 12.6 - - - -
242A GLU 4.8 1.3 - - - -
243A THR* 3.7 20.9 - - + -
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Residues in contact with THR 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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164A HIS* 5.9 0.7 - - - -
173A ARG* 4.9 5.5 + - - +
175A GLN* 4.6 17.6 - - - +
176A HIS* 3.3 32.0 + - - -
203A VAL 4.0 0.2 + - - -
204A CYS* 1.3 70.5 - - - +
206A GLU* 1.3 75.9 + - - +
208A LEU* 3.3 5.0 + - - +
209A HIS* 3.0 49.8 + - - -
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Residues in contact with GLU 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ARG* 3.1 30.2 + - - -
204A CYS* 3.4 10.2 - - + +
205A THR* 1.3 98.9 + - - +
207A GLU* 1.3 58.5 + - - +
209A HIS* 3.4 13.1 + - - +
210A SER* 3.0 26.9 + - - -
243A THR* 3.3 26.2 - - + +
245A PHE* 4.4 7.7 - - + -
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Residues in contact with GLU 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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178A LEU* 5.0 0.7 - - - +
203A VAL* 4.2 12.2 - - + +
204A CYS* 3.0 31.1 + - + +
206A GLU* 1.3 74.3 - - - +
208A LEU* 1.3 65.7 + - - +
210A SER* 3.5 10.3 + - - -
211A ALA* 3.3 19.6 + - - +
219A ILE* 4.1 10.1 - - + +
223A LEU* 3.4 28.8 - - - +
240A ARG* 3.0 25.0 + - - -
243A THR* 3.4 5.5 - - - -
244A ILE* 3.4 39.5 + - + +
245A PHE* 4.0 9.6 - - + -
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Residues in contact with LEU 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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160A HIS* 3.7 41.3 - - + -
161A VAL 4.2 6.5 - - - +
162A SER* 3.6 15.0 - - - +
164A HIS* 4.9 4.0 - - + -
176A HIS* 3.5 49.1 - - + +
177A MET 4.4 3.6 - - - +
178A LEU* 4.5 2.9 - - + -
203A VAL* 4.3 5.5 - - + +
204A CYS 2.9 11.7 + - - +
205A THR 3.4 9.0 - - - +
207A GLU* 1.3 77.0 - - - +
209A HIS* 1.3 62.7 + - + +
211A ALA* 3.0 7.6 + - - +
212A GLN* 2.9 38.2 + - - +
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Residues in contact with HIS 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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164A HIS* 5.7 7.8 - + - -
205A THR* 3.0 40.6 + - - -
206A GLU* 3.6 12.1 - - - +
207A GLU 3.3 0.2 - - - -
208A LEU* 1.3 81.7 - - + +
210A SER* 1.3 57.2 + - - +
212A GLN* 3.0 28.9 + - - +
213A GLN* 3.1 48.1 + - - +
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Residues in contact with SER 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 GLU 3.0 15.9 + - - -
207A GLU 3.5 9.0 - - - -
208A LEU 3.2 0.2 - - - -
209A HIS* 1.3 77.7 - - - +
211A ALA* 1.3 56.4 + - - +
213A GLN* 3.2 9.9 + - - +
214A TRP* 2.8 33.6 + - - +
219A ILE* 3.6 21.3 - - - -
245A PHE* 3.3 24.4 - - - -
252A GLN* 5.9 0.7 + - - -
255A VAL* 5.1 9.6 - - - +
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Residues in contact with ALA 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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160A HIS* 4.6 12.6 + - + +
178A LEU* 4.1 32.1 - - + -
207A GLU 3.3 10.3 + - - +
208A LEU 3.0 9.5 + - - +
210A SER* 1.3 74.9 - - - +
212A GLN* 1.3 56.6 + - - +
214A TRP 2.4 25.9 - - - +
215A ASN 4.0 4.5 - - - -
216A GLY* 4.1 6.3 + - - -
219A ILE* 3.8 17.9 - - + +
265A ASN* 4.5 4.0 + - - +
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Residues in contact with GLN 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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160A HIS* 3.7 36.4 + - + +
162A SER* 3.9 16.0 + - - -
208A LEU* 2.9 20.2 + - - +
209A HIS* 3.0 40.3 + - - +
210A SER 3.2 0.2 - - - -
211A ALA* 1.3 78.2 - - - +
213A GLN* 1.3 59.6 - - + +
265A ASN* 3.6 9.9 - - - +
266A LEU* 3.2 38.8 + - + +
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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 HIS* 3.1 35.3 + - - +
210A SER* 3.7 7.0 - - - +
212A GLN* 1.3 79.3 - - + +
214A TRP* 1.3 56.5 + - - +
255A VAL* 6.1 0.2 - - + -
259A ILE* 3.9 16.4 - - + +
264A SER* 2.5 34.9 + - - -
265A ASN 4.2 0.9 - - - -
266A LEU* 4.2 16.0 - - + +
380A LEU* 4.3 12.4 - - - +
383A LEU* 3.7 31.3 - - + +
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Residues in contact with TRP 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 SER 2.8 11.8 + - - +
211A ALA 2.4 31.7 - - - +
212A GLN 3.8 0.7 - - - -
213A GLN* 1.3 75.1 - - - +
215A ASN* 1.3 84.1 + - - +
218A GLY* 3.7 35.2 - - - -
219A ILE* 3.7 26.2 - - + -
222A LEU* 4.2 11.0 - - + -
254A ARG* 4.2 11.9 - - + -
255A VAL* 3.9 26.7 - - + -
258A GLY* 3.5 25.6 - - - -
259A ILE* 3.6 14.8 - - + -
262A ASP* 2.7 30.1 + - - -
263A GLY 3.6 19.5 - - - -
265A ASN* 3.8 9.2 + - - +
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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