Contacts of the helix formed by residues 203 - 217 (chain A) in PDB entry 6EKK
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 LYS 203 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A VAL* 3.6 22.0 - - + +
68A GLY* 3.8 19.8 - - - -
69A GLN 4.5 2.6 - - - +
70A ASN 5.6 0.2 - - - +
174A GLU* 4.2 3.9 + - - +
201A CYS* 3.5 5.6 - - - -
202A SER* 1.3 83.6 + - - +
204A LEU* 1.3 61.0 + - - +
205A SER* 2.5 40.1 + - - +
206A THR* 3.5 19.6 - - - +
207A LEU* 2.8 30.1 + - - +
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Residues in contact with LEU 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PRO* 3.9 31.2 - - + +
57A PHE* 4.0 12.3 - - + -
67A VAL 3.1 21.7 + - - +
70A ASN 4.8 0.2 - - - +
71A PHE* 3.5 42.6 - - + +
89A LEU* 4.0 12.1 - - + -
203A LYS* 1.3 68.3 - - - +
205A SER* 1.3 66.5 + - - +
207A LEU* 3.5 8.0 - - + +
208A THR* 3.0 26.9 + - + +
230A VAL* 4.1 12.3 - - + -
250A HIS* 3.9 30.7 - - + -
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Residues in contact with SER 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL 4.2 1.4 + - - -
69A GLN 5.3 0.9 - - - -
70A ASN* 3.0 29.4 + - - -
71A PHE* 4.0 0.2 - - - -
170A ARG* 5.9 0.9 - - - -
174A GLU* 2.9 13.0 + - - -
203A LYS* 2.5 36.0 + - - +
204A LEU* 1.3 77.5 - - - +
206A THR* 1.3 70.4 + - - +
209A ALA* 3.0 16.3 + - - +
404A EDO 2.7 33.2 + - - -
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Residues in contact with THR 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A GLU* 2.6 28.6 + - + +
178A ALA* 3.6 30.7 - - + -
201A CYS* 3.8 19.5 - - - -
203A LYS* 3.3 25.4 + - - +
204A LEU 3.2 0.2 - - - -
205A SER* 1.3 78.7 + - - +
207A LEU* 1.3 66.3 + - - +
209A ALA* 3.3 1.2 + - - +
210A CYS* 2.9 31.1 + - - -
270A VAL* 3.9 7.9 - - + -
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Residues in contact with LEU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ILE* 3.3 38.4 - - + +
201A CYS* 3.9 16.3 - - + +
203A LYS 2.8 17.5 + - - +
204A LEU* 3.3 12.5 + - + +
206A THR* 1.3 80.2 - - - +
208A THR* 1.3 62.2 + - - +
210A CYS* 3.3 4.9 + - - +
211A ILE* 3.2 21.1 + - - +
229A PRO 3.9 6.3 - - - +
230A VAL* 3.7 28.0 - - + -
248A GLY* 3.8 6.5 - - - -
249A ILE 3.5 34.5 - - - +
250A HIS* 3.7 5.4 - - - +
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Residues in contact with THR 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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71A PHE* 3.8 4.4 - - + +
72A THR* 3.3 43.8 + - - +
171A ASN* 5.2 0.2 + - - -
204A LEU* 3.0 14.4 + - + +
207A LEU* 1.3 74.5 - - + +
209A ALA* 1.3 63.5 + - - +
211A ILE* 3.3 2.9 + - - +
212A HIS* 2.9 41.3 + - - -
229A PRO* 3.8 22.0 - - - +
230A VAL* 3.9 20.6 - - + -
404A EDO 3.3 12.0 + - - -
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Residues in contact with ALA 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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171A ASN* 3.5 33.4 - - - +
174A GLU* 3.6 29.4 - - + -
175A TYR* 3.9 1.5 - - - +
205A SER 3.0 19.8 + - - +
206A THR 3.6 3.4 - - - +
207A LEU 3.3 0.2 - - - -
208A THR* 1.3 78.6 + - - +
210A CYS* 1.3 53.8 + - - +
213A GLY* 2.7 34.1 + - - -
404A EDO 4.0 3.3 + - - -
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Residues in contact with CYS 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 3.8 22.3 - - + -
178A ALA* 4.5 0.7 - - - -
179A VAL* 3.6 29.4 - - + -
199A ILE* 4.2 22.0 - - + +
206A THR* 2.9 35.4 + - - +
207A LEU 3.6 5.4 - - - +
208A THR 3.2 0.2 - - - -
209A ALA* 1.3 76.5 - - - +
211A ILE* 1.3 51.7 + - - +
214A SER* 2.7 40.2 + - - -
270A VAL* 4.1 13.9 - - + -
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Residues in contact with ILE 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ILE* 3.8 21.8 - - + -
207A LEU 3.2 14.2 + - - +
208A THR 3.8 6.1 - - - +
209A ALA 3.3 0.2 - - - -
210A CYS* 1.3 77.2 - - - +
212A HIS* 1.3 64.3 + - - +
214A SER* 3.3 5.3 + - - -
215A ALA* 3.1 23.7 + - - +
227A TYR* 3.6 26.2 - - + +
229A PRO* 3.7 34.3 - - + +
246A LEU* 3.8 20.7 - - + +
247A ILE* 3.6 11.0 - - - +
248A GLY* 3.6 24.5 - - - +
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Residues in contact with HIS 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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72A THR* 3.2 24.5 + - - +
74A VAL* 3.5 18.2 - - + -
84A PHE* 3.9 13.2 - + - -
106A PHE* 3.9 21.5 - + - -
171A ASN* 3.5 24.0 - - - +
208A THR* 2.9 32.3 + - - +
211A ILE* 1.3 77.1 - - - +
213A GLY* 1.3 63.8 + - - +
215A ALA* 3.4 1.9 + - - +
216A ALA* 3.0 23.7 + - - +
227A TYR* 2.9 21.6 + - - -
229A PRO* 3.5 23.7 - - + +
405A EDO 3.5 18.9 - - - -
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Residues in contact with GLY 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ASN* 4.3 12.7 - - - +
172A LEU* 4.7 5.2 - - - -
175A TYR* 3.7 16.8 - - - -
209A ALA 2.7 23.6 + - - -
212A HIS* 1.3 73.7 - - - +
214A SER* 1.3 60.5 + - - +
216A ALA* 3.3 18.4 + - - +
217A MET* 3.5 15.9 - - - +
405A EDO 4.9 0.4 - - - -
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Residues in contact with SER 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 3.5 34.4 - - - -
187A LEU* 4.1 6.7 - - - -
191A MET* 3.2 32.5 - - - +
199A ILE* 4.4 5.5 - - - +
210A CYS 2.7 25.6 + - - -
211A ILE* 3.3 6.4 + - - -
213A GLY* 1.3 76.2 - - - +
215A ALA* 1.3 64.1 + - - +
217A MET* 3.1 20.0 + - - +
218A LEU* 4.1 1.2 + - - +
246A LEU* 4.6 0.7 - - - +
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Residues in contact with ALA 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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191A MET* 4.2 11.2 - - - -
211A ILE 3.1 15.2 + - - +
212A HIS 3.9 3.1 - - - +
214A SER* 1.3 81.0 + - - +
216A ALA* 1.3 62.6 - - - +
218A LEU* 3.1 23.6 + - - +
219A TYR 4.5 0.5 + - - -
221A MET 4.7 1.7 - - - +
222A TYR* 6.0 0.5 - - - -
223A TRP* 4.8 3.1 - - + -
227A TYR* 3.9 14.1 - - + +
246A LEU* 4.0 8.7 - - + -
403A EDO 3.5 33.0 + - - +
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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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164A PRO* 5.2 8.6 - - + +
212A HIS 3.0 18.2 + - - +
213A GLY* 3.5 9.2 - - - +
214A SER 3.2 0.4 - - - -
215A ALA* 1.3 77.3 - - - +
217A MET* 1.3 73.8 + - + +
218A LEU 3.1 0.9 - - - -
219A TYR* 3.2 22.7 + - - +
403A EDO 5.8 1.6 - - - -
405A EDO 4.4 19.7 - - - +
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Residues in contact with MET 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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164A PRO* 4.2 17.7 - - + -
172A LEU* 4.0 23.8 - - + -
175A TYR* 4.5 7.6 - - + +
188A TYR* 4.3 8.0 - - + -
213A GLY 3.5 18.2 - - - +
214A SER* 3.4 13.7 - - - +
215A ALA 3.1 1.4 - - - -
216A ALA* 1.3 90.7 - - + +
218A LEU* 1.3 63.4 + - - +
219A TYR* 3.2 2.0 + - - +
308A VAL* 4.4 1.6 - - - -
309A ALA* 4.2 16.6 - - + -
312A PHE* 3.4 66.7 - - + +
316A GLN* 3.9 10.9 - - - +
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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