Contacts of the helix formed by residues 194 - 214 (chain A) in PDB entry 1C7C
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 SER 194 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A ASP* 2.6 42.8 + - - +
191A SER* 3.0 19.4 + - - -
192A HIS 3.3 1.4 + - - -
193A GLY* 1.3 78.6 - - - +
195A ALA* 1.3 61.6 + - - +
196A GLN* 3.0 17.2 + - - +
197A VAL* 3.2 13.3 + - - +
198A LYS* 3.1 21.5 + - - +
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Residues in contact with ALA 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A GLY 3.2 3.0 + - - +
194A SER* 1.3 70.8 + - - +
196A GLN* 1.3 60.6 + - + +
198A LYS* 3.8 17.4 - - - +
199A GLY* 3.0 24.4 + - - -
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Residues in contact with GLN 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A HIS* 3.5 19.4 + - - +
188A PHE* 3.5 31.6 - - + +
189A ASP* 2.6 39.5 + - - +
194A SER* 3.0 7.4 + - - +
195A ALA* 1.3 77.7 - - + +
197A VAL* 1.3 62.1 + - - +
199A GLY* 3.5 0.6 + - - -
200A HIS* 3.0 29.1 + - - +
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Residues in contact with VAL 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ALA* 4.0 23.6 - - + +
171A LEU* 3.8 17.8 - - + +
172A GLU* 4.7 6.7 - - + +
175A PHE* 4.6 7.6 - - + -
188A PHE* 4.7 4.3 - - + -
189A ASP 3.7 20.6 - - - +
190A LEU* 4.2 26.0 - - + +
191A SER 4.7 1.6 - - - +
194A SER* 3.2 14.8 + - - +
196A GLN* 1.3 75.9 - - - +
198A LYS* 1.3 61.0 + - + +
200A HIS* 3.3 5.2 + - - +
201A GLY* 2.7 28.4 + - - -
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Residues in contact with LYS 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A GLY 4.7 2.1 - - - +
168A ALA* 3.9 20.3 - - + +
193A GLY* 3.5 27.3 + - - +
194A SER 3.1 12.2 + - - +
195A ALA* 4.0 13.7 - - - +
196A GLN 3.3 0.2 - - - -
197A VAL* 1.3 78.6 - - + +
199A GLY* 1.3 61.4 + - - +
201A GLY* 3.4 1.0 + - - -
202A LYS* 3.1 23.4 + - - +
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Residues in contact with GLY 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ALA 3.0 17.0 + - - -
196A GLN* 4.0 1.1 - - - -
198A LYS* 1.3 76.4 - - - +
200A HIS* 1.3 61.6 + - - +
202A LYS* 3.5 7.9 + - - +
203A LYS* 3.2 30.9 + - - +
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Residues in contact with HIS 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LEU* 3.6 25.0 - - + +
185A PHE* 3.9 22.0 - + - -
188A PHE* 3.9 15.0 - + + -
196A GLN 3.0 19.4 + - - +
197A VAL* 3.8 3.6 - - - +
199A GLY* 1.3 74.9 - - - +
201A GLY* 1.3 63.9 + - - +
203A LYS* 2.9 18.3 + - - +
204A VAL* 2.9 37.1 + - + +
285A HEM 3.3 69.3 + + + +
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Residues in contact with GLY 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A GLY 4.0 6.7 - - - -
167A GLY* 3.7 19.6 - - - -
168A ALA 3.7 2.2 - - - -
171A LEU* 3.5 18.7 - - - +
197A VAL 2.7 18.6 + - - -
198A LYS 3.8 0.9 - - - -
200A HIS* 1.3 72.7 - - - +
202A LYS* 1.3 56.6 + - - +
204A VAL* 3.3 4.5 + - - +
205A ALA* 2.9 30.5 + - - +
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Residues in contact with LYS 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ALA 5.8 1.4 + - - -
163A ALA* 5.6 3.6 - - - +
164A GLY* 4.0 29.9 + - - +
198A LYS 3.1 16.3 + - - +
199A GLY* 3.7 7.9 - - - +
200A HIS 3.1 0.2 - - - -
201A GLY* 1.3 74.4 - - - +
203A LYS* 1.3 62.5 + - + +
206A ASP* 2.8 72.5 + - - +
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Residues in contact with LYS 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A GLY 3.2 17.8 + - - +
200A HIS* 2.9 17.5 + - - +
202A LYS* 1.3 81.6 - - + +
204A VAL* 1.3 62.3 + - - +
206A ASP* 3.5 7.4 + - - +
207A ALA* 3.1 17.7 + - - +
285A HEM 3.5 70.9 + - + +
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Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLY* 5.5 4.0 - - - +
171A LEU* 4.9 9.0 - - + -
200A HIS* 2.9 43.7 + - + +
201A GLY* 3.7 9.6 - - - +
203A LYS* 1.3 78.0 - - - +
205A ALA* 1.3 61.8 + - - +
207A ALA* 3.2 4.7 + - - +
208A LEU* 3.0 34.4 + - + +
243A LEU* 4.5 16.4 - - + -
247A LEU* 5.2 7.0 - - + -
285A HEM 4.1 40.5 - - + +
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Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A TRP* 3.9 5.9 - - + -
163A ALA* 3.2 41.3 - - + +
164A GLY* 3.9 2.2 - - - +
167A GLY* 4.5 4.7 - - - -
201A GLY 2.9 17.7 + - - +
202A LYS 3.8 3.1 - - - +
204A VAL* 1.3 75.8 - - - +
206A ASP* 1.3 60.5 + - - +
208A LEU* 3.0 13.5 + - - +
209A THR* 2.8 32.5 + - - -
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Residues in contact with ASP 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ALA* 5.7 1.4 - - - +
202A LYS* 2.8 64.3 + - - +
203A LYS* 3.7 6.7 - - - +
205A ALA* 1.3 75.7 - - - +
207A ALA* 1.3 62.0 + - - +
209A THR* 3.3 10.5 + - - -
210A ASN* 3.1 21.3 + - - +
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Residues in contact with ALA 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A LYS 3.1 14.6 + - - +
204A VAL 3.6 8.1 - - - +
205A ALA 3.2 0.2 - - - -
206A ASP* 1.3 76.3 - - - +
208A LEU* 1.3 59.4 + - - +
210A ASN* 3.2 8.3 + - - +
211A ALA* 3.0 26.3 + - - +
222A LEU* 4.2 7.0 - - + +
225A LEU* 3.6 31.0 - - + -
285A HEM 4.0 16.2 - - + -
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Residues in contact with LEU 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A TRP* 3.7 30.7 - - + -
204A VAL* 3.0 23.8 + - + +
205A ALA* 3.0 10.6 + - - +
207A ALA* 1.3 73.0 - - - +
209A THR* 1.3 60.3 + - - +
211A ALA* 3.2 4.7 + - + +
212A VAL* 2.9 35.6 + - - +
247A LEU* 3.9 32.8 - - + -
270A PHE* 4.3 11.1 - - + -
271A LEU* 4.2 18.2 - - + -
274A VAL* 4.2 26.2 - - + -
285A HEM 4.5 11.9 - - + -
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Residues in contact with THR 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A TRP* 2.9 30.0 + - + +
163A ALA* 4.5 7.8 - - - +
205A ALA 2.8 15.7 + - - -
206A ASP* 3.4 13.8 + - - -
208A LEU* 1.3 79.3 - - - +
210A ASN* 1.3 60.9 + - - +
212A VAL* 3.4 3.6 + - - +
213A ALA* 3.1 22.1 + - + +
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Residues in contact with ASN 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ASP 3.1 12.9 + - - +
207A ALA* 3.2 11.9 + - - +
209A THR* 1.3 73.4 - - - +
211A ALA* 1.3 65.4 + - - +
213A ALA* 3.3 4.0 + - - +
214A HIS* 2.8 60.5 + - - +
221A ALA* 3.5 36.2 + - - +
222A LEU* 4.7 5.0 - - + +
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Residues in contact with ALA 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A ALA 3.0 14.0 + - - +
208A LEU* 3.5 12.3 - - + +
210A ASN* 1.3 76.9 - - - +
212A VAL* 1.3 64.7 + - - +
214A HIS* 3.3 3.5 + - - -
215A VAL* 3.1 24.6 + - - +
218A MET* 3.6 25.0 - - - +
221A ALA* 5.5 1.1 - - - -
222A LEU* 4.3 21.7 - - + +
270A PHE* 4.1 10.5 - - + -
274A VAL* 4.4 4.3 - - + -
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Residues in contact with VAL 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A VAL* 4.0 13.9 - - + -
153A LYS* 3.8 40.6 - - + +
156A TRP* 4.0 29.6 - - + -
208A LEU 2.9 20.6 + - - +
209A THR 3.7 4.7 - - - +
211A ALA* 1.3 75.9 - - - +
213A ALA* 1.3 64.3 + - - +
214A HIS 3.2 0.7 + - - -
215A VAL* 3.4 19.4 + - + +
270A PHE* 3.6 27.4 - - + -
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Residues in contact with ALA 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LYS* 6.4 0.2 - - - -
209A THR* 3.1 17.8 + - + +
210A ASN* 3.6 9.0 - - - +
211A ALA 3.3 0.4 - - - -
212A VAL* 1.3 77.7 - - - +
214A HIS* 1.3 71.8 + - + +
215A VAL 3.6 1.0 + - - -
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Residues in contact with HIS 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ASN* 2.8 48.5 + - - +
211A ALA* 3.3 4.5 - - - +
212A VAL 3.1 0.2 - - - -
213A ALA* 1.3 90.2 + - + +
215A VAL* 1.3 55.9 + - - +
216A ASP 3.0 5.8 - - - -
217A ASP* 2.8 35.0 + - + +
218A MET* 3.0 9.9 + - - +
221A ALA* 3.7 23.9 - - + +
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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
------------------------------------------------------------
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