Contacts of the helix formed by residues 209 - 219 (chain A) in PDB entry 1EKP
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 PRO 209 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A GLY* 3.3 24.0 - - - +
206A ASN* 4.1 2.7 - - - +
207A TYR 3.4 4.7 - - - +
208A GLY* 1.3 88.9 - - - +
210A THR* 1.3 61.8 + - + +
211A VAL 3.4 0.6 + - - -
212A LEU* 4.1 5.8 + - - +
213A VAL* 4.1 4.0 - - - +
71B SER 5.6 0.9 - - - +
106B ARG* 3.0 43.3 + - - +
107B LEU* 4.2 11.9 - - + -
198B VAL* 4.2 22.0 - - + -
203B LEU* 5.0 2.7 - - + -
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Residues in contact with THR 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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192A ARG* 4.6 11.2 - - + -
206A ASN 3.5 21.3 - - - +
207A TYR* 2.5 26.7 + - + +
209A PRO* 1.3 79.2 - - + +
211A VAL* 1.3 65.5 + - - +
212A LEU 3.4 0.4 - - - -
213A VAL* 3.2 4.2 + - - +
214A GLN* 3.0 22.9 + - - +
227A TRP* 3.6 37.4 - - + -
239A GLY 6.2 0.2 - - - +
240A THR* 5.9 1.2 - - - +
155B VAL* 4.1 12.8 - - - +
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Residues in contact with VAL 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 TYR 4.2 6.7 - - - +
208A GLY* 3.3 16.2 + - - +
210A THR* 1.3 76.7 + - - +
212A LEU* 1.3 64.4 + - - +
214A GLN* 3.2 17.1 + - + +
215A GLN* 3.2 16.5 + - + +
70B TYR* 6.2 1.3 - - + -
72B LEU* 4.2 15.5 - - + -
107B LEU 4.6 4.9 - - - +
108B CYS* 3.8 20.6 - - + -
155B VAL* 4.6 12.1 - - + -
156B SER* 4.0 20.4 - - - +
157B GLN* 3.7 30.1 - - + +
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Residues in contact with LEU 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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190A PHE* 6.1 4.5 - - + -
209A PRO 4.1 1.6 + - - -
210A THR 3.4 0.4 - - - -
211A VAL* 1.3 78.1 - - - +
213A VAL* 1.3 65.8 + - + +
215A GLN* 3.2 8.7 + - + +
216A GLU* 3.0 23.0 + - + +
105B MET 4.2 9.6 - - - +
106B ARG* 3.4 55.2 + - - +
108B CYS* 3.7 21.4 - - - -
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Residues in contact with VAL 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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185A LEU* 4.7 2.3 - - + +
190A PHE* 3.6 48.5 - - + -
209A PRO 4.1 12.6 - - - +
210A THR 3.2 7.7 + - - +
212A LEU* 1.3 77.7 - - + +
214A GLN* 1.3 57.9 + - - +
216A GLU* 3.3 8.3 + - - +
217A ALA* 3.0 26.0 + - - +
225A VAL* 3.7 28.7 - - + -
227A TRP* 3.9 18.6 - - + -
106B ARG* 4.2 10.3 - - - +
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Residues in contact with GLN 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 THR* 3.0 12.6 + - - +
211A VAL* 3.5 12.1 - - + +
213A VAL* 1.3 74.0 - - - +
215A GLN* 1.3 64.3 + - - +
217A ALA* 3.2 3.3 + - - +
218A LEU* 3.0 46.8 + - + +
223A GLU 2.9 24.7 + - - +
224A GLN* 3.4 26.1 + - - +
225A VAL* 4.0 12.4 - - + +
239A GLY* 5.7 0.3 - - - -
155B VAL 5.3 8.5 - - - +
156B SER* 6.4 0.9 - - - -
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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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211A VAL* 3.2 19.2 + - + +
212A LEU* 3.2 10.7 + - + +
214A GLN* 1.3 76.0 - - + +
216A GLU* 1.3 66.6 + - - +
218A LEU* 3.1 21.4 + - - +
219A LYS* 3.0 24.8 + - - +
108B CYS* 4.5 13.5 - - - -
156B SER* 5.8 0.9 - - - -
157B GLN* 4.1 32.8 + - - +
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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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185A LEU* 4.3 3.8 - - + +
190A PHE* 4.3 18.2 - - + -
212A LEU* 3.0 15.3 + - + +
213A VAL* 3.5 13.0 - - - +
215A GLN* 1.3 77.3 - - - +
217A ALA* 1.3 62.0 + - - +
219A LYS* 2.6 48.6 + - - +
220A ARG* 2.8 51.4 + - - +
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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* 3.6 30.0 - - + +
213A VAL 3.0 12.7 + - - +
214A GLN* 3.3 10.8 - - - +
215A GLN 3.1 0.4 - - - -
216A GLU* 1.3 75.8 - - - +
218A LEU* 1.3 66.9 + - - +
220A ARG* 2.9 13.9 + - - +
221A GLY 3.0 0.5 + - - -
222A CYS* 3.0 26.9 + - - +
224A GLN 4.1 7.9 - - - +
225A VAL* 4.0 15.0 - - + -
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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 GLN* 3.0 38.7 + - + +
215A GLN* 3.1 27.3 + - - +
217A ALA* 1.3 76.1 - - - +
219A LYS* 1.3 57.2 + - - +
221A GLY* 2.9 19.6 + - - -
222A CYS 3.4 16.1 + - - +
223A GLU* 4.3 10.1 - - + +
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Residues in contact with LYS 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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215A GLN 3.0 12.4 + - - +
216A GLU* 2.6 54.2 + - - +
218A LEU* 1.3 74.6 - - - +
220A ARG* 1.3 63.0 + - - +
221A GLY 3.3 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