Contacts of the helix formed by residues 164 - 180 (chain E) in PDB entry 5LEZ
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 ARG 164 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E LEU* 5.9 1.6 - - - +
162E GLY 3.4 0.8 + - - -
163E ALA* 1.3 94.4 + - - +
165E SER* 1.3 62.0 + - - +
166E GLN* 3.2 6.6 + - - +
167E SER* 3.4 17.1 + - - +
198E THR* 2.8 47.9 + - - +
199E LEU* 4.8 3.8 - - - +
200E PRO* 3.8 24.8 - - - +
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Residues in contact with SER 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E ALA* 4.8 0.9 - - - -
160E SER* 3.4 22.2 - - - -
161E ILE* 3.5 14.1 - - - -
162E GLY 2.6 26.6 + - - -
163E ALA 3.1 2.5 - - - -
164E ARG* 1.3 75.1 - - - +
166E GLN* 1.3 61.0 + - - +
167E SER 3.2 0.4 - - - -
168E ALA* 3.1 4.7 + - - +
169E ARG* 2.8 53.5 + - - +
198E THR* 4.2 5.8 - - - -
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Residues in contact with GLN 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164E ARG* 3.2 3.6 - - - +
165E SER* 1.3 78.8 + - - +
167E SER* 1.3 57.3 + - - +
169E ARG* 3.3 30.3 + - + +
170E THR* 2.9 38.9 + - - +
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Residues in contact with SER 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164E ARG* 3.4 15.5 + - - +
165E SER 3.2 0.6 - - - -
166E GLN* 1.3 78.0 - - - +
168E ALA* 1.3 62.1 + - - +
170E THR* 3.5 7.4 + - - -
171E TYR* 3.1 21.8 + - - +
197E GLU* 3.3 44.7 + - - +
198E THR* 4.7 0.5 - - - -
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Residues in contact with ALA 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E VAL* 4.1 5.8 - - + -
160E SER* 3.4 28.0 - - - +
164E ARG 4.3 0.8 + - - -
165E SER 3.1 4.9 + - - +
167E SER* 1.3 77.8 - - - +
169E ARG* 1.3 58.0 + - - +
171E TYR* 3.0 4.9 + - - +
172E LEU* 2.8 34.2 + - + +
194E ALA* 3.3 32.2 + - + +
198E THR* 3.9 11.4 - - + +
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Residues in contact with ARG 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148E 6V1 6.0 0.6 + - - -
159E MET* 3.9 15.7 - - - -
160E SER* 2.9 39.2 + - - +
161E ILE* 4.4 1.8 - - - +
165E SER* 2.8 35.4 + - - +
166E GLN* 3.3 42.1 + - + +
168E ALA* 1.3 75.7 - - - +
170E THR* 1.3 55.9 + - - +
172E LEU* 3.3 5.1 + - - +
173E GLU* 2.9 38.9 + - - +
55F SER* 5.4 2.7 - - - -
57F LEU* 3.8 21.2 - - + +
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Residues in contact with THR 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E GLN* 2.9 23.4 + - - +
167E SER* 3.7 8.1 - - - -
169E ARG* 1.3 73.0 - - - +
171E TYR* 1.3 66.9 + - - +
173E GLU* 3.6 8.6 + - - +
174E ARG* 3.1 38.1 + - - +
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Residues in contact with TYR 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E SER 3.1 10.2 + - - +
168E ALA 3.0 8.3 + - - +
170E THR* 1.3 79.3 - - - +
172E LEU* 1.3 69.7 + - + +
174E ARG* 3.1 35.7 + - - +
175E HIS* 3.2 43.0 + + + -
179E PHE* 5.1 0.4 - + - -
190E HIS* 2.9 47.7 + - + -
193E ARG* 3.4 39.0 + - + +
194E ALA* 3.6 23.1 - - + -
197E GLU* 3.7 20.6 - - + +
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Residues in contact with LEU 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E VAL* 3.9 18.4 - - + -
38E LEU* 4.4 8.1 - - + -
158E ALA* 4.2 7.9 - - + -
159E MET* 3.7 38.1 - - - +
160E SER* 4.3 2.9 - - - +
168E ALA 2.8 29.1 + - - +
169E ARG* 3.7 6.5 - - - +
171E TYR* 1.3 76.9 - - + +
173E GLU* 1.3 63.3 + - - +
175E HIS 3.3 1.2 + - - -
176E MET* 3.0 28.1 + - - +
179E PHE* 3.8 24.4 - - + -
190E HIS 4.9 0.9 - - - +
194E ALA* 3.7 20.0 - - + -
57F LEU* 3.8 14.4 - - + -
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Residues in contact with GLU 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169E ARG* 2.9 23.4 + - - +
170E THR* 3.8 7.0 - - - +
172E LEU* 1.3 77.2 - - - +
174E ARG* 1.3 61.4 + - - +
175E HIS 3.3 0.7 + - - -
176E MET* 3.6 23.0 + - + +
55F SER* 4.0 16.3 + - - -
56F LYS* 3.3 38.9 + - + +
57F LEU* 3.8 20.8 - - + +
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Residues in contact with ARG 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E THR* 3.1 36.5 + - - +
171E TYR* 3.1 34.0 + - - +
173E GLU* 1.3 79.4 - - - +
175E HIS* 1.3 78.5 + - + +
176E MET 3.7 0.4 + - - -
177E SER* 5.4 2.4 + - - -
178E GLU* 5.1 0.9 - - - +
197E GLU* 3.4 25.9 + - - -
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Residues in contact with HIS 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E TYR* 3.2 63.0 + + + +
172E LEU 3.7 1.1 - - - -
174E ARG* 1.3 105.1 + - + +
176E MET* 1.3 63.3 + - - +
177E SER* 3.3 3.1 - - - -
178E GLU* 3.1 42.3 + - - +
179E PHE* 3.2 24.7 - - + -
190E HIS* 3.9 12.7 - + + +
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Residues in contact with MET 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157E ARG* 3.4 49.8 + - + +
158E ALA* 5.7 0.2 - - + -
172E LEU 3.0 12.7 + - - +
173E GLU* 3.6 20.5 + - + +
174E ARG 3.7 0.4 - - - -
175E HIS* 1.3 78.5 - - - +
177E SER* 1.3 60.4 + - - +
178E GLU 3.0 0.4 - - - -
179E PHE* 3.0 42.0 + - + +
180E MET* 4.4 2.8 + - - +
56F LYS* 3.6 38.4 - - + +
57F LEU* 4.3 18.6 - - + -
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Residues in contact with SER 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157E ARG* 3.9 11.9 - - - +
174E ARG 5.4 2.6 + - - -
175E HIS* 4.9 1.4 - - - -
176E MET* 1.3 80.5 - - - +
178E GLU* 1.3 65.0 + - - +
179E PHE 3.5 0.2 - - - -
180E MET* 5.0 3.9 + - - +
181E GLU* 5.7 1.2 + - - +
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Residues in contact with GLU 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174E ARG 5.1 0.5 - - - +
175E HIS* 3.2 39.2 + - - +
176E MET 3.0 1.4 - - - -
177E SER* 1.3 82.9 - - - +
179E PHE* 1.3 64.1 + - - +
180E MET 3.4 1.7 + - - -
181E GLU* 3.6 12.1 + - - +
182E CYS* 3.2 16.7 + - - -
190E HIS* 3.2 27.4 + - - +
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Residues in contact with PHE 179 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E LEU* 3.9 19.5 - - + -
39E LYS 3.4 17.9 - - - +
40E SER* 3.3 13.9 - - - -
157E ARG* 4.6 5.4 - - + -
158E ALA* 3.9 26.0 - - + -
171E TYR* 5.1 0.9 - + - -
172E LEU* 3.8 36.8 - - + -
175E HIS* 3.2 20.4 - - + -
176E MET* 3.0 30.7 + - + +
178E GLU* 1.3 78.8 - - - +
180E MET* 1.3 66.4 + - + +
182E CYS* 3.0 19.7 + - - +
187E LEU* 4.0 4.4 - - + +
190E HIS* 3.8 33.2 - + + -
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Residues in contact with MET 180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E LYS* 4.3 29.6 - - + +
40E SER* 3.7 25.8 - - - +
41E LYS* 2.9 42.0 + - + +
157E ARG* 4.8 23.6 - - + +
176E MET 4.4 2.6 + - - +
177E SER 5.0 3.0 + - - +
178E GLU 3.4 1.2 + - - -
179E PHE* 1.3 79.0 - - + +
181E GLU* 1.3 65.6 + - + +
182E CYS 3.7 0.7 + - - +
59F GLU* 4.5 7.6 - - - +
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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
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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