Contacts of the helix formed by residues 213 - 230 (chain A) in PDB entry 1DG3
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 SER 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A GLY* 3.6 2.0 - - - -
212A THR* 1.3 79.5 - - - +
214A GLN* 1.3 65.1 + - - +
215A LYS* 4.0 5.3 + - - +
216A ASP* 2.4 47.8 + - - +
217A GLU* 3.1 12.2 + - - +
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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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212A THR 3.7 1.4 + - - -
213A SER* 1.3 72.5 - - - +
215A LYS* 1.3 57.3 + - - +
217A GLU* 3.3 15.7 + - - +
218A THR* 2.7 37.2 + - - +
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Residues in contact with LYS 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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136A GLN* 4.2 26.4 + - - +
209A LYS* 6.5 0.4 - - + -
213A SER* 3.2 4.8 + - - +
214A GLN* 1.3 82.1 - - - +
216A ASP* 1.3 62.1 + - - +
218A THR* 3.4 24.2 - - - +
219A PHE* 3.1 25.5 + - + +
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Residues in contact with ASP 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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209A LYS* 3.7 22.4 - - - +
210A LYS 2.7 27.9 - - - +
211A GLY* 4.1 10.8 - - - +
213A SER* 2.4 36.6 + - - +
215A LYS* 1.3 78.8 - - - +
217A GLU* 1.3 57.0 + - - +
218A THR 3.1 1.6 - - - -
219A PHE* 2.9 7.8 + - - +
220A ASN* 2.7 42.4 + - - +
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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
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212A THR* 4.3 21.4 - - - +
213A SER 3.1 10.1 + - - +
214A GLN* 3.3 16.8 + - - +
216A ASP* 1.3 75.1 - - + +
218A THR* 1.3 57.5 + - - +
220A ASN* 4.1 8.6 - - - +
221A LEU* 3.0 32.4 + - - +
567A LYS* 5.2 7.3 + - - -
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Residues in contact with THR 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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136A GLN* 5.9 1.8 - - - +
140A ASP* 5.5 6.1 - - - +
214A GLN* 2.7 26.7 + - - +
215A LYS* 3.4 29.4 + - - +
216A ASP 3.1 0.2 - - - -
217A GLU* 1.3 78.6 - - - +
219A PHE* 1.3 60.5 + - - +
221A LEU* 4.2 4.3 - - - +
222A PRO* 3.4 19.4 - - - +
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Residues in contact with PHE 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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136A GLN* 4.4 19.7 - - - +
205A SER 5.2 0.4 - - - -
207A LYS 3.6 16.8 - - - -
208A LEU 4.5 0.2 - - - -
209A LYS* 3.8 44.6 - - + -
215A LYS* 3.1 19.0 + - + +
216A ASP* 2.9 11.2 + - - +
218A THR* 1.3 80.2 - - - +
220A ASN* 1.3 73.2 + - - +
222A PRO* 3.7 5.4 - - - +
223A ARG* 2.7 72.2 + - - +
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Residues in contact with ASN 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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208A LEU* 3.3 23.4 - - + +
209A LYS 2.6 46.5 + - - +
211A GLY 4.9 2.8 + - - -
216A ASP* 2.7 31.5 + - - +
217A GLU* 3.4 7.8 + - - +
219A PHE* 1.3 84.7 - - - +
221A LEU* 1.3 65.9 + - - +
222A PRO 3.5 0.2 - - - -
223A ARG* 3.1 4.3 + - - +
224A LEU* 2.8 34.1 + - + +
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Residues in contact with LEU 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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146A THR* 3.5 33.4 - - + +
217A GLU 3.0 18.2 + - - +
218A THR* 4.2 4.7 - - - +
220A ASN* 1.3 76.1 - - - +
222A PRO* 1.3 70.1 - - + +
224A LEU* 3.1 11.7 + - + +
225A CYS* 3.0 36.5 + - - -
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Residues in contact with PRO 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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139A MET* 4.0 36.8 - - + +
142A LEU* 5.0 1.6 - - + +
143A TYR* 5.8 0.2 - - - -
145A VAL* 3.8 25.5 - - + +
146A THR* 3.8 11.2 - - + -
218A THR 3.4 15.5 - - - +
219A PHE* 3.7 9.4 - - - +
220A ASN 3.7 0.9 - - - -
221A LEU* 1.3 94.5 - - + +
223A ARG* 1.3 59.6 + - - +
225A CYS* 3.4 1.6 + - + +
226A ILE* 3.0 36.7 + - + +
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Residues in contact with ARG 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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134A ILE* 5.0 7.1 + - - +
135A ASN* 5.1 6.3 + - - +
136A GLN* 5.9 1.2 - - - +
139A MET* 3.6 41.9 - - + +
205A SER 2.8 24.4 + - - +
206A LEU* 3.7 27.6 - - - +
207A LYS 3.4 20.8 + - - -
208A LEU* 3.8 6.5 - - + -
219A PHE* 2.7 74.6 + - - +
220A ASN 3.1 7.5 + - - +
222A PRO* 1.3 75.1 - - - +
224A LEU* 1.3 66.3 + - - +
226A ILE* 3.4 1.6 + - - +
227A ARG* 3.0 31.8 + - - +
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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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208A LEU* 3.8 26.2 - - + +
220A ASN* 2.8 30.4 + - + +
221A LEU* 3.5 10.8 - - + +
223A ARG* 1.3 73.4 - - - +
225A CYS* 1.3 63.5 + - - +
227A ARG* 3.4 6.1 + - + +
228A LYS* 2.9 55.0 + - + +
560A LEU* 4.7 7.6 - - + -
568A GLU* 3.7 42.6 - - + +
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Residues in contact with CYS 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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145A VAL* 3.7 28.3 - - + +
146A THR* 4.1 13.5 - - - -
149A THR* 5.6 2.2 - - - -
221A LEU* 3.0 29.7 + - - -
222A PRO 3.6 7.6 - - - +
224A LEU* 1.3 79.5 - - - +
226A ILE* 1.3 56.9 + - - +
229A PHE* 2.9 70.6 + - + +
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Residues in contact with ILE 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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139A MET* 4.3 9.4 - - + -
142A LEU* 3.9 27.6 - - + -
145A VAL* 4.1 15.3 - - + -
178A PHE* 4.3 32.5 - - + -
180A TRP* 4.3 5.4 - - + -
206A LEU* 3.9 35.9 - - + -
222A PRO 3.0 18.8 + - - +
223A ARG 3.8 3.8 - - - +
225A CYS* 1.3 76.3 - - - +
227A ARG* 1.3 63.6 + - - +
228A LYS 3.5 0.2 + - - -
230A PHE* 3.5 21.9 + - + -
233A LYS* 3.2 20.6 - - + -
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Residues in contact with ARG 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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172A VAL* 6.0 0.2 - - - +
203A THR 5.7 0.2 + - - -
206A LEU* 3.1 51.7 + - + -
207A LYS* 3.8 13.1 - - - +
208A LEU* 3.9 14.9 - - - +
223A ARG 3.0 18.4 + - - +
224A LEU* 3.9 7.1 - - + +
226A ILE* 1.3 76.6 - - - +
228A LYS* 1.3 60.8 + - + +
230A PHE 4.1 0.3 - - - +
233A LYS* 2.8 27.5 + - - +
556A GLU* 3.4 48.6 + - - +
559A GLN* 4.5 5.9 - - - +
560A LEU* 3.8 13.6 - - - +
563A GLU* 3.0 36.3 + - - -
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Residues in contact with LYS 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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168A SER 5.6 0.3 - - - +
172A VAL* 3.5 21.4 + - - +
224A LEU* 2.9 41.8 + - + +
227A ARG* 1.3 82.5 - - + +
229A PHE* 1.3 77.3 + - + +
553A LYS* 4.8 6.6 + - - +
556A GLU* 4.9 5.6 - - + +
560A LEU* 5.3 1.8 - - + -
568A GLU* 4.4 8.0 + - - +
571A ILE* 4.0 13.3 - - - +
572A MET* 3.5 40.7 - - + +
575A GLU* 2.9 32.7 + - - +
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Residues in contact with PHE 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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145A VAL 4.3 5.8 - - - -
148A LEU* 4.2 16.6 - - + -
149A THR* 3.6 28.7 - - + -
168A SER* 3.9 17.0 - - - -
171A PHE* 3.8 33.2 - + + -
172A VAL* 3.2 22.0 - - - +
175A PHE* 3.2 29.6 - - + +
225A CYS* 2.9 56.9 + - + +
228A LYS* 1.3 93.3 - - + +
230A PHE* 1.3 63.3 + + + +
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Residues in contact with PHE 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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116A PHE* 5.5 2.2 - + - -
120A VAL* 4.5 10.8 - - + -
126A PHE* 4.5 9.2 - + + -
145A VAL* 4.2 21.8 - - + -
148A LEU* 4.4 8.5 - - + -
172A VAL* 4.0 4.3 - - - +
175A PHE* 3.8 24.0 - + - -
176A PRO* 3.2 33.4 - - + +
178A PHE* 3.7 48.0 - + + -
226A ILE* 3.5 23.4 + - - +
227A ARG 4.1 1.0 - - - +
229A PHE* 1.3 91.0 - - + +
231A PRO* 1.3 64.8 - - + +
232A LYS 4.1 2.7 - - - +
233A LYS* 2.8 32.9 + - - -
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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