Contacts of the helix formed by residues 211 - 231 (chain A) in PDB entry 1TKD
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 LEU 211 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A HIS* 3.7 26.9 - - + +
191A TYR* 3.1 41.0 + - + +
193A PRO* 5.2 1.0 - - - +
210A SER* 1.3 79.2 + - - +
212A GLU* 1.3 69.7 + - - +
213A ALA* 4.3 3.6 - - + +
214A VAL* 2.9 18.9 + - + +
215A ASP* 3.9 1.4 + - - +
597A ASP 3.7 8.1 - - - +
598A GLY* 3.4 39.0 - - - +
599A ARG* 3.6 3.6 - - - +
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Residues in contact with GLU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A TRP 5.8 0.7 - - - -
210A SER 3.4 2.9 + - - -
211A LEU* 1.3 74.0 - - - +
213A ALA* 1.3 54.1 + - - +
215A ASP* 2.8 33.0 + - + +
216A ILE* 3.1 31.6 + - + +
596A LEU 4.2 0.7 - - - +
597A ASP* 3.7 15.8 - - + +
624A LEU* 4.6 1.0 - - - +
683A HIS* 2.7 32.4 + - - -
684A TRP* 3.2 26.1 + - - -
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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
----------------------------------------------------------
97A LEU* 3.9 13.0 - - + -
191A TYR* 4.6 0.2 - - + -
211A LEU* 3.0 8.9 + - + -
212A GLU* 1.3 78.9 - - - +
214A VAL* 1.3 56.8 + - - +
216A ILE* 3.8 2.3 - - - +
217A GLU* 2.9 34.8 + - - +
597A ASP* 3.3 41.3 + - - +
599A ARG* 3.9 22.2 - - + +
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Residues in contact with VAL 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 4.2 4.7 - - + -
97A LEU* 4.1 17.7 - - + -
191A TYR* 4.4 15.9 - - + -
192A PHE* 3.9 29.6 - - + -
206A PHE* 4.3 5.4 - - + -
207A TRP* 3.7 10.0 - - + -
210A SER* 3.7 20.4 - - - +
211A LEU 2.9 16.4 + - - +
213A ALA* 1.3 77.2 - - - +
215A ASP* 1.3 62.6 + - - +
217A GLU* 3.8 1.0 + - - +
218A HIS* 2.8 51.0 + - + +
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Residues in contact with ASP 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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85A ARG* 4.2 4.5 + - - -
207A TRP* 3.9 45.2 - - + +
211A LEU 3.9 0.6 + - - +
212A GLU* 2.8 15.5 + - + +
214A VAL* 1.3 79.5 - - - +
216A ILE* 1.3 65.2 + - + +
218A HIS* 3.5 2.1 + - - +
219A ARG* 3.1 54.4 + - - +
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Residues in contact with ILE 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A GLU* 3.1 33.4 + - + +
213A ALA 3.8 6.1 - - - +
215A ASP* 1.3 75.7 - - + +
217A GLU* 1.3 62.7 + - - +
219A ARG* 3.3 4.1 + - - +
220A ALA* 2.9 27.5 + - - +
597A ASP* 3.7 27.1 - - + +
599A ARG* 5.1 0.2 - - - +
620A LEU* 5.5 2.9 - - + +
623A LYS* 4.1 29.2 - - + -
624A LEU* 4.1 18.2 - - + +
627A ILE* 3.5 13.8 - - + +
684A TRP* 3.8 20.0 - - + -
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Residues in contact with GLU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A VAL* 3.7 21.1 - - + +
97A LEU* 4.0 24.4 - - + +
213A ALA 2.9 20.5 + - - +
214A VAL 4.2 3.1 - - - +
216A ILE* 1.3 77.1 - - - +
218A HIS* 1.3 57.9 + - + +
220A ALA* 3.2 4.4 + - - +
221A ALA* 2.9 30.3 + - - +
422A PRO* 4.5 6.6 - - - +
423A ASN* 3.3 23.2 + - - +
599A ARG* 2.8 33.5 + - - +
623A LYS* 3.0 29.9 + - - +
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Residues in contact with HIS 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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62A HIS* 3.6 19.5 + + - +
85A ARG* 5.0 5.5 - - + +
88A CYS 3.9 0.7 - - - +
89A ILE* 3.7 17.2 - - + +
90A ASP* 3.2 40.6 + - + -
93A VAL* 4.3 12.7 - - + +
94A LEU* 4.0 19.3 - - + -
206A PHE* 5.2 0.4 - + - -
207A TRP* 3.5 26.0 - + + -
214A VAL* 2.8 40.6 + - + +
215A ASP* 4.1 2.2 - - - +
216A ILE 3.3 0.4 - - - -
217A GLU* 1.3 74.6 - - + +
219A ARG* 1.3 65.8 + - + +
221A ALA* 4.5 0.9 - - - +
222A TRP* 3.0 25.6 + - - +
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Residues in contact with ARG 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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85A ARG* 3.4 51.4 - - - +
215A ASP* 3.1 47.5 + - - +
216A ILE* 5.0 2.0 - - - +
218A HIS* 1.3 76.0 - - + +
220A ALA* 1.3 63.3 + - - +
222A TRP* 3.5 4.5 + - - +
223A LEU* 3.0 26.0 + - - +
627A ILE* 3.6 35.8 - - + +
631A GLU* 3.4 28.6 + - - -
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Residues in contact with ALA 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 ILE 2.9 17.7 + - - +
217A GLU* 3.5 5.2 - - - +
219A ARG* 1.3 78.4 - - - +
221A ALA* 1.3 57.9 + - - +
223A LEU* 3.3 3.6 + - - +
224A LEU* 2.8 47.7 + - + +
422A PRO* 4.7 5.2 - - + -
623A LYS* 3.7 32.8 - - + -
626A ILE* 5.4 1.8 - - + -
627A ILE* 3.6 11.1 - - + +
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Residues in contact with ALA 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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62A HIS* 4.0 12.5 - - + +
63A LYS* 5.1 4.5 - - + +
93A VAL* 3.7 29.6 - - + -
217A GLU 2.9 15.7 + - - +
218A HIS 4.0 3.1 - - - +
219A ARG 3.3 0.2 - - - -
220A ALA* 1.3 78.2 - - - +
222A TRP* 1.3 56.8 + - - +
224A LEU* 4.1 0.5 - - - +
225A ALA* 2.9 31.5 + - - +
422A PRO* 4.0 22.1 - - + +
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Residues in contact with TRP 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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62A HIS* 3.6 33.8 - + + -
66A VAL* 3.5 32.5 - - + -
83A LEU 3.4 26.2 - - - -
84A PRO 4.2 0.9 - - - -
85A ARG* 3.4 44.8 - - + +
88A CYS* 3.9 20.6 - - + -
218A HIS 3.0 18.6 + - - +
219A ARG 3.9 3.1 - - - +
221A ALA* 1.3 76.6 - - - +
223A LEU* 1.3 66.3 + - - +
225A ALA* 3.6 6.2 + - - +
226A LYS* 3.4 19.5 + - + +
229A ARG* 4.3 7.5 + - - +
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Residues in contact with LEU 223 (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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219A ARG 3.0 18.6 + - - +
220A ALA 3.7 2.5 - - - +
222A TRP* 1.3 82.7 - - + +
224A LEU* 1.3 58.3 + - + +
226A LYS* 3.1 11.5 - - + +
227A GLN* 3.1 21.8 + - - +
626A ILE* 3.4 51.4 - - + +
627A ILE* 4.0 9.9 - - + -
630A GLU* 3.8 32.8 - - + +
640A HIS* 3.8 18.4 - - + -
648A TYR* 3.9 20.9 - - + -
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Residues in contact with LEU 224 (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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220A ALA* 2.8 26.7 + - + +
221A ALA 4.1 2.5 - - - +
223A LEU* 1.3 73.7 - - + +
225A ALA* 1.3 66.0 + - - +
227A GLN* 3.2 34.0 + - + +
228A GLU* 3.0 28.4 + - - +
420A VAL* 4.1 17.0 - - + +
422A PRO* 3.9 29.6 - - + -
626A ILE* 4.4 12.8 - - + -
648A TYR* 5.6 0.7 - - + -
651A TRP* 3.5 44.4 - - + -
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Residues in contact with ALA 225 (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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62A HIS 3.6 19.7 - - - +
63A LYS* 4.0 22.6 - - + +
221A ALA 2.9 18.5 + - - +
222A TRP* 3.7 4.7 - - - +
223A LEU 3.3 0.2 - - - -
224A LEU* 1.3 75.6 - - - +
226A LYS* 1.3 63.1 + - - +
228A GLU* 3.0 11.6 + - - +
229A ARG* 3.0 41.2 + - - +
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Residues in contact with LYS 226 (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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222A TRP* 3.4 10.4 + - + +
223A LEU* 3.1 15.2 + - + +
225A ALA* 1.3 79.8 - - - +
227A GLN* 1.3 55.2 + - - +
229A ARG* 3.2 30.9 + - + +
230A ASN* 2.9 48.5 + - - +
630A GLU* 5.3 0.9 - - - +
640A HIS* 3.0 59.8 + - + +
641A GLY* 4.1 4.2 - - - -
643A ASP* 5.6 0.8 + - - -
904A SO4 2.8 34.4 + - - +
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Residues in contact with GLN 227 (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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223A LEU 3.1 11.3 + - - +
224A LEU* 3.4 21.6 - - + +
226A LYS* 1.3 76.6 - - - +
228A GLU* 1.3 64.4 + - - +
230A ASN* 3.1 13.8 + - - +
231A GLY* 2.9 20.8 + - - +
418A GLY 5.6 1.6 + - - -
420A VAL* 4.1 23.6 - - - +
437A LEU* 6.3 0.6 - - - +
648A TYR* 3.7 34.2 - - + +
649A MET 3.7 10.0 + - - +
650A ALA* 3.4 28.1 + - - +
651A TRP* 3.4 24.5 + - - +
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Residues in contact with GLU 228 (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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63A LYS* 2.8 43.1 + - - +
224A LEU* 3.0 17.0 + - - +
225A ALA* 3.0 11.4 + - - +
227A GLN* 1.3 79.0 - - + +
229A ARG* 1.3 52.6 + - + +
231A GLY* 3.2 3.9 + - - -
417A HIS* 2.7 43.8 + - + +
418A GLY 3.3 21.0 - - - +
419A SER* 3.8 14.5 + - - -
420A VAL* 3.0 23.4 + - + +
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Residues in contact with ARG 229 (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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12A LEU* 4.0 25.4 - - + +
62A HIS 4.3 1.6 + - - -
63A LYS 5.4 0.4 + - - -
67A PRO* 3.8 31.3 - - - +
222A TRP* 4.3 9.3 + - - +
225A ALA* 3.0 24.7 + - - +
226A LYS* 3.2 49.4 + - + +
228A GLU* 1.3 76.7 - - + +
230A ASN* 1.3 64.2 + - - +
417A HIS* 3.1 17.2 - - - -
642A TRP* 4.9 1.0 + - - -
904A SO4 2.6 34.6 + - - +
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Residues in contact with ASN 230 (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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226A LYS* 2.9 39.7 + - - +
227A GLN* 3.1 5.5 + - - +
229A ARG* 1.3 79.0 - - - +
231A GLY* 1.3 64.5 + - - +
415A LYS* 3.4 11.3 - - - +
417A HIS* 3.7 1.7 - - - -
640A HIS* 3.1 28.5 + - - -
641A GLY* 4.5 5.2 - - - -
642A TRP* 2.9 37.3 + - + +
647A ALA* 4.0 8.6 - - - +
648A TYR 3.0 30.3 + - - +
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Residues in contact with GLY 231 (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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227A GLN 2.9 12.4 + - - -
228A GLU* 3.2 5.5 + - - -
230A ASN* 1.3 83.2 - - - +
232A PHE* 1.3 61.1 + - - -
233A PRO* 3.6 8.5 - - - +
415A LYS* 4.1 2.2 - - - -
416A ILE 3.5 8.7 - - - -
417A HIS* 3.4 21.3 - - - -
642A TRP* 3.7 5.5 - - - -
649A MET* 3.9 15.9 - - - -
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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
------------------------------------------------------------
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