Contacts of the helix formed by residues 218 - 227 (chain D) in PDB entry 3C6Q
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 THR 218 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12D HIS* 4.1 16.2 - - + -
13D PRO* 4.1 6.7 - - + -
14D TYR* 4.1 27.6 - - + +
17D GLN* 4.0 19.7 - - - +
191D ALA* 4.8 1.0 + - + -
216D ASP* 3.7 7.1 - - + -
217D THR* 1.3 82.6 - - - +
219D PRO* 1.3 71.3 - - - +
220D ASP* 3.2 11.1 + - - -
221D ILE* 3.2 26.8 + - - +
222D LEU* 2.8 25.8 + - - +
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Residues in contact with PRO 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D PRO* 4.9 10.8 - - + -
17D GLN* 4.9 5.8 - - - +
218D THR* 1.3 92.2 - - + +
220D ASP* 1.3 60.3 + - - +
222D LEU* 3.6 6.9 + - + +
223D GLN* 3.1 25.3 + - - +
304D LYS* 3.8 53.1 - - + +
305D PHE* 3.9 26.5 - - + +
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Residues in contact with ASP 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D HIS* 5.5 4.6 + - - -
13D PRO* 5.3 5.3 - - - +
195D PRO* 3.1 30.2 - - + +
218D THR* 3.4 16.2 + - - -
219D PRO* 1.3 79.5 - - - +
221D ILE* 1.3 66.4 + - - -
223D GLN* 2.9 17.0 + - - +
224D TYR* 2.9 26.8 + - + -
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Residues in contact with ILE 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D ALA 3.7 18.2 - - - +
194D GLY* 4.6 3.8 - - - -
195D PRO* 3.3 27.6 - - + -
214D CYS* 4.0 11.9 - - - -
215D PHE 3.2 24.0 - - - +
216D ASP* 3.5 25.6 - - + +
217D THR* 4.7 1.1 - - - -
218D THR* 3.2 23.2 + - - +
220D ASP* 1.3 77.5 - - - +
222D LEU* 1.3 58.3 + - - +
223D GLN 3.1 0.3 + - - -
224D TYR* 3.2 2.5 + - - +
225D VAL* 3.0 34.2 + - + +
230D ILE* 4.3 9.8 - - + +
233D THR* 4.0 16.6 - - + +
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Residues in contact with LEU 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D THR* 3.0 54.3 - - + +
218D THR 2.8 16.4 + - - +
219D PRO* 3.6 6.5 - - + +
221D ILE* 1.3 75.9 - - + +
223D GLN* 1.3 59.9 + - - +
225D VAL* 3.8 7.6 - - + +
226D LYS* 3.2 20.6 + - - +
233D THR* 5.1 4.3 - - + -
284D VAL* 5.1 2.0 - - + -
289D LEU* 4.2 27.9 - - + +
292D TYR* 5.0 4.3 - - + -
293D LEU* 4.3 11.9 - - + -
303D ILE* 4.2 23.8 - - + -
304D LYS 4.5 6.5 - - - +
305D PHE* 4.4 17.0 - - + -
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Residues in contact with GLN 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D PRO 3.1 12.5 + - - +
220D ASP* 2.9 12.8 + - - +
222D LEU* 1.3 74.7 - - - +
224D TYR* 1.3 70.5 + - + +
225D VAL 3.0 1.1 - - - -
226D LYS* 2.9 20.4 + - - +
227D GLU* 2.9 52.5 + - - +
305D PHE* 4.8 17.8 - - + +
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Residues in contact with TYR 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D PRO* 3.8 28.7 - - + -
198D ALA* 3.4 29.2 - - + -
199D LEU* 3.3 30.3 - - - +
202D LYS* 3.9 24.7 + - + +
220D ASP* 2.9 31.0 + - + +
223D GLN* 1.3 78.4 - - + +
225D VAL* 1.3 57.2 + - - +
227D GLU* 3.8 12.6 - - - -
228D GLY 3.1 2.9 + - - -
229D VAL* 2.7 49.9 + - + +
230D ILE* 3.1 22.0 + - + -
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Residues in contact with VAL 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D ILE* 3.0 28.8 + - + +
222D LEU* 3.8 7.9 - - + +
224D TYR* 1.3 74.8 - - - +
226D LYS* 1.3 59.1 - - - +
228D GLY* 2.6 27.0 + - - -
230D ILE* 3.4 33.7 - - + +
232D ALA 5.2 2.0 - - - +
233D THR* 4.4 12.8 - - + +
284D VAL* 5.1 2.7 - - + +
285D THR* 4.3 4.0 - - - -
286D PRO* 3.6 37.9 - - + +
289D LEU* 4.3 17.9 - - + -
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Residues in contact with LYS 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C VAL* 5.7 3.0 - - - +
270C ASP* 3.2 51.7 + - - +
222D LEU 3.2 11.7 + - - +
223D GLN* 2.9 22.2 + - - +
225D VAL* 1.3 82.3 - - - +
227D GLU* 1.3 63.0 + - + +
228D GLY* 3.4 0.5 + - - -
286D PRO* 5.2 6.1 - - - +
289D LEU* 4.0 20.7 - - + +
290D ASP* 5.6 5.4 + - - -
305D PHE* 4.7 21.3 - - + -
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Residues in contact with GLU 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C ASP 6.0 2.7 - - - +
202D LYS* 3.4 32.3 + - - -
207D VAL* 5.5 2.8 - - - +
223D GLN* 2.9 49.8 + - - +
224D TYR* 3.8 7.9 - - - +
226D LYS* 1.3 76.6 - - + +
228D GLY* 1.3 61.2 + - - +
229D VAL* 3.7 20.2 - - + +
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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