Contacts of the helix formed by residues 182 - 193 (chain D) in PDB entry 1EQB
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 ASP 182 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155D TYR* 2.9 24.4 + - + +
180D VAL* 3.9 2.1 + - - -
181D VAL* 1.3 72.0 - - - +
183D TRP* 1.3 60.5 - - - +
184D ALA* 3.3 10.6 + - - +
185D LYS* 2.8 45.1 + - + +
186D MET* 3.1 22.3 + - - +
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Residues in contact with TRP 183 (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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172D GLY* 4.1 12.3 - - - -
173D GLY* 4.4 10.5 - - - -
174D PHE* 4.6 4.3 - + - -
181D VAL* 3.1 41.3 + - + -
182D ASP* 1.3 71.0 + - - +
184D ALA* 1.3 64.4 + - - +
186D MET* 3.1 10.4 + - - +
187D ARG* 3.0 22.3 + - - +
197D LEU* 3.7 6.1 - - + +
199D VAL* 3.7 36.6 - - + -
200D ASP 5.6 0.4 - - - -
201D MET* 5.4 1.3 - - + -
204D VAL* 5.0 7.4 - - + -
213D TYR* 3.9 19.9 - + - -
214D PRO* 2.8 39.9 + - + +
215D ASN 3.6 5.6 - - - -
216D PRO* 3.4 37.5 - - + +
219D HIS* 3.9 22.4 - + + -
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Residues in contact with ALA 184 (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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182D ASP* 3.3 7.0 + - - +
183D TRP* 1.3 77.9 - - - +
185D LYS* 1.3 57.8 + - - +
187D ARG* 3.3 4.8 + - - +
188D GLU* 3.0 32.9 + - - +
219D HIS* 3.6 34.5 - - + +
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Residues in contact with LYS 185 (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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155D TYR* 3.9 35.7 - - + -
159D GLU* 4.0 19.6 + - - -
182D ASP* 2.8 38.4 + - + +
184D ALA* 1.3 71.1 - - - +
186D MET* 1.3 64.5 + - - +
188D GLU* 3.3 34.6 + - - +
189D ILE* 3.2 29.3 + - + +
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Residues in contact with MET 186 (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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145D TYR* 3.6 25.4 - - + +
153D ILE* 5.8 2.5 - - + -
155D TYR* 4.1 14.8 - - + -
158D LEU* 3.9 18.6 - - + -
170D ILE* 3.9 26.9 - - + +
172D GLY* 3.8 20.9 - - - +
181D VAL* 3.7 25.1 - - - -
182D ASP 3.1 10.8 + - - +
183D TRP* 3.1 13.9 + - - +
185D LYS* 1.3 73.5 - - - +
187D ARG* 1.3 60.7 + - - +
189D ILE* 3.3 10.0 + - - +
190D ALA* 2.9 28.1 + - - +
197D LEU* 3.8 17.0 - - + +
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Residues in contact with ARG 187 (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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183D TRP 3.0 12.9 + - - +
184D ALA* 3.5 10.5 - - - +
185D LYS 3.2 0.2 - - - -
186D MET* 1.3 75.0 - - - +
188D GLU* 1.3 65.5 + - - +
190D ALA* 3.2 2.0 + - - -
191D ASP* 2.8 52.5 + - - +
197D LEU* 3.5 8.7 - - + +
218D PRO 5.1 1.8 + - - -
219D HIS* 2.6 59.6 + - + +
220D ALA 4.2 6.7 + - - +
221D HIS* 3.5 38.4 + - - +
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Residues in contact with GLU 188 (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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184D ALA* 3.0 17.1 + - - +
185D LYS* 3.3 40.7 + - + +
187D ARG* 1.3 78.9 - - - +
189D ILE* 1.3 64.1 + - + +
191D ASP* 3.1 15.1 + - - +
192D SER* 3.1 13.8 + - - -
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Residues in contact with ILE 189 (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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155D TYR* 3.7 28.9 - - + +
158D LEU* 3.8 25.8 - - + +
159D GLU* 3.9 30.7 - - + +
162D ALA* 3.6 27.8 - - + -
163D LYS* 6.4 0.2 - - + -
170D ILE* 4.0 9.2 - - + -
185D LYS* 3.2 22.4 + - - +
186D MET* 3.5 9.4 - - - +
187D ARG 3.3 0.2 - - - -
188D GLU* 1.3 77.4 - - + +
190D ALA* 1.3 61.7 + - - +
192D SER* 2.7 24.6 + - - +
193D ILE* 3.8 7.4 + - - +
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Residues in contact with ALA 190 (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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170D ILE* 4.1 15.9 - - + +
186D MET 2.9 14.9 + - - +
187D ARG* 3.5 11.2 - - - +
189D ILE* 1.3 75.3 - - - +
191D ASP* 1.3 65.2 + - - +
193D ILE* 3.0 5.0 + - - +
194D GLY 2.9 17.5 + - - -
195D ALA* 2.9 33.0 + - + +
196D TYR 4.5 0.4 - - - -
197D LEU* 4.2 19.3 - - + +
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Residues in contact with ASP 191 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A ASN* 5.8 1.2 + - - -
144A PRO* 3.6 13.2 - - - +
187D ARG* 2.8 55.6 + - - +
188D GLU* 3.1 7.7 + - - +
190D ALA* 1.3 77.3 - - - +
192D SER* 1.3 62.0 + - - +
193D ILE 3.2 0.5 + - - -
194D GLY* 3.2 11.9 + - - +
195D ALA 4.9 0.9 - - - +
221D HIS* 4.4 5.9 + - - -
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Residues in contact with SER 192 (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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143A VAL* 4.2 10.4 - - - +
144A PRO* 3.9 12.5 - - - +
161A GLN* 4.3 11.1 + - - +
165A HIS* 5.1 1.7 + - - -
159D GLU* 5.3 1.7 - - - +
162D ALA* 5.9 0.2 - - - +
163D LYS* 3.7 26.2 + - - +
188D GLU 3.1 10.5 + - - -
189D ILE* 2.7 26.6 + - - +
191D ASP* 1.3 75.8 - - - +
193D ILE* 1.3 64.6 + - - +
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Residues in contact with ILE 193 (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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142A ILE 4.2 0.9 - - - +
143A VAL* 5.3 2.2 - - - -
144A PRO* 4.1 7.6 - - - -
165A HIS* 4.4 14.8 - - + +
162D ALA* 3.6 26.2 - - + +
163D LYS* 4.2 17.0 - - + +
166D LYS* 2.8 40.3 - - + +
167D PRO* 3.4 47.6 - - + +
170D ILE* 4.5 2.2 - - + -
189D ILE 3.8 6.7 - - - +
190D ALA 3.4 10.3 - - - +
192D SER* 1.3 88.1 + - - +
194D GLY* 1.3 62.0 + - - +
195D ALA* 3.8 8.8 - - + -
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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