Contacts of the helix formed by residues 197 - 212 (chain E) in PDB entry 1H4L
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 THR 197 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ARG* 4.0 31.9 - - + +
148E THR* 3.6 4.3 - - - -
194E GLY 4.2 8.1 - - - +
195E PHE 3.0 16.6 + - - +
196E ILE* 1.3 77.6 - - - +
198E PRO* 1.3 77.8 - - - +
199E ALA* 3.6 7.0 + - - +
200E ASN* 3.2 25.3 + - - +
201E VAL* 2.8 24.0 + - - +
239E ASN* 6.0 3.4 - - - +
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Residues in contact with PRO 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ARG* 4.6 9.6 - - - +
147E SER* 4.0 12.1 - - - +
148E THR* 3.3 29.6 - - - +
151E LEU* 3.5 23.2 - - + +
197E THR* 1.3 87.1 - - - +
199E ALA* 1.3 60.3 + - - +
201E VAL* 3.3 4.6 + - + +
202E VAL* 3.0 31.4 + - - +
286E PHE* 5.8 2.2 - - + -
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Residues in contact with ALA 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ILE* 3.3 34.3 - - + +
154B PRO* 4.7 8.3 - - + +
197E THR* 3.2 5.7 + - - +
198E PRO* 1.3 78.7 - - - +
200E ASN* 1.3 63.1 + - - +
202E VAL* 3.1 5.9 + - - +
203E PHE* 2.8 26.7 + - - +
282E PHE* 3.9 20.7 - - + -
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Residues in contact with ASN 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195E PHE* 2.9 60.6 - - + +
196E ILE* 4.8 1.1 - - - -
197E THR* 3.1 19.1 + - - +
199E ALA* 1.3 79.9 - - - +
201E VAL* 1.3 66.6 + - - +
203E PHE* 3.3 5.2 + - - +
204E LEU* 2.8 22.7 + - - +
233E SER* 5.0 2.8 + - - -
237E MET* 3.4 37.2 + - - +
239E ASN* 5.4 3.3 + - - -
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Residues in contact with VAL 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148E THR* 4.3 8.1 - - + -
151E LEU* 4.0 23.6 - - + +
152E LEU* 4.3 10.3 - - + +
155E LEU* 4.3 17.9 - - + -
196E ILE* 3.7 26.7 - - + -
197E THR 2.8 25.6 + - - +
198E PRO* 3.6 6.3 - - + +
200E ASN* 1.3 74.7 - - - +
202E VAL* 1.3 53.3 + - - +
204E LEU* 2.8 12.4 + - + +
205E TYR* 2.7 32.1 + - - +
289E LEU* 4.0 18.8 - - + -
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Residues in contact with VAL 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E LEU* 4.5 1.8 - - + -
198E PRO 3.0 17.9 - - - +
199E ALA* 3.3 9.2 - - - +
201E VAL* 1.3 76.8 - - - +
203E PHE* 1.3 62.8 + - - +
205E TYR* 3.0 10.0 + - + +
206E MET* 2.8 21.8 + - - +
275E ILE* 4.1 1.8 - - + -
282E PHE* 3.9 17.9 - - + -
285E VAL* 3.8 14.3 - - + +
286E PHE* 3.6 56.5 - - + +
289E LEU* 4.3 11.7 - - + -
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Residues in contact with PHE 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ILE* 5.2 0.9 - - + -
199E ALA 2.8 16.2 + - - +
200E ASN* 3.5 12.3 - - - +
202E VAL* 1.3 72.5 - - - +
204E LEU* 1.3 63.7 + - - +
206E MET* 3.1 24.1 + - - +
207E LEU* 3.3 22.5 + - + +
233E SER* 3.7 33.2 - - - -
236E TYR* 3.5 35.9 - + + -
237E MET* 3.7 28.7 - - + -
272E MET* 3.7 38.4 - - + -
275E ILE* 3.8 20.6 - - + +
276E ASN* 3.9 1.6 - - - -
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Residues in contact with LEU 204 (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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152E LEU* 6.1 0.2 - - + -
155E LEU* 3.5 26.0 - - + -
178E LEU* 3.8 26.7 - - + -
200E ASN 2.8 12.4 + - - +
201E VAL* 2.8 17.3 + - + +
203E PHE* 1.3 74.7 - - - +
205E TYR* 1.3 62.1 + - - +
207E LEU* 3.1 11.8 + - + -
208E CYS* 3.1 27.0 + - - -
226E LEU* 4.7 3.4 - - + +
229E CYS* 3.7 20.9 - - + -
230E LEU* 4.1 16.4 - - + +
233E SER* 3.7 19.3 - - - +
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Residues in contact with TYR 205 (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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155E LEU* 4.4 16.8 - - + +
158E PHE* 3.9 35.4 - + - -
201E VAL 2.7 14.5 + - - +
202E VAL* 3.4 7.4 - - + +
204E LEU* 1.3 72.4 - - - +
206E MET* 1.3 61.4 + - - +
208E CYS* 4.5 0.7 - - - -
209E ARG* 3.0 56.2 + - - +
285E VAL* 3.7 21.8 - - + -
288E ASP* 3.5 11.1 - - - +
289E LEU* 3.5 51.8 - - + -
292E GLU* 2.5 30.7 + - - -
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Residues in contact with MET 206 (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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202E VAL 2.8 11.2 + - - +
203E PHE* 3.1 18.4 - - - +
204E LEU 3.0 0.2 - - - -
205E TYR* 1.3 79.8 - - - +
207E LEU* 1.3 81.2 + - + +
209E ARG* 3.7 16.6 + - - +
210E ASP* 3.9 1.9 + - - +
268E MET* 3.0 44.2 - - + +
271E LYS* 3.7 37.0 - - + +
272E MET* 4.2 5.8 - - + -
275E ILE* 4.3 12.3 - - + -
281E TYR* 3.7 17.0 - - - +
285E VAL* 4.0 19.1 - - + -
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Residues in contact with LEU 207 (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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203E PHE* 3.3 17.9 + - + +
204E LEU* 3.1 6.4 + - + +
206E MET* 1.3 97.0 - - + +
208E CYS* 1.3 67.7 + - - +
210E ASP* 2.9 15.8 + - - -
211E VAL* 3.1 15.2 + - - +
229E CYS* 3.5 42.8 - - + +
232E LEU* 4.0 17.3 - - + -
233E SER* 3.9 11.2 - - - +
264E VAL* 4.2 6.3 - - + -
268E MET* 3.7 26.7 - - + +
272E MET* 3.8 15.7 - - + -
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Residues in contact with CYS 208 (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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155E LEU* 4.3 11.0 - - + -
158E PHE* 4.3 12.7 - - + -
159E LEU* 4.4 2.7 - - + -
162E ARG* 3.9 2.3 + - - -
204E LEU* 3.1 36.5 + - - +
205E TYR* 3.9 5.8 - - - +
207E LEU* 1.3 77.1 - - - +
209E ARG* 1.3 63.9 + - - +
212E ILE* 2.9 51.0 + - + +
226E LEU* 3.9 22.9 - - - -
229E CYS* 4.2 8.4 - - - -
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Residues in contact with ARG 209 (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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158E PHE* 3.8 20.6 - - + -
162E ARG* 3.1 27.6 + - - +
205E TYR* 3.0 44.2 + - + +
206E MET* 3.7 10.8 + - - +
207E LEU 2.9 0.2 + - - -
208E CYS* 1.3 76.8 - - - +
210E ASP* 1.3 74.9 + - - +
281E TYR* 4.0 14.5 + - - -
285E VAL* 3.8 28.3 - - - +
288E ASP* 2.7 38.4 + - - +
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Residues in contact with ASP 210 (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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206E MET* 4.3 3.3 - - - +
207E LEU 2.9 6.7 + - - -
209E ARG* 1.3 92.1 + - - +
211E VAL* 1.3 63.9 + - - +
212E ILE 5.0 0.9 - - - -
267E LEU* 3.7 14.1 - - + +
268E MET* 3.1 28.6 - - + +
271E LYS* 2.4 34.6 + - - +
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Residues in contact with VAL 211 (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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207E LEU 3.1 17.8 + - - +
208E CYS 3.1 0.6 + - - -
209E ARG 3.5 0.4 - - - -
210E ASP* 1.3 84.9 - - - +
212E ILE* 1.3 69.2 + - - +
213E SER* 3.2 5.4 + - - -
225E VAL* 3.5 26.3 - - + +
229E CYS* 3.8 13.5 - - - -
260E ARG* 5.9 0.2 - - - -
264E VAL* 3.7 42.4 - - + -
267E LEU* 4.6 4.3 - - + -
268E MET* 4.3 9.6 - - + -
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Residues in contact with ILE 212 (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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158E PHE* 5.3 0.4 - - + -
159E LEU* 4.0 11.2 - - + -
162E ARG* 2.9 34.6 + - + +
163E CYS* 3.9 18.8 - - - -
208E CYS* 2.9 37.1 + - + +
210E ASP 5.0 0.5 - - - -
211E VAL* 1.3 76.6 + - - +
213E SER* 1.3 62.6 + - - +
214E SER 3.8 0.2 + - - -
216E VAL* 3.9 5.8 - - + -
222E LEU* 3.6 25.4 - - + -
225E VAL* 3.4 35.0 - - + +
226E LEU* 4.0 15.5 - - + +
229E CYS* 4.5 1.8 - - - -
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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