Contacts of the helix formed by residues 191 - 205 (chain D) in PDB entry 1F5Q
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 191 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28D GLU* 2.5 38.0 + - - +
31D HIS* 3.5 23.5 + - + +
32D ASP* 2.7 35.6 + - - -
189D MET 3.9 0.2 + - - -
190D LYS* 1.3 77.5 - - - +
192D PRO* 1.3 74.0 - - + +
193D VAL* 4.7 3.6 - - + +
194D LEU* 3.2 21.2 + - + +
195D ILE* 3.1 20.6 + - - +
224D ILE* 6.2 5.2 - - - -
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Residues in contact with PRO 192 (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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27D SER* 3.9 22.7 - - - +
28D GLU* 4.7 3.1 - - - +
31D HIS* 3.8 19.7 - - + +
34D ARG* 4.1 19.3 - - - +
147D CYS 4.6 9.2 - - - +
149D SER* 2.7 30.3 + - - +
152D LEU* 3.8 15.3 - - + -
190D LYS 3.5 2.6 - - - +
191D ARG* 1.3 85.6 - - + +
193D VAL* 1.3 58.5 + - - +
195D ILE* 3.1 6.0 + - + -
196D THR* 2.8 19.4 + - - -
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Residues in contact with VAL 193 (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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24D ILE* 3.4 35.0 - - + -
27D SER* 3.7 5.2 - - - +
28D GLU* 4.6 17.0 - - - +
152D LEU* 3.1 30.1 - - + -
156D ILE* 4.9 5.6 - - + -
191D ARG* 5.1 3.6 - - + -
192D PRO* 1.3 73.7 - - - +
194D LEU* 1.3 60.5 + - + +
196D THR* 3.4 8.9 - - - -
197D LEU* 2.7 41.0 + - + +
222D LEU* 4.6 8.1 - - + -
224D ILE* 4.3 18.2 - - + -
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Residues in contact with LEU 194 (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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190D LYS* 4.0 30.3 - - + +
191D ARG* 3.2 25.5 + - + +
192D PRO 3.1 0.6 - - - -
193D VAL* 1.3 79.8 - - - +
195D ILE* 1.3 61.3 - - - +
197D LEU* 3.5 2.4 + - + -
198D ALA* 2.9 29.6 + - - +
224D ILE* 3.9 36.6 - - + -
228D GLU* 4.3 17.7 - - + +
229D LEU* 4.1 23.8 - - + +
232D CYS* 3.8 16.4 - - + -
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Residues in contact with ILE 195 (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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149D SER* 3.8 17.3 - - - +
178D ILE* 4.7 7.6 - - + -
181D ALA* 4.2 21.5 - - + -
182D LEU* 5.1 10.1 - - + -
187D SER* 3.3 26.2 - - - +
188D ALA* 4.5 8.1 - - - +
190D LYS* 3.6 27.6 - - + +
191D ARG 3.1 11.5 + - - +
192D PRO* 3.3 7.6 - - + +
194D LEU* 1.3 75.8 - - - +
196D THR* 1.3 64.1 + - - +
198D ALA* 3.3 2.1 + - - +
199D CYS* 3.1 33.5 + - - -
232D CYS* 4.0 10.8 - - - -
236D VAL* 4.8 3.1 - - + -
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Residues in contact with THR 196 (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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149D SER* 2.9 38.4 + - - +
152D LEU* 3.6 6.7 - - - +
153D ILE* 3.6 23.1 - - + +
156D ILE* 3.3 24.7 - - + -
174D CYS* 5.1 0.3 - - - -
178D ILE* 5.0 2.9 - - - -
192D PRO 2.8 17.6 + - - -
193D VAL* 3.4 11.4 - - - -
195D ILE* 1.3 79.1 - - - +
197D LEU* 1.3 56.6 + - - +
199D CYS* 3.3 5.8 + - - +
200D MET* 2.9 32.7 + - - +
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Residues in contact with LEU 197 (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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156D ILE* 3.7 36.6 - - + -
160D MET* 5.4 0.2 - - + -
193D VAL* 2.7 24.9 + - + +
194D LEU* 4.1 3.8 - - + +
196D THR* 1.3 72.0 - - - +
198D ALA* 1.3 56.8 + - - +
200D MET* 3.7 8.1 - - + +
201D HIS* 2.7 35.5 + - - +
211D TYR* 4.6 2.2 + - + -
215D ILE* 3.8 23.1 - - + -
218D VAL* 4.4 9.4 - - + -
219D CYS* 4.7 11.4 - - - -
222D LEU* 4.2 17.9 - - + -
224D ILE* 4.0 26.2 - - + -
229D LEU* 3.7 12.6 - - + +
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Residues in contact with ALA 198 (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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194D LEU 2.9 19.7 + - - +
195D ILE 3.3 5.4 + - - +
197D LEU* 1.3 76.2 - - - +
199D CYS* 1.3 57.5 + - - +
201D HIS* 3.2 4.7 - - - +
202D LEU* 3.0 32.8 + - - +
229D LEU* 3.5 12.7 - - + +
232D CYS* 3.6 38.1 - - + +
233D CYS* 3.6 7.4 - - - +
236D VAL* 4.1 6.3 - - + -
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Residues in contact with CYS 199 (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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174D CYS* 3.8 20.0 - - + -
177D LYS* 3.5 31.4 - - + -
178D ILE* 3.7 22.2 - - + -
195D ILE* 3.1 22.2 + - - +
196D THR 3.7 4.0 - - - +
198D ALA* 1.3 74.9 - - - +
200D MET* 1.3 65.1 + - - +
202D LEU* 3.3 7.4 + - - +
203D THR* 3.1 28.9 + - - +
236D VAL* 4.1 17.5 - - - -
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Residues in contact with MET 200 (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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153D ILE* 4.0 11.4 - - + +
156D ILE* 3.5 53.6 - - + -
157D LEU* 3.3 37.7 - - + -
160D MET* 4.9 3.4 - - - -
170D ILE* 4.9 0.4 - - + -
174D CYS* 4.0 12.8 - - - -
196D THR* 2.9 25.9 + - + +
197D LEU* 3.7 8.1 - - + +
199D CYS* 1.3 72.9 - - - +
201D HIS* 1.3 57.5 + - - +
203D THR* 3.7 6.7 - - - -
204D MET* 2.7 54.3 + - + +
211D TYR* 4.7 8.3 - - + -
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Residues in contact with HIS 201 (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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197D LEU 2.7 18.6 + - - +
198D ALA 3.2 6.1 - - - +
200D MET* 1.3 77.2 - - - +
202D LEU* 1.3 64.6 + - + +
205D ASN* 2.9 65.0 + - + +
211D TYR* 2.8 29.3 + - - +
215D ILE* 5.3 1.3 - - + +
229D LEU* 4.2 13.4 - - + +
230D HIS* 4.2 25.2 + + - -
233D CYS* 3.5 25.8 - - - -
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Residues in contact with LEU 202 (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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177D LYS* 4.2 21.6 - - + +
198D ALA 3.0 18.0 + - - +
199D CYS 3.3 8.0 + - - +
201D HIS* 1.3 82.5 - - + +
203D THR* 1.3 59.0 + - - +
205D ASN 5.0 0.2 - - - -
207D LYS* 5.5 4.7 + - - -
233D CYS* 4.0 29.6 - - + +
236D VAL* 4.0 20.6 - - + -
237D ASP* 3.8 29.2 - - - +
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Residues in contact with THR 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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170D ILE* 4.3 5.6 - - - +
173D LEU* 3.9 38.7 - - + +
174D CYS* 3.6 15.0 - - - -
177D LYS* 3.6 24.7 - - + -
199D CYS 3.1 17.5 + - - +
200D MET* 3.4 4.5 + - - -
202D LEU* 1.3 81.5 - - - +
204D MET* 1.3 67.5 + - - +
205D ASN 4.0 0.2 - - - -
207D LYS* 4.0 14.9 - - - +
208D TYR* 3.9 12.8 + - - -
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Residues in contact with MET 204 (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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157D LEU* 3.7 13.5 - - + -
160D MET* 4.9 1.3 - - - -
170D ILE* 3.9 21.3 - - + -
200D MET* 2.7 52.5 + - + +
203D THR* 1.3 85.0 - - - +
205D ASN* 1.3 65.6 + - - +
206D GLN 3.4 0.2 + - - -
207D LYS* 3.0 14.7 + - - -
208D TYR* 3.2 27.3 + - + +
210D TYR* 3.5 33.9 - - + -
211D TYR* 3.8 31.3 - - + -
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Residues in contact with ASN 205 (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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201D HIS* 2.9 52.4 + - + +
202D LEU 5.0 0.2 - - - -
204D MET* 1.3 72.8 - - - +
206D GLN* 1.3 86.6 + - - +
207D LYS* 3.0 18.1 + - - +
211D TYR* 3.2 27.4 - - + -
212D GLU* 5.1 7.5 - - - +
215D ILE* 5.5 3.0 - - - +
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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