Contacts of the helix formed by residues 211 - 222 (chain A) in PDB entry 3KTC
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 SER 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A GLY 4.1 0.2 + - - -
210A GLU* 1.3 71.0 - - - +
212A PRO* 1.3 69.7 - - - +
213A ALA* 3.6 4.9 + - - +
214A ASP* 3.0 27.3 + - - -
215A SER* 2.9 18.5 + - - -
250A GLU* 5.8 1.3 - - - -
253A GLU* 4.4 4.9 + - - -
342A EDO 3.2 14.2 - - - -
132B TRP* 3.9 27.4 - - - -
140B HIS* 3.6 15.4 + - - -
175B LYS* 4.9 2.0 - - - +
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Residues in contact with PRO 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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200A LEU* 4.2 0.3 - - - +
202A PHE* 3.5 49.8 - - + +
205A ALA* 3.9 22.7 - - + -
206A LEU* 3.8 22.9 - - + +
210A GLU 3.3 9.6 - - - +
211A SER* 1.3 82.4 - - - +
213A ALA* 1.3 57.0 + - - +
215A SER* 3.2 2.6 + - - -
216A ALA* 2.9 29.8 + - - +
250A GLU* 4.9 9.9 - - + +
253A GLU* 6.1 0.7 - - - +
254A PHE* 3.6 14.0 - - + -
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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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211A SER* 3.8 2.2 - - - +
212A PRO* 1.3 76.4 - - - +
214A ASP* 1.3 64.8 + - - +
216A ALA* 3.3 6.0 + - - +
217A GLN* 3.0 19.2 + - - +
250A GLU 5.3 0.8 + - - +
253A GLU* 3.6 47.3 - - + +
254A PHE* 4.1 9.2 - - - +
257A VAL* 3.6 24.8 - - + +
140B HIS* 4.0 6.1 - - + -
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Residues in contact with ASP 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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211A SER* 3.0 22.9 + - - +
213A ALA* 1.3 76.2 - - - +
215A SER* 1.3 59.0 + - - +
217A GLN* 3.1 3.5 + - - +
218A LEU* 2.8 27.7 + - - +
342A EDO 2.5 27.0 + - - -
140B HIS* 3.6 41.4 + - - +
144B TRP* 5.1 0.2 - - - +
183B ARG* 2.8 36.7 + - - -
341B EDO 3.8 10.5 + - - +
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Residues in contact with SER 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 TYR* 3.7 11.0 - - - -
181A ALA* 3.7 8.8 - - - +
200A LEU* 3.9 6.3 - - - -
210A GLU* 2.7 28.7 + - - -
211A SER 2.9 9.4 + - - -
212A PRO* 3.6 10.5 - - - -
214A ASP* 1.3 76.6 - - - +
216A ALA* 1.3 63.8 + - - +
218A LEU* 3.3 5.0 + - - +
219A ILE* 3.0 30.3 + - - +
342A EDO 2.7 25.4 + - - -
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Residues in contact with ALA 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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200A LEU* 3.4 20.1 - - + +
212A PRO 2.9 14.4 + - - +
213A ALA 3.5 8.5 - - - +
214A ASP 3.2 0.2 - - - -
215A SER* 1.3 76.5 - - - +
217A GLN* 1.3 62.3 + - - +
219A ILE* 4.0 1.6 - - - +
220A ILE* 2.9 31.2 + - + +
225A LEU* 4.8 1.8 - - + -
254A PHE* 4.1 8.5 - - + -
257A VAL* 4.0 12.1 - - + -
258A LEU* 4.1 21.3 - - + -
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Residues in contact with GLN 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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213A ALA 3.0 12.7 + - - +
214A ASP* 3.4 11.7 - - - +
216A ALA* 1.3 76.7 - - - +
218A LEU* 1.3 57.7 + - - +
220A ILE* 3.3 3.5 + - - +
221A ASP* 2.8 71.5 + - - +
257A VAL* 3.8 10.3 - - + +
260A ILE* 4.9 2.3 - - - +
261A ASN* 2.8 38.8 + - - +
344A EDO 3.7 9.4 - - - -
140B HIS* 4.4 6.9 - - + +
141B LYS* 3.6 37.4 + - + +
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Residues in contact with LEU 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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181A ALA* 4.9 3.8 - - + -
182A ALA* 4.5 14.1 - - + +
185A LEU* 3.7 27.1 - - + +
214A ASP* 2.8 21.2 + - - +
215A SER* 3.6 4.7 - - - +
217A GLN* 1.3 74.5 - - - +
219A ILE* 1.3 61.9 + - + +
221A ASP* 3.4 13.4 + - + +
222A ARG* 3.5 16.0 + - - +
342A EDO 4.8 5.4 - - - +
144B TRP* 3.8 32.8 - - + +
183B ARG* 3.7 27.8 - - + +
186B LEU* 4.0 20.2 - - + -
190B ASP* 6.1 0.2 - - - +
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Residues in contact with ILE 219 (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 TYR* 4.2 0.7 - - + -
181A ALA* 3.9 20.4 - - + -
185A LEU* 4.0 24.9 - - + -
198A VAL* 3.9 29.4 - - + -
200A LEU* 3.9 22.9 - - + -
215A SER 3.0 18.0 + - - +
216A ALA 4.0 2.2 - - - +
218A LEU* 1.3 74.3 - - + +
220A ILE* 1.3 64.7 + - - +
222A ARG* 3.1 9.9 + - - +
224A ARG* 3.1 54.8 + - + +
225A LEU* 3.4 13.7 - - + +
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Residues in contact with ILE 220 (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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216A ALA* 2.9 25.7 + - + +
217A GLN* 3.7 4.0 - - - +
219A ILE* 1.3 74.5 - - - +
221A ASP* 1.3 62.1 + - - +
223A GLY* 2.8 19.4 + - - -
225A LEU* 3.7 32.3 - - + -
257A VAL* 4.9 0.2 - - + -
258A LEU* 3.9 16.8 - - + -
261A ASN* 3.7 48.0 - - + +
263A TRP* 4.1 13.5 - - + -
336A CL 4.0 11.2 - - + +
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Residues in contact with ASP 221 (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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217A GLN* 2.8 50.7 + - - +
218A LEU* 3.7 9.3 - - + +
219A ILE 3.2 0.4 - - - -
220A ILE* 1.3 78.5 - - - +
222A ARG* 1.3 60.7 + - + +
223A GLY 3.4 0.4 + - - -
261A ASN* 4.5 1.2 - - - +
141B LYS* 2.9 35.5 + - - +
144B TRP* 6.1 0.9 - - - -
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Residues in contact with ARG 222 (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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185A LEU* 3.6 34.3 + - + +
189A GLU* 2.7 45.2 + - - +
218A LEU* 3.5 10.0 + - - +
219A ILE 3.1 7.7 + - - +
220A ILE 3.1 0.6 - - - -
221A ASP* 1.3 82.9 - - + +
223A GLY* 1.3 60.2 + - - +
224A ARG* 3.3 27.7 + - + +
186B LEU* 3.4 31.1 + - - +
189B GLU* 4.8 2.0 - - - +
190B ASP* 3.1 30.4 + - - -
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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