Contacts of the helix formed by residues 169 - 177 (chain D) in PDB entry 2E52
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 TRP 169 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43D VAL* 3.4 38.6 - - + +
44D ARG* 5.3 3.1 - - - +
46D ILE* 3.6 29.4 - - + -
47D GLY* 3.5 20.1 - - - -
67D GLY* 3.5 26.2 - - - -
70D VAL* 4.4 5.2 - - + -
71D LEU* 4.1 19.5 - - + -
109D ALA* 3.6 25.1 - - + -
110D LYS 2.8 30.3 + - - -
111D SER* 4.9 2.2 - - - -
142D THR* 3.6 22.8 + - + +
143D ALA 3.2 26.3 + - - -
144D PRO* 3.6 4.9 - - + -
168D SER* 1.3 72.0 - - - +
170D GLU* 1.3 64.8 + - - +
172D LEU* 3.4 5.3 + - + -
173D ALA* 2.8 27.5 + - - +
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Residues in contact with GLU 170 (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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44D ARG* 5.3 5.3 - - - +
144D PRO* 3.7 9.0 - - - +
145D PHE* 2.8 42.5 + - + +
146D PHE* 4.3 11.5 - - + -
168D SER* 3.1 6.0 - - - +
169D TRP* 1.3 86.2 + - - +
171D HIS* 1.3 57.4 + - - +
173D ALA* 3.3 7.1 + - - +
174D ILE* 3.1 33.9 + - - +
234D LEU* 4.5 11.4 - - + -
237D GLU* 4.1 35.8 - - + +
241D ILE* 3.9 18.4 - - + +
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Residues in contact with HIS 171 (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 PHE* 3.6 35.7 - + - -
167D PHE* 3.6 23.1 - - + -
168D SER* 2.6 30.5 + - - +
170D GLU* 1.3 72.8 - - - +
172D LEU* 1.3 65.5 + - - +
174D ILE* 3.2 14.4 + - + +
175D LEU* 3.1 26.2 + - - +
212D MET* 6.0 0.2 - - + -
215D PHE* 3.7 29.0 - + - -
216D ASN* 2.8 27.7 + - - -
219D PHE* 3.8 27.2 - + + -
230D LEU* 5.3 1.5 - - + +
234D LEU* 5.4 6.8 - - + +
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Residues in contact with LEU 172 (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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43D VAL* 4.0 15.0 - - + -
71D LEU* 3.6 31.2 - - + -
74D ALA* 3.7 27.4 - - + -
75D PHE* 5.3 3.1 - - + +
78D LEU* 3.9 30.1 - - + -
142D THR* 4.5 4.0 - - + -
167D PHE* 3.8 20.5 - - + -
168D SER 3.0 16.6 + - - +
169D TRP* 3.5 15.0 - - + +
171D HIS* 1.3 77.8 - - - +
173D ALA* 1.3 61.8 + - - +
175D LEU* 3.3 4.3 + - + +
176D LEU* 3.1 30.2 + - + +
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Residues in contact with ALA 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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40D ILE* 4.4 9.8 - - + +
43D VAL* 3.8 11.6 - - + +
44D ARG* 3.8 28.0 - - + -
169D TRP 2.8 21.0 + - - +
170D GLU 3.6 5.4 - - - +
171D HIS 3.3 0.2 - - - -
172D LEU* 1.3 73.9 - - - +
174D ILE* 1.3 57.1 + - - +
176D LEU* 3.4 7.3 + - - +
177D GLN* 2.9 30.9 + - - +
237D GLU* 3.9 11.0 - - - +
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Residues in contact with ILE 174 (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 GLU 3.1 21.7 + - - +
171D HIS* 3.5 13.2 - - + +
172D LEU 3.2 0.2 - - - -
173D ALA* 1.3 73.9 - - - +
175D LEU* 1.3 65.1 + - - +
177D GLN* 3.3 5.6 + - - +
178D LEU* 3.0 36.3 + - + +
219D PHE* 4.0 20.4 - - + -
225D ILE* 4.2 3.4 - - + -
230D LEU* 3.6 26.2 - - + -
233D LEU* 3.8 38.4 - - + +
234D LEU* 3.8 22.4 - - + +
237D GLU* 5.0 7.2 - - + +
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Residues in contact with LEU 175 (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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78D LEU* 4.0 21.5 - - + -
167D PHE* 4.0 26.2 - - + -
171D HIS 3.1 15.3 + - - +
172D LEU* 3.3 7.6 + - - +
174D ILE* 1.3 76.4 - - - +
176D LEU* 1.3 62.2 + - - +
178D LEU 3.4 0.7 + - - -
179D ASP 3.3 3.3 + - - -
180D LEU* 2.9 47.2 + - + +
188D PHE* 4.1 17.3 - - + -
191D LEU* 4.1 11.7 - - + -
219D PHE* 3.7 22.2 - - + -
223D PHE* 3.8 30.3 - - + -
225D ILE* 5.0 0.4 - - + -
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Residues in contact with LEU 176 (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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36D ARG* 2.8 37.7 + - - +
39D VAL* 4.5 7.0 - - + -
40D ILE* 3.7 25.2 - - + +
43D VAL* 3.9 20.4 - - + -
74D ALA* 3.8 33.0 - - + +
77D LEU* 3.6 32.5 - - + -
78D LEU* 3.9 15.0 - - + -
172D LEU* 3.1 21.8 + - + +
173D ALA* 3.8 2.2 - - - +
175D LEU* 1.3 76.9 - - - +
177D GLN* 1.3 63.9 + - - +
179D ASP* 3.1 3.8 + - - +
180D LEU 5.3 0.2 - - - -
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Residues in contact with GLN 177 (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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37D ASN* 5.0 7.1 + - - +
40D ILE* 3.6 32.0 - - + +
44D ARG* 4.7 6.5 - - - +
173D ALA 2.9 19.6 + - - +
174D ILE* 3.7 7.2 - - - +
176D LEU* 1.3 77.0 - - - +
178D LEU* 1.3 61.6 + - + +
179D ASP* 3.2 11.3 + - - +
233D LEU* 4.2 25.1 - - + -
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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