Contacts of the helix formed by residues 172 - 187 (chain D) in PDB entry 1EJH
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 ASN 172 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D ASP* 2.8 33.9 + - - +
168D THR* 5.4 1.0 - - - -
169D GLU* 3.0 30.7 + - - +
171D GLU* 1.3 77.5 - - - +
173D ARG* 1.3 63.9 + - - +
174D ASP 3.2 3.1 - - - -
175D ALA* 2.9 18.5 + - + +
176D VAL* 3.0 15.6 + - - +
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Residues in contact with ARG 173 (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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46C TRP* 3.4 29.9 - - - -
60C LEU* 5.3 4.8 + - - +
62C LEU* 3.5 33.1 - - + +
99C GLU* 3.4 30.1 + - - +
171D GLU 2.9 15.4 + - - +
172D ASN* 1.3 70.0 - - - +
174D ASP* 1.3 83.9 + - - +
176D VAL* 4.1 0.8 - - - +
177D THR* 2.8 35.5 + - - -
215D PHE* 3.9 25.3 - - + -
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Residues in contact with ASP 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LEU* 4.4 1.4 - - - +
65C LYS* 3.0 36.0 + - - +
145D TYR* 3.4 25.1 - - + +
172D ASN 3.1 1.0 + - - -
173D ARG* 1.3 96.0 + - - +
175D ALA* 1.3 57.7 + - - +
177D THR* 3.8 2.1 - - - +
178D HIS* 3.1 30.3 + - - +
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Residues in contact with ALA 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D TYR* 3.3 35.1 - - + -
148D ASP* 3.6 33.0 - - + +
172D ASN* 2.9 13.5 + - + +
174D ASP* 1.3 77.1 - - - +
176D VAL* 1.3 65.6 + - - +
178D HIS* 3.4 1.2 + - - +
179D ILE* 2.9 32.1 + - - +
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Residues in contact with VAL 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D TRP* 2.9 31.4 + - + +
148D ASP* 5.5 0.7 - - + +
167D THR* 3.8 17.5 - - - +
169D GLU 3.6 24.5 - - - +
170D CYS* 4.2 6.5 - - - -
172D ASN 3.0 15.2 + - - +
173D ARG 4.1 3.1 - - - +
175D ALA* 1.3 76.7 - - + +
177D THR* 1.3 63.0 + - - +
179D ILE* 3.5 5.3 + - - +
180D GLY 3.0 6.4 + - - -
197D TYR* 3.5 41.3 - - + -
215D PHE* 3.6 20.6 - - + -
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Residues in contact with THR 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LEU* 3.7 14.4 - - - +
64C SER* 4.7 4.4 - - - -
65C LYS* 3.2 53.3 - - + +
113D TRP* 4.5 6.5 - - - -
173D ARG 2.8 22.7 + - - -
174D ASP 3.8 3.6 - - - -
176D VAL* 1.3 75.0 - - - +
178D HIS* 1.3 69.0 + - - +
180D GLY* 3.3 3.1 + - - -
181D ARG* 3.1 25.1 + - + +
215D PHE* 4.1 11.9 - - - +
217D VAL* 4.2 6.6 - - + +
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Residues in contact with HIS 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ARG* 5.8 9.4 + - - -
142D PHE* 4.0 25.9 + - - +
143D ASP* 4.3 17.9 + - + +
144D ASP* 5.8 0.8 + - - +
145D TYR* 3.5 26.8 - + + +
174D ASP 3.1 16.5 + - - +
175D ALA 3.7 0.7 - - - +
177D THR* 1.3 80.5 - - - +
179D ILE* 1.3 66.6 + - - +
181D ARG* 3.0 17.8 + - + +
182D VAL* 3.0 38.0 + - + +
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Residues in contact with ILE 179 (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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113D TRP* 3.7 18.4 - - + +
142D PHE* 3.4 31.5 - - + -
145D TYR* 3.5 26.9 - - + +
148D ASP* 4.1 12.1 - - + -
149D VAL* 3.8 10.8 - - + -
165D ILE* 4.1 21.5 - - + -
167D THR* 3.8 21.1 - - + -
175D ALA 2.9 24.2 + - - +
176D VAL 3.7 3.8 - - - +
178D HIS* 1.3 76.1 + - - +
180D GLY* 1.3 64.3 + - - +
183D TYR* 3.0 27.1 + - + +
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Residues in contact with GLY 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D TRP* 3.2 37.4 - - - +
176D VAL 3.0 11.5 + - - -
177D THR 3.3 2.4 + - - -
179D ILE* 1.3 76.4 - - - +
181D ARG* 1.3 55.8 + - - +
183D TYR* 3.6 3.4 - - - +
184D LYS* 2.8 32.2 + - - +
195D ILE* 4.2 4.0 - - - +
217D VAL* 4.1 6.3 - - - -
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Residues in contact with ARG 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LYS* 5.8 0.2 - - - +
42C ARG* 6.0 4.5 - - - +
64C SER* 4.2 3.8 + - - -
65C LYS* 3.0 30.9 + - + +
66C PHE* 3.8 9.8 - - - +
67C ASP* 5.7 6.1 - - - +
71C ASP* 3.2 53.2 + - - +
75C LEU* 5.4 2.6 - - - +
177D THR* 3.1 17.8 + - + +
178D HIS* 3.0 12.0 + - + +
180D GLY* 1.3 75.6 - - - +
182D VAL* 1.3 58.7 + - + +
184D LYS* 3.2 11.5 + - - +
185D GLU* 2.9 33.9 + - - +
217D VAL* 2.9 47.8 - - + +
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Residues in contact with VAL 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D SER* 3.5 24.5 - - - +
142D PHE* 3.6 21.5 - - + -
143D ASP* 6.1 0.2 - - - -
178D HIS* 3.0 39.8 + - + +
181D ARG* 1.3 79.2 - - + +
183D TYR* 1.3 51.7 + - - +
185D GLU* 3.1 7.4 + - - +
186D ARG* 2.7 56.6 + - + +
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Residues in contact with TYR 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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113D TRP* 4.6 14.1 - + + -
115D ILE* 3.8 19.7 - - + -
133D THR* 2.6 37.1 + - + +
136D CYS* 4.6 8.3 - - - -
142D PHE* 3.7 11.9 - + + -
163D ILE* 3.2 21.4 - - - +
165D ILE* 3.6 45.5 - - + +
179D ILE* 3.0 21.3 + - + +
180D GLY* 3.6 3.8 - - - +
182D VAL* 1.3 75.1 - - - +
184D LYS* 1.3 66.2 + - - +
186D ARG* 3.1 3.2 + - - +
187D LEU* 2.9 59.3 + - + +
195D ILE* 4.8 2.2 - - + -
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Residues in contact with LYS 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LYS* 5.2 4.0 - - - +
71C ASP* 4.9 4.1 + - - +
74C ALA* 5.1 1.4 - - - +
180D GLY 2.8 20.6 + - - +
181D ARG* 3.5 14.2 - - - +
183D TYR* 1.3 74.3 - - - +
185D GLU* 1.3 61.8 + - - +
187D LEU 3.6 0.2 + - - -
188D GLY 3.3 2.9 + - - -
189D LEU* 3.2 53.4 + - + +
190D PRO 3.8 11.5 + - - -
191D PRO* 4.4 11.0 + - - -
193D ILE* 3.3 20.6 - - - -
194D VAL* 3.3 20.2 - - - +
195D ILE* 4.1 12.1 - - + -
217D VAL* 2.8 47.4 + - + +
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Residues in contact with GLU 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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33C HIS* 3.8 31.6 + - - -
34C TYR 5.4 0.5 - - - +
36C LYS* 4.0 27.4 - - + +
181D ARG* 2.9 14.3 + - - +
182D VAL* 3.4 11.4 - - + +
184D LYS* 1.3 76.8 - - + +
186D ARG* 1.3 66.4 + - + +
188D GLY* 3.2 13.6 + - - -
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Residues in contact with ARG 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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132D GLU* 2.8 39.7 + - + +
135D LEU* 4.4 12.7 - - - +
136D CYS* 3.7 29.2 - - - -
141D SER* 3.9 22.4 + - - -
182D VAL* 2.7 44.0 + - + +
183D TYR* 3.1 4.0 + - + +
185D GLU* 1.3 75.6 - - + +
187D LEU* 1.3 60.7 + - + +
188D GLY 3.2 0.8 + - - -
626H ARG* 3.7 38.6 - - - +
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Residues in contact with LEU 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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115D ILE* 4.0 18.2 - - + -
129D PHE* 3.7 56.2 - - + +
132D GLU* 4.1 14.6 - - + -
133D THR* 4.0 7.9 - - - +
136D CYS* 6.4 0.2 - - - -
163D ILE* 5.9 1.3 - - + -
183D TYR* 2.9 56.2 + - + +
186D ARG* 1.3 78.5 - - + +
188D GLY* 1.3 64.0 + - - +
189D LEU* 3.4 30.3 + - + +
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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
------------------------------------------------------------
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