Contacts of the helix formed by residues 164 - 183 (chain E) in PDB entry 6M04
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 TYR 164 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154E TYR* 5.8 1.3 - - - -
155E HIS* 5.7 0.9 + - - -
160E TRP* 3.8 21.3 - - - +
161E TYR 3.9 4.7 + - - +
162E SER 3.4 0.8 - - - -
163E LYS* 1.3 117.8 + - + +
165E PHE* 1.3 63.3 + - - +
166E PRO* 3.7 2.7 - - - -
167E TYR* 4.0 11.2 + - + +
168E LEU* 3.5 20.1 + - - +
360F TYR* 3.5 27.4 - - - +
361F MET* 3.6 42.1 + - + +
364F LYS* 3.5 34.2 - - + -
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Residues in contact with PHE 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E ALA* 5.7 3.8 - - + -
161E TYR 4.2 3.0 + - - +
162E SER 4.1 8.0 + - - +
163E LYS 3.4 0.6 - - - -
164E TYR* 1.3 76.8 - - - +
166E PRO* 1.4 75.6 - - + +
168E LEU* 3.1 18.9 + - + +
169E ALA* 2.9 37.3 + - + +
325E TYR* 5.5 4.7 - + - -
326E THR* 5.0 5.6 - - + -
329E PHE* 3.5 40.2 - + + -
362E LEU* 4.8 17.3 - - + -
365E LEU* 5.5 8.5 - - + -
366E LEU* 3.6 31.6 - - + -
369E TYR* 3.8 31.9 - + + -
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Residues in contact with PRO 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E ALA 4.6 4.6 - - - +
42E ALA* 3.7 34.5 - - + +
43E GLY* 3.9 8.7 - - - +
45E MET* 6.2 0.9 - - + -
46E GLN* 3.9 30.5 - - + +
163E LYS 4.6 4.5 - - - +
164E TYR 3.9 1.8 - - - -
165E PHE* 1.4 99.0 - - + +
167E TYR* 1.3 63.7 + - + +
169E ALA* 3.3 5.5 + - + +
170E LEU* 3.0 29.9 + - - +
362E LEU* 4.9 11.0 - - + -
365E LEU* 6.0 0.7 - - + -
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Residues in contact with TYR 167 (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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2E PHE* 6.4 0.9 - - + -
43E GLY* 5.6 8.7 + - - -
46E GLN* 2.9 35.4 + - - -
47E LEU* 5.2 9.5 - - + +
163E LYS 5.1 2.9 - - - -
164E TYR* 4.4 14.8 - - + +
165E PHE 3.3 0.6 - - - -
166E PRO* 1.3 79.0 - - + +
168E LEU* 1.3 58.0 + - - +
170E LEU* 3.3 10.8 + - + +
171E ILE* 3.0 37.2 + - + +
41F PHE* 3.5 39.5 - + + -
45F MET* 4.3 12.6 - - + +
49F LYS* 5.2 5.4 + - - -
361F MET* 3.7 30.6 - - + +
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Residues in contact with LEU 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164E TYR 3.5 13.8 + - - +
165E PHE* 3.1 21.6 + - + +
167E TYR* 1.3 78.7 - - - +
169E ALA* 1.3 58.9 + - - +
171E ILE* 3.4 10.0 + - + +
172E HIS* 3.0 36.7 + - + +
322E ILE* 5.3 11.0 - - + -
325E TYR* 4.9 22.0 - - + -
369E TYR* 5.7 2.2 - - + +
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Residues in contact with ALA 169 (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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39E ALA* 4.2 11.4 - - + -
42E ALA* 6.1 1.1 - - + -
165E PHE* 2.9 31.1 + - + +
166E PRO* 3.8 5.8 - - + +
168E LEU* 1.3 79.1 - - - +
170E LEU* 1.3 54.1 + - - +
172E HIS* 3.4 2.4 + - - +
173E THR* 2.6 38.4 + - - -
369E TYR* 4.0 33.7 + - + -
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Residues in contact with LEU 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E PHE 4.3 13.5 - - - +
3E THR* 4.3 21.5 - - + +
36E LEU* 6.4 2.0 - - + -
39E ALA* 4.0 21.0 - - + +
40E ILE* 3.7 30.1 - - + -
43E GLY* 6.0 3.6 - - - -
166E PRO 3.0 16.4 + - - +
167E TYR* 3.7 11.2 - - + +
169E ALA* 1.3 75.7 - - - +
171E ILE* 1.3 76.3 + - + +
173E THR* 3.3 4.4 + - - -
174E ILE* 3.0 42.4 + - + +
37F MET* 6.4 1.8 - - - -
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Residues in contact with ILE 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 TYR* 3.0 24.1 + - + +
168E LEU* 3.8 11.2 - - + +
170E LEU* 1.3 86.0 - - + +
172E HIS* 1.3 58.7 + - - +
174E ILE* 3.3 7.7 + - + +
175E ILE* 3.0 37.8 + - + +
37F MET* 4.4 23.8 - - + -
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Residues in contact with HIS 172 (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 MET* 5.1 6.1 - - + -
168E LEU* 3.0 23.4 + - + +
169E ALA 3.9 3.6 - - - +
170E LEU 3.3 0.2 - - - -
171E ILE* 1.3 77.4 - - - +
173E THR* 1.3 57.4 + - - +
175E ILE* 3.4 13.6 + - + +
176E LEU* 3.0 36.5 + - + +
318E LYS* 3.4 36.0 + - + +
319E PHE* 5.2 0.6 - - - -
321E PHE* 5.8 1.8 - + - -
322E ILE* 3.4 50.2 - - + +
369E TYR* 4.0 11.2 - - - +
373E ILE* 5.7 0.9 - - + -
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Residues in contact with THR 173 (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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32E ALA* 4.0 5.6 - - + +
35E MET* 2.6 37.7 - - + +
36E LEU* 3.6 44.9 - - + +
39E ALA* 4.1 4.7 - - - +
169E ALA 2.6 22.9 + - - -
170E LEU* 3.4 9.0 - - - -
172E HIS* 1.3 75.1 - - - +
174E ILE* 1.3 66.0 + - - +
176E LEU* 3.2 2.4 + - - +
177E MET* 3.0 26.6 + - + +
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Residues in contact with ILE 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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3E THR* 5.3 6.7 - - + -
8E ALA* 4.4 17.3 - - + +
36E LEU* 4.3 22.0 - - + -
170E LEU* 3.0 32.3 + - + +
171E ILE* 3.3 8.0 + - + +
173E THR* 1.3 74.6 - - + +
175E ILE* 1.3 67.1 + - + +
177E MET* 4.8 5.4 - - - -
178E VAL* 3.0 45.5 + - + +
37F MET* 5.7 14.4 - - + -
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Residues in contact with ILE 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 ILE* 3.0 31.7 + - + +
172E HIS* 3.6 17.9 - - + +
174E ILE* 1.3 80.6 - - + +
176E LEU* 1.3 58.7 + - - +
178E VAL* 4.4 1.3 - - - +
179E SER* 2.9 36.7 + - - -
182E PHE* 5.6 0.2 - - - -
314E ILE* 6.4 3.6 - - + -
318E LYS* 5.4 7.2 - - + -
30F TYR* 6.1 1.1 - - - +
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Residues in contact with LEU 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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32E ALA* 4.7 6.7 - - + -
35E MET* 4.0 22.4 - - + -
172E HIS* 3.0 28.0 + - + +
173E THR* 3.2 4.9 + - - +
175E ILE* 1.3 77.8 - - - +
177E MET* 1.3 57.9 + - - +
179E SER* 2.5 24.4 + - - +
180E SER* 3.0 14.4 + - - -
315E LYS* 4.1 20.9 - - + +
318E LYS* 5.5 4.5 - - + -
373E ILE* 4.7 5.6 - - + -
376E TYR* 3.4 55.6 - - + +
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Residues in contact with MET 177 (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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8E ALA 3.9 17.5 - - - +
9E SER* 4.0 6.1 - - - +
11E ASN 5.7 0.2 - - - -
12E ASP* 3.3 46.5 - - + +
29E ASP* 4.5 1.6 - - - +
32E ALA* 4.7 21.8 - - + +
33E VAL* 3.8 27.8 - - + +
36E LEU* 4.0 24.5 - - + -
173E THR* 3.0 16.0 + - - +
174E ILE* 4.1 5.4 - - - +
176E LEU* 1.3 77.3 - - - +
178E VAL* 1.3 66.8 + - + +
180E SER* 2.4 27.5 + - - +
181E ASN* 3.2 8.3 + - - +
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Residues in contact with VAL 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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11E ASN* 5.7 10.3 - - + +
174E ILE* 3.0 33.8 + - + +
175E ILE* 4.4 2.2 - - + +
177E MET* 1.3 81.1 - - + +
179E SER* 1.3 56.4 + - - +
181E ASN* 3.3 3.7 + - - +
182E PHE* 2.8 37.6 + - + -
30F TYR* 4.1 26.9 - - + +
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Residues in contact with SER 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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175E ILE* 2.9 20.3 + - - -
176E LEU* 2.5 30.5 + - - +
178E VAL* 1.3 75.4 - - - +
180E SER* 1.3 63.6 + - - +
181E ASN 3.1 1.4 + - - -
182E PHE* 3.5 18.0 - - - -
183E TRP* 3.2 13.3 + - - +
311E GLN* 2.9 28.5 + - - +
314E ILE* 4.7 14.9 - - - +
315E LYS* 5.5 4.7 - - - +
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Residues in contact with SER 180 (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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12E ASP* 4.6 1.9 + - - -
25E ASP* 5.0 11.0 - - - +
28E MET* 5.7 7.4 - - - -
29E ASP* 5.7 4.1 + - - -
176E LEU* 3.0 7.4 + - - -
177E MET* 2.4 33.0 + - - +
179E SER* 1.3 80.2 + - - +
181E ASN* 1.3 69.9 + - - +
183E TRP* 4.1 15.8 - - - +
311E GLN* 6.0 1.8 - - - -
376E TYR* 4.9 10.3 - - - -
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Residues in contact with ASN 181 (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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12E ASP* 2.3 49.8 + - - +
14E GLN* 4.3 11.8 + - - +
25E ASP* 5.3 7.8 + - - +
29E ASP* 5.2 3.8 + - - -
177E MET 3.2 6.1 + - - +
178E VAL* 3.3 3.8 + - - +
179E SER 3.1 0.4 - - - -
180E SER* 1.3 87.7 + - - +
182E PHE* 1.3 56.4 + - - +
183E TRP* 3.2 5.7 - - - -
184E PHE* 3.3 14.4 + - - +
185E LYS* 3.0 37.6 + - + +
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Residues in contact with PHE 182 (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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178E VAL* 2.8 36.6 + - + +
179E SER* 3.3 23.5 + - - -
181E ASN* 1.3 72.4 - - - +
183E TRP* 1.3 64.0 + - - +
184E PHE 3.7 0.9 - - - +
185E LYS* 4.0 6.5 - - + +
186E TYR* 3.7 35.6 - + + +
307E LEU* 4.8 1.9 - - + +
311E GLN* 3.9 22.4 + - - -
314E ILE* 5.5 10.3 - - + -
27F PHE* 5.7 10.8 - + - -
30F TYR* 3.9 30.1 - + + +
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Residues in contact with TRP 183 (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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20E LEU* 4.8 14.4 - - + -
25E ASP* 5.9 2.7 - - - -
179E SER 3.2 8.6 + - - +
180E SER* 4.1 16.8 - - - +
181E ASN* 5.6 1.3 - - - -
182E PHE* 1.3 78.1 - - - +
184E PHE* 1.3 94.1 + + + +
186E TYR* 4.7 0.9 - - - -
193E VAL* 6.0 1.3 - - + -
304E ILE* 3.9 29.2 + - + +
307E LEU* 3.3 26.9 - - + +
308E TYR* 3.2 65.9 - + + +
311E GLN* 3.7 21.8 - - + +
419E LEU* 5.8 2.9 - - + -
422E MET* 3.9 27.6 - - + -
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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
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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