Contacts of the helix formed by residues 214 - 221 (chain A) in PDB entry 4K8T
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 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A ASN* 1.3 74.7 - - - +
215A GLN* 1.3 70.4 + - + +
217A ALA* 3.2 3.3 + - - +
218A LEU* 3.0 42.7 + - + +
224A ASP 5.6 2.2 + - - -
226A PHE* 3.3 69.8 - - + +
243A THR 3.0 12.3 + - - +
244A MSE 4.9 17.5 - - - +
247A ASN* 5.6 6.1 - - - +
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Residues in contact with GLN 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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31A ALA* 5.8 5.3 - - - +
188A SER* 4.0 19.0 - - - +
213A ASN* 3.3 27.6 - - - +
214A ARG* 1.3 83.9 + - + +
216A GLU* 1.3 58.5 + - + +
218A LEU* 3.5 9.8 + - - +
219A SER* 3.0 28.8 + - - -
245A SER* 5.2 9.2 + - - -
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Residues in contact with GLU 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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184A THR* 4.4 2.5 + - - -
185A LEU* 3.6 25.6 - - + +
186A SER 3.0 31.2 + - - +
187A ASP* 3.2 30.6 + - - +
188A SER* 3.8 4.0 - - - +
191A VAL* 4.2 2.7 - - + +
211A PHE 4.1 0.5 - - - +
212A ALA* 3.3 9.4 - - - -
213A ASN* 2.9 47.8 + - - +
215A GLN* 1.3 74.0 - - - +
217A ALA* 1.3 60.9 + - - +
219A SER* 3.7 5.6 - - - -
220A LEU* 2.8 30.3 + - - +
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Residues in contact with ALA 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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185A LEU* 4.9 1.1 - - - -
212A ALA* 4.3 10.2 - - + +
213A ASN 3.0 16.1 + - - +
214A ARG 3.2 4.7 + - - +
216A GLU* 1.3 78.2 - - - +
218A LEU* 1.3 62.2 - - - +
220A LEU* 3.3 13.4 + - - +
221A TYR* 3.4 21.8 + - + -
226A PHE* 4.4 12.6 - - + -
229A ALA* 3.9 19.7 - - + +
230A LEU* 6.0 0.4 - - + -
233A ILE* 5.0 10.1 - - + -
242A VAL* 4.5 10.3 - - + -
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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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214A ARG* 3.0 41.2 + - + +
215A GLN* 3.8 7.9 - - - +
217A ALA* 1.3 76.7 - - - +
219A SER* 1.3 51.4 + - - +
221A TYR 3.5 1.2 + - - -
222A GLN* 2.8 28.6 + - - -
223A THR* 2.9 36.4 + - + +
224A ASP* 3.9 11.4 - - + +
225A ASP 3.8 7.2 - - - +
226A PHE* 3.7 37.9 - - + +
229A ALA* 4.3 2.9 - - + -
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Residues in contact with SER 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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188A SER* 3.1 33.7 + - - -
191A VAL* 3.5 5.5 - - - +
192A ASP* 3.2 16.8 + - - -
195A ARG* 2.9 27.5 + - - +
215A GLN 3.0 18.1 + - - -
216A GLU 3.8 3.6 - - - -
217A ALA 3.3 0.2 - - - -
218A LEU* 1.3 72.0 - - - +
220A LEU* 1.3 67.5 + - - +
221A TYR 3.0 2.9 + - - -
222A GLN* 3.1 8.5 + - - +
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Residues in contact with LEU 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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185A LEU* 3.8 22.2 - - + -
191A VAL* 3.4 19.2 - - + +
195A ARG* 3.4 28.8 - - + +
198A PHE* 4.6 12.8 - - + -
199A LEU* 3.7 35.0 - - + +
202A MSE 4.2 17.3 - - + -
216A GLU 2.8 17.9 + - - +
217A ALA 3.6 7.0 - - - +
219A SER* 1.3 76.7 - - - +
221A TYR* 1.3 87.4 + - + +
233A ILE* 4.3 5.2 - - + -
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Residues in contact with TYR 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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195A ARG* 5.4 0.4 - - - +
199A LEU* 3.6 16.5 - - + +
202A MSE 4.2 0.3 - - - +
203A ARG* 4.5 0.2 - - - -
217A ALA* 3.4 15.2 + - - -
219A SER 3.0 0.4 - - - -
220A LEU* 1.3 106.2 - - + +
222A GLN* 1.3 70.8 + - - +
223A THR* 3.2 21.4 + - + -
228A GLU* 4.6 0.7 - - - +
229A ALA* 3.8 15.5 - - + -
232A ARG* 3.3 61.2 + - + +
233A ILE* 3.3 35.4 - - + +
236A ASP* 2.7 33.3 + - - +
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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