Contacts of the helix formed by residues 184 - 197 (chain E) in PDB entry 5L5E
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 184 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42E HIS* 4.7 2.7 - - - -
181E ILE* 3.4 21.0 + - + +
182E ASP* 3.2 6.2 - - - +
183E GLY* 1.3 79.6 + - - +
185E PRO* 1.3 68.7 - - - +
186E ASP* 3.4 10.0 + - - +
187E GLU* 3.2 34.8 - - - +
188E LEU* 3.4 17.5 + - - +
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Residues in contact with PRO 185 (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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42E HIS* 4.3 21.1 - - + +
183E GLY 3.8 5.4 - - - +
184E ASN* 1.3 89.6 - - - +
186E ASP* 1.3 71.9 + - - +
188E LEU* 3.2 7.3 + - + +
189E ILE* 3.1 30.2 + - + +
214E ILE* 3.7 25.9 - - + +
219E THR* 6.5 0.7 - - + -
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Residues in contact with ASP 186 (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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184E ASN* 3.3 9.0 - - - +
185E PRO* 1.3 87.0 - - - +
187E GLU* 1.3 59.4 + - + +
189E ILE* 3.4 3.8 + - - +
190E LYS* 3.0 36.3 + - - +
231E LYS* 4.1 15.4 - - - +
232E TYR* 3.4 31.5 + - + +
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Residues in contact with GLU 187 (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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181E ILE* 3.8 22.5 - - + +
184E ASN* 3.2 32.1 + - - +
185E PRO 3.3 0.6 - - - -
186E ASP* 1.3 75.5 - - + +
188E LEU* 1.3 63.5 + - - +
190E LYS* 3.5 30.9 + - - +
191E ALA* 3.2 21.8 + - - +
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Residues in contact with LEU 188 (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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37E LEU* 3.6 33.6 - - + +
38E ARG* 4.4 7.2 - - - -
39E SER* 3.6 31.2 - - - +
42E HIS* 3.7 33.7 - - + +
44E VAL* 4.0 14.1 - - + -
178E PHE* 4.6 9.0 - - + +
181E ILE* 3.8 16.3 - - + +
184E ASN 3.4 9.6 + - - +
185E PRO* 3.2 11.1 + - + +
187E GLU* 1.3 75.6 - - - +
189E ILE* 1.3 64.4 + - - +
191E ALA* 3.4 2.1 + - - +
192E GLY* 3.2 17.3 + - - -
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Residues in contact with ILE 189 (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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44E VAL* 4.1 28.0 - - + -
46E VAL* 4.7 0.8 - - + +
185E PRO* 3.1 17.2 + - + +
186E ASP* 3.7 6.1 - - - +
187E GLU 3.4 0.2 - - - -
188E LEU* 1.3 73.9 - - - +
190E LYS* 1.3 55.7 + - - +
192E GLY* 2.9 3.0 + - - +
193E VAL* 2.7 34.5 + - + +
212E ILE* 3.7 40.4 - - + -
214E ILE* 4.2 18.8 - - + -
224E TYR* 5.0 6.3 - - + -
232E TYR* 3.4 42.6 - - + +
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Residues in contact with LYS 190 (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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186E ASP* 3.0 20.3 + - - +
187E GLU* 3.5 36.1 + - - +
189E ILE* 1.3 76.7 - - - +
191E ALA* 1.3 52.2 + - - +
193E VAL* 3.2 8.2 + - - +
194E GLU* 2.8 37.4 + - - +
231E LYS* 5.4 6.7 + - - +
232E TYR* 4.7 18.4 - - + +
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Residues in contact with ALA 191 (chain E).
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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37E LEU* 4.1 14.1 - - + +
170E TYR* 3.6 21.1 - - + +
174E THR* 5.5 3.4 - - + -
178E PHE* 4.3 16.6 - - + -
181E ILE* 4.5 5.6 - - + -
187E GLU 3.2 11.3 + - - +
188E LEU 3.6 9.4 - - - +
189E ILE 3.2 0.4 - - - -
190E LYS* 1.3 79.1 - - - +
192E GLY* 1.3 58.2 + - - +
194E GLU* 3.6 1.6 + - - +
195E ALA* 3.0 26.7 + - - +
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Residues in contact with GLY 192 (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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35E VAL* 4.3 2.5 - - - +
37E LEU* 3.7 26.1 - - - +
46E VAL* 3.8 15.5 - - - +
188E LEU 3.2 7.8 + - - -
189E ILE* 2.9 7.4 + - - -
191E ALA* 1.3 76.1 - - - +
193E VAL* 1.3 58.4 + - - +
195E ALA* 3.3 6.2 + - - +
196E ILE* 3.0 29.5 + - - +
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Residues in contact with VAL 193 (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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46E VAL* 4.5 6.5 - - + -
189E ILE* 2.7 28.0 + - + +
190E LYS* 3.6 6.5 - - - +
192E GLY* 1.3 71.0 - - - +
194E GLU* 1.3 56.2 + - - +
196E ILE* 3.2 8.7 - - - +
197E SER* 2.7 35.8 + - - +
205E LEU* 3.7 23.3 - - + -
210E LEU* 4.5 7.0 - - + -
212E ILE* 4.0 26.7 - - + -
232E TYR* 3.9 28.7 - - + +
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Residues in contact with GLU 194 (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 TYR* 3.2 35.8 + - + +
190E LYS* 2.8 18.1 + - - +
191E ALA* 3.9 1.9 - - - +
193E VAL* 1.3 76.3 - - - +
195E ALA* 1.3 61.8 + - - +
197E SER* 3.6 10.4 - - - -
198E GLN* 3.2 32.7 + - - +
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Residues in contact with ALA 195 (chain E).
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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35E VAL* 4.2 8.3 - - + -
167E ALA* 3.2 20.5 - - + +
170E TYR* 3.5 25.8 - - + -
171E LEU* 4.0 20.0 - - + -
191E ALA 3.0 19.3 + - - +
192E GLY* 3.5 8.1 - - - +
193E VAL 3.2 0.4 - - - -
194E GLU* 1.3 75.6 - - - +
196E ILE* 1.3 65.5 + - - +
198E GLN* 3.1 16.1 + - - +
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Residues in contact with ILE 196 (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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33E VAL* 3.8 24.2 - - + +
34E THR* 4.4 0.4 - - - -
35E VAL* 3.6 20.8 - - + +
46E VAL* 3.7 34.5 - - + +
47E ALA* 3.9 3.8 - - - -
48E LEU* 3.5 32.3 - - + +
167E ALA* 4.4 2.5 - - - -
192E GLY 3.0 13.7 + - - +
193E VAL* 3.2 14.8 - - - +
195E ALA* 1.3 76.0 - - - +
197E SER* 1.3 64.0 + - - +
198E GLN 3.1 0.2 - - - -
199E SER* 3.1 16.5 + - - -
200E LEU* 3.7 11.1 - - + +
205E LEU* 4.3 18.4 - - + -
210E LEU* 5.4 0.9 - - + -
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Residues in contact with SER 197 (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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193E VAL* 2.7 24.3 + - - +
194E GLU* 3.6 12.8 - - - -
195E ALA 3.1 0.8 - - - -
196E ILE* 1.3 77.8 - - - +
198E GLN* 1.3 64.3 + - - +
199E SER 3.1 1.8 + - - -
200E LEU* 3.5 31.6 + - - +
205E LEU* 3.6 17.0 - - - +
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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