Contacts of the helix formed by residues 194 - 211 (chain K) in PDB entry 5A31
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 CYS 194 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192K LYS* 3.5 16.8 - - - +
193K LEU* 1.3 85.2 + - - +
195K ASN* 1.3 77.7 + - - +
196K GLU* 3.4 19.5 - - + +
197K GLU* 4.1 8.1 - - + +
198K GLN* 3.5 13.5 + - - +
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Residues in contact with ASN 195 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192K LYS* 4.0 28.3 + - - +
194K CYS* 1.3 84.1 - - - +
196K GLU* 1.3 66.6 + - + +
198K GLN* 3.6 3.5 + - - +
199K GLU* 3.4 24.5 + - - +
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Residues in contact with GLU 196 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2J ASN* 2.8 37.7 - - - +
194K CYS* 4.1 12.6 - - + +
195K ASN* 1.3 79.1 - - + +
197K GLU* 1.3 67.0 + - + +
199K GLU* 3.3 7.3 + - - +
200K LEU* 2.9 29.0 + - + +
224K VAL* 6.1 4.7 - - + -
225K ASP* 5.5 5.9 - - - +
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Residues in contact with GLU 197 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2J ASN* 6.1 1.6 - - - -
5J ARG* 4.8 13.2 - - - +
162K TYR* 2.4 38.4 + - - +
190K LEU* 5.5 0.4 - - - -
193K LEU* 3.2 37.8 - - + +
194K CYS* 3.8 5.9 + - + +
195K ASN 3.4 0.6 - - - -
196K GLU* 1.3 83.5 - - + +
198K GLN* 1.3 66.6 + - - +
200K LEU* 4.1 13.5 - - + -
201K LEU* 2.9 37.9 + - + +
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Residues in contact with GLN 198 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190K LEU* 2.4 47.2 + - - +
191K SER* 4.2 0.6 - - - +
192K LYS* 3.2 49.6 - - + +
193K LEU 4.9 1.4 - - - +
194K CYS 3.5 5.8 + - - +
195K ASN 3.8 9.4 - - - +
196K GLU 3.3 0.4 - - - -
197K GLU* 1.3 78.2 - - - +
199K GLU* 1.3 63.5 - - + +
201K LEU* 4.4 0.7 - - - +
202K ARG* 3.2 68.2 + - - +
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Residues in contact with GLU 199 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195K ASN 3.4 11.4 + - - +
196K GLU* 3.3 9.2 + - - +
198K GLN* 1.3 81.0 - - + +
200K LEU* 1.3 59.0 + - - +
202K ARG* 3.7 14.0 - - - +
203K PHE* 2.9 32.8 + - - +
220K ILE* 5.1 8.5 - - - +
221K PRO* 5.1 9.0 - - - +
224K VAL* 4.3 28.4 - - + +
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Residues in contact with LEU 200 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J LEU* 4.7 6.1 - - + -
25J TRP* 4.3 18.6 - - + -
28J LYS* 6.4 0.2 - - + -
32J LEU* 4.2 21.5 - - + -
162K TYR* 6.5 0.4 - - + -
196K GLU* 2.9 19.0 + - + +
197K GLU* 3.3 15.0 + - + +
199K GLU* 1.3 77.5 - - - +
201K LEU* 1.3 60.8 + - + +
203K PHE* 3.4 5.5 + - + +
204K LEU* 3.0 40.9 + - + +
225K ASP* 4.6 14.1 - - - +
227K LEU* 3.4 33.2 - - + -
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Residues in contact with LEU 201 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25J TRP* 3.5 39.5 - - + -
161K VAL* 4.0 24.0 - - + -
162K TYR* 4.2 28.3 - - + -
190K LEU* 4.1 18.8 - - + -
193K LEU* 5.9 3.1 - - + -
197K GLU* 2.9 26.3 + - + +
200K LEU* 1.3 74.1 - - + +
202K ARG* 1.3 67.4 + - - +
204K LEU* 3.9 3.8 - - + +
205K PHE* 3.0 54.2 + - + -
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Residues in contact with ARG 202 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185K LEU* 4.7 5.1 - - + +
190K LEU* 4.1 19.8 - - + +
192K LYS* 6.1 0.8 - - - +
198K GLN* 3.2 55.9 + - - +
199K GLU* 3.7 12.5 - - - +
201K LEU* 1.3 77.0 - - - +
203K PHE* 1.3 52.7 + - - +
205K PHE* 4.3 2.0 - - - +
206K GLU* 2.8 48.4 + - + +
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Residues in contact with PHE 203 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199K GLU 2.9 19.4 + - - +
200K LEU* 3.5 6.1 - - + +
202K ARG* 1.3 77.2 - - - +
204K LEU* 1.3 85.4 + - + +
206K GLU* 3.4 7.5 + - - +
207K ASN* 3.2 42.8 + - - +
218K THR* 3.6 28.5 - - + -
221K PRO* 3.1 43.7 - - + -
222K GLU* 5.8 3.6 - - + -
227K LEU* 3.7 29.8 - - + -
228K GLU 5.8 1.1 - - - -
233K VAL* 3.9 15.7 - - + -
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Residues in contact with LEU 204 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J PHE* 4.3 9.6 - - + -
25J TRP* 3.6 31.4 - - + -
28J LYS* 3.5 37.7 - - + +
200K LEU* 3.0 37.9 + - + +
201K LEU* 3.9 4.9 - - + +
203K PHE* 1.3 97.6 - - + +
205K PHE* 1.3 72.9 + - + +
207K ASN* 3.3 16.1 + - - +
208K LYS* 3.7 21.9 + - - +
227K LEU* 4.5 3.8 - - + -
233K VAL* 4.9 4.5 - - + -
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Residues in contact with PHE 205 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J PHE* 5.0 3.1 - + - -
25J TRP* 5.3 2.9 - + - -
157K LEU* 5.8 0.7 - - + -
161K VAL* 4.0 25.6 - - + -
162K TYR 4.9 5.8 - - - -
164K PHE* 4.2 19.3 - + + -
167K PHE* 3.5 51.1 - + + -
185K LEU* 3.3 26.2 - - + -
188K LEU* 4.8 18.8 - - + -
190K LEU* 5.4 2.0 - - + -
201K LEU* 3.0 49.0 + - + +
204K LEU* 1.3 83.1 - - + +
206K GLU* 1.3 64.1 + - - +
207K ASN 3.3 0.3 + - - -
208K LYS* 3.3 6.1 + - - +
209K LEU* 3.3 26.2 + - - +
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Residues in contact with GLU 206 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185K LEU* 4.2 14.9 - - - +
202K ARG* 2.8 34.3 + - + +
203K PHE* 3.5 8.5 - - - +
205K PHE* 1.3 73.0 - - - +
207K ASN* 1.3 64.3 + - - +
209K LEU* 4.7 6.4 - - - +
210K LYS* 3.0 67.6 + - - +
218K THR* 5.6 3.4 - - + -
240K ARG* 4.3 1.1 - - - -
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Residues in contact with ASN 207 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203K PHE* 3.2 41.1 + - - +
204K LEU* 3.7 10.8 + - - +
205K PHE 3.2 0.6 - - - -
206K GLU* 1.3 76.5 - - - +
208K LYS* 1.3 70.4 + - - +
211K LYS* 3.8 14.2 + - - -
218K THR* 3.2 30.1 - - - +
232K ASP 5.4 0.2 - - - -
233K VAL* 4.0 18.6 + - - +
236K SER* 3.3 34.8 + - - +
239K GLU* 5.0 3.1 - - - +
240K ARG* 3.6 9.1 + - - +
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Residues in contact with LYS 208 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J PHE* 4.4 11.1 - - - -
28J LYS* 4.4 6.1 - - - +
164K PHE* 4.0 30.5 - - + -
167K PHE* 4.5 17.5 - - + -
168K ASP* 4.6 9.4 - - - +
171K THR* 5.0 6.7 + - + +
204K LEU* 3.7 23.5 + - - +
205K PHE* 3.3 7.8 + - - +
206K GLU 3.3 0.2 - - - -
207K ASN* 1.3 90.1 - - + +
209K LEU* 1.3 59.0 + - + +
211K LYS* 2.8 32.5 - - - +
232K ASP* 3.8 26.5 + - - +
236K SER* 5.8 2.8 - - - -
239K GLU* 5.0 11.5 - - - +
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Residues in contact with LEU 209 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167K PHE* 4.0 15.3 - - + -
171K THR* 3.1 28.3 - - + +
176K LEU* 5.1 1.1 - - + -
178K ALA* 5.8 1.0 - - - +
181K GLU* 3.2 54.1 - - + +
182K LYS* 4.5 2.7 - - - +
185K LEU* 3.2 43.5 - - + -
205K PHE 3.3 12.2 + - - +
206K GLU* 4.4 7.6 - - - +
208K LYS* 1.3 76.2 - - - +
210K LYS* 1.3 69.4 + - + +
211K LYS* 3.5 7.1 - - - +
212K TYR* 5.8 0.3 - - - -
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Residues in contact with LYS 210 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206K GLU* 3.0 52.9 + - - +
209K LEU* 1.3 79.4 - - - +
211K LYS* 1.3 52.0 - - - +
212K TYR* 2.2 32.5 + - - +
213K ASN* 4.0 28.4 + - + +
217K GLU* 2.6 45.2 + - + +
218K THR* 5.0 4.8 - - - +
240K ARG* 3.5 26.0 - - - +
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Residues in contact with LYS 211 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171K THR* 4.0 11.7 + - - -
174K HIS* 3.0 71.9 + - + +
181K GLU* 3.9 13.8 + - - -
207K ASN 3.8 10.7 + - - -
208K LYS 2.8 26.0 - - - +
209K LEU* 3.5 10.8 - - - +
210K LYS* 1.3 72.4 - - - +
212K TYR* 1.3 59.6 + - + +
213K ASN 3.6 1.3 - - - -
236K SER* 5.9 0.2 - - - -
239K GLU* 3.5 24.0 - - - +
240K ARG* 3.1 38.1 + - - +
243K TYR* 4.2 10.1 - - + -
366K GLY* 5.8 0.2 - - - -
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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
------------------------------------------------------------
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