Contacts of the helix formed by residues 197 - 212 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A ARG* 3.8 34.3 - - + +
148D THR* 3.8 5.8 - - - -
194D GLY 4.0 7.0 - - - +
195D PHE 2.9 23.0 + - - +
196D ILE* 1.3 76.3 - - - +
198D PRO* 1.3 81.6 - - - +
199D ALA* 3.9 5.8 + - - +
200D ASN* 3.0 27.2 + - - +
201D VAL* 2.8 21.9 + - - +
239D ASN* 6.0 2.0 - - - +
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Residues in contact with PRO 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ARG* 4.8 8.1 - - - +
147D SER* 4.3 11.2 - - - +
148D THR* 3.9 24.7 - - - +
151D LEU* 3.5 24.0 - - + +
197D THR* 1.3 92.9 - - - +
199D ALA* 1.3 63.5 + - - +
201D VAL* 3.0 4.7 + - + +
202D VAL* 3.0 24.4 + - + +
286D PHE* 5.6 4.7 - - + -
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Residues in contact with ALA 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ILE* 3.4 34.2 - - + +
154A PRO 5.1 4.7 - - - +
197D THR* 4.3 4.7 - - - +
198D PRO* 1.3 79.3 - - + +
200D ASN* 1.3 55.8 + - - +
202D VAL* 3.1 5.9 + - - +
203D PHE* 2.7 34.6 + - - +
282D PHE* 4.1 22.3 - - + -
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Residues in contact with ASN 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D PHE* 3.0 50.1 - - + +
196D ILE* 4.7 1.1 - - - -
197D THR* 3.0 25.2 + - - +
199D ALA* 1.3 75.3 - - - +
201D VAL* 1.3 67.7 + - - +
203D PHE* 3.1 5.3 + - - +
204D LEU* 2.7 24.1 + - - +
233D SER* 5.0 1.9 + - - -
237D MET* 3.5 41.5 + - - +
239D ASN* 4.9 4.2 + - - -
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Residues in contact with VAL 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D THR* 4.5 3.1 - - + -
151D LEU* 4.1 28.3 - - + +
152D LEU* 3.8 24.0 - - + -
155D LEU* 4.1 20.2 - - + -
196D ILE* 3.7 25.6 - - + -
197D THR 2.8 26.6 + - - +
198D PRO* 3.5 6.7 - - + +
200D ASN* 1.3 70.8 - - - +
202D VAL* 1.3 53.8 + - - +
204D LEU* 2.8 12.7 + - + +
205D TYR* 2.6 33.7 + - - +
289D LEU* 4.3 4.3 - - + -
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Residues in contact with VAL 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D LEU* 4.1 3.8 - - + -
198D PRO 3.0 18.1 + - - +
199D ALA* 3.2 9.0 - - - +
201D VAL* 1.3 76.9 - - - +
203D PHE* 1.3 64.6 + - - +
205D TYR* 2.9 2.4 + - - +
206D MET* 2.8 22.2 + - - +
275D ILE* 4.4 2.5 - - + -
282D PHE* 4.1 16.8 - - + -
285D VAL* 3.6 25.2 - - + +
286D PHE* 3.7 42.0 - - + +
289D LEU* 3.9 21.5 - - + -
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Residues in contact with PHE 203 (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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153A ILE* 4.6 2.2 - - + -
199D ALA 2.7 17.5 + - - +
200D ASN* 3.4 13.2 - - - +
202D VAL* 1.3 71.9 - - - +
204D LEU* 1.3 58.3 + - - +
206D MET* 3.0 27.3 - - - +
207D LEU* 3.4 19.4 + - + +
233D SER* 3.4 38.6 - - - -
236D TYR* 3.6 22.0 - + - -
237D MET* 3.6 31.0 - - + -
272D MET* 3.6 43.7 - - + -
275D ILE* 3.8 24.7 - - + +
276D ASN* 3.9 2.0 - - - -
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Residues in contact with LEU 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D LEU* 3.8 9.9 - - + -
178D LEU* 3.7 33.9 - - + -
195D PHE* 6.3 0.2 - - + -
196D ILE* 6.4 0.9 - - + -
200D ASN 2.7 13.0 + - - +
201D VAL* 3.1 13.5 - - + +
203D PHE* 1.3 74.3 - - - +
205D TYR* 1.3 63.6 + - - +
206D MET 3.0 1.8 - - - -
207D LEU* 3.1 3.7 + - + +
208D CYS* 3.1 28.8 + - - -
226D LEU* 4.6 3.4 - - + +
229D CYS* 3.7 13.0 - - + -
230D LEU* 3.6 43.1 - - + +
233D SER* 3.5 24.0 - - - +
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Residues in contact with TYR 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D LEU* 4.4 17.0 - - + +
158D PHE* 3.7 41.4 - + + -
201D VAL 2.6 15.1 + - - +
202D VAL 3.5 5.4 - - - +
204D LEU* 1.3 73.3 - - - +
206D MET* 1.3 57.0 + - - +
208D CYS* 4.4 0.9 - - - -
209D ARG* 2.8 62.3 + - + +
285D VAL* 3.8 19.5 - - + -
288D ASP* 4.0 10.1 - - + +
289D LEU* 3.3 58.1 - - + -
292D GLU* 2.6 24.1 + - - -
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Residues in contact with MET 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D VAL 2.8 12.3 + - - +
203D PHE* 3.0 18.8 - - - +
205D TYR* 1.3 77.2 - - - +
207D LEU* 1.3 79.7 + - + +
209D ARG* 3.0 24.0 - - - +
210D ASP* 3.7 3.6 + - - +
268D MET* 3.0 41.5 - - + +
271D LYS* 3.8 35.4 - - + +
272D MET* 4.4 5.8 - - - +
275D ILE* 4.3 17.9 - - + -
281D TYR* 3.9 16.2 - - - +
285D VAL* 4.1 16.2 - - + -
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Residues in contact with LEU 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D PHE* 3.4 16.5 + - + +
204D LEU* 3.1 6.7 + - + +
206D MET* 1.3 95.5 - - + +
208D CYS* 1.3 68.5 + - - +
209D ARG 3.0 1.0 + - - -
210D ASP* 3.0 12.6 + - - +
211D VAL* 3.0 19.7 + - + +
229D CYS* 3.5 41.5 - - + +
232D LEU* 4.0 18.8 - - + -
233D SER* 3.7 12.8 - - - +
264D VAL* 4.1 6.5 - - + -
268D MET* 3.7 24.9 - - + -
272D MET* 3.9 14.6 - - + -
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Residues in contact with CYS 208 (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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155D LEU* 4.2 10.3 - - + -
158D PHE* 4.2 12.8 - - + -
159D LEU* 4.2 2.7 - - + -
162D ARG* 3.9 1.2 + - - -
204D LEU* 3.1 29.7 + - - +
205D TYR* 3.8 5.8 - - - +
207D LEU* 1.3 76.8 - - - +
209D ARG* 1.3 66.2 + - - +
211D VAL 2.9 10.4 + - - -
212D ILE* 2.9 35.9 + - + +
226D LEU* 3.4 33.7 - - - -
229D CYS* 4.0 10.1 - - - -
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Residues in contact with ARG 209 (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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158D PHE* 4.0 14.3 - - + -
162D ARG* 2.8 35.1 + - - +
205D TYR* 2.8 41.8 + - + +
206D MET* 3.0 19.4 - - - +
208D CYS* 1.3 74.4 - - - +
210D ASP* 1.3 72.8 + - - +
281D TYR* 4.2 13.7 + - - -
285D VAL* 3.8 25.2 - - - +
288D ASP* 2.3 44.0 + - - +
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Residues in contact with ASP 210 (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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162D ARG* 5.3 0.7 - - - -
206D MET* 3.7 1.8 + - - +
207D LEU 3.0 3.4 + - - -
209D ARG* 1.3 96.5 + - - +
211D VAL* 1.3 63.0 + - - +
267D LEU* 4.2 12.4 - - + +
268D MET* 3.4 26.6 - - + +
271D LYS* 2.5 32.3 + - - +
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Residues in contact with VAL 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D LEU* 3.3 21.1 - - - +
208D CYS 2.9 5.8 + - - +
209D ARG 3.3 0.2 - - - -
210D ASP* 1.3 84.5 - - - +
212D ILE* 1.3 64.3 + - - +
213D SER* 3.0 5.7 + - - -
225D VAL* 3.8 25.6 - - + +
229D CYS* 4.1 9.9 - - - -
260D ARG* 6.3 0.2 - - + -
264D VAL* 4.0 41.1 - - + -
267D LEU* 5.0 2.7 - - + -
268D MET* 4.2 11.2 - - + -
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Residues in contact with ILE 212 (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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158D PHE* 5.1 0.4 - - + -
159D LEU* 4.1 11.0 - - + -
162D ARG* 3.0 31.5 + - + -
163D CYS* 3.6 10.8 - - - -
208D CYS* 2.9 41.8 + - + +
211D VAL* 1.3 68.7 - - - +
213D SER* 1.3 77.2 + - - +
216D VAL* 4.0 3.6 - - + -
222D LEU* 3.4 28.9 - - + -
225D VAL* 3.1 37.2 - - + +
226D LEU* 4.2 12.1 - - - +
229D CYS* 4.7 2.5 - - - -
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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