Contacts of the helix formed by residues 210 - 231 (chain A) in PDB entry 3SPD
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 HIS 210 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A LEU* 4.0 2.9 - - - -
207A PHE* 2.8 27.7 + - + +
208A GLY* 3.4 2.0 - - - -
209A ARG* 1.3 78.2 - - - +
211A PHE* 1.3 64.4 + - - +
212A THR 3.3 1.1 - - - -
213A LYS* 3.2 39.5 + - + +
214A LEU* 3.1 18.5 + - - +
11E G 6.1 5.2 - - - -
7F A 5.6 1.8 + - - -
8F T 3.3 16.2 + - - +
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Residues in contact with PHE 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LEU* 3.5 29.6 - - + -
161A LYS* 3.3 23.8 - - - -
162A ASN* 3.2 37.9 - - - -
163A SER* 3.6 23.8 - - - +
166A TYR* 4.6 5.8 - - + -
198A LEU* 3.6 8.1 - - - -
209A ARG 3.0 8.6 + - - +
210A HIS* 1.3 72.1 - - - +
212A THR* 1.3 61.6 + - - +
214A LEU* 3.2 14.4 + - + +
215A LYS* 2.8 56.5 + - + +
8F T 2.8 22.1 + - - +
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Residues in contact with THR 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A PHE* 1.3 78.1 - - - +
213A LYS* 1.3 65.2 + - + +
215A LYS* 3.4 8.7 + - + +
216A ALA* 3.2 21.4 + - + +
7F A 3.5 34.8 + - - +
8F T 2.8 31.3 + - - -
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Residues in contact with LYS 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A PHE* 3.9 19.0 - - + -
210A HIS* 3.2 40.0 + - + +
212A THR* 1.3 78.3 - - + +
214A LEU* 1.3 65.2 + - - +
216A ALA* 3.3 7.0 + - - +
217A HIS* 3.1 22.2 + - - +
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Residues in contact with LEU 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A TYR* 3.6 43.3 - - + +
198A LEU* 4.1 21.1 - - + -
199A LYS 4.5 1.3 - - - -
200A CYS* 4.2 20.0 - - + +
207A PHE* 3.7 36.8 - - + -
210A HIS 3.1 12.8 + - - +
211A PHE* 3.4 16.2 - - + +
213A LYS* 1.3 76.1 - - - +
215A LYS* 1.3 58.1 + - - +
217A HIS* 3.0 5.6 + - + +
218A LEU* 2.8 44.8 + - + +
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Residues in contact with LYS 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A HIS 5.4 0.8 + - - +
156A VAL* 5.5 0.6 - - - +
157A SER 2.9 26.1 + - - +
158A PRO* 4.5 4.8 + - - +
160A LEU* 2.8 30.1 + - + +
161A LYS* 5.3 0.2 - - - -
211A PHE* 2.8 53.9 + - + +
212A THR* 3.5 12.8 - - + +
213A LYS 3.3 0.2 - - - -
214A LEU* 1.3 72.3 - - - +
216A ALA* 1.3 60.9 + - - +
218A LEU* 3.2 18.0 + - - +
219A GLN* 3.2 12.5 + - - +
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Residues in contact with ALA 216 (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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212A THR* 3.2 10.8 + - + +
213A LYS* 3.7 9.4 - - - +
214A LEU 3.2 0.2 - - - -
215A LYS* 1.3 78.6 - - - +
217A HIS* 1.3 62.5 + - - +
219A GLN* 3.3 10.5 + - - +
220A GLU* 3.2 27.0 + - - +
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Residues in contact with HIS 217 (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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200A CYS* 3.6 14.5 - - + +
203A CYS* 3.7 3.5 - - - -
205A GLU* 3.2 25.8 + - - -
207A PHE* 3.4 28.3 - + + -
213A LYS 3.1 7.8 + - - +
214A LEU* 3.0 9.6 + - + +
216A ALA* 1.3 76.0 - - - +
218A LEU* 1.3 60.9 + - - +
220A GLU* 3.2 23.4 + - + +
221A GLU* 2.9 34.0 + - + +
601A ZN 2.1 36.4 - - - -
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Residues in contact with LEU 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ASP 3.8 12.2 - - - +
155A HIS* 3.7 17.5 - - + +
156A VAL* 3.3 15.5 - - + +
160A LEU* 4.2 8.5 - - + -
166A TYR* 3.8 29.2 - - + +
200A CYS* 4.6 11.0 - - - -
201A TRP* 3.7 33.4 - - + +
214A LEU* 2.8 35.5 + - + +
215A LYS* 3.2 12.3 + - + +
217A HIS* 1.3 72.1 - - - +
219A GLN* 1.3 60.8 + - - +
221A GLU* 3.3 6.4 + - + +
222A TYR* 2.9 24.1 + - - +
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Residues in contact with GLN 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LYS* 5.2 2.5 + - - +
156A VAL* 3.2 30.2 - - + +
215A LYS 3.2 9.6 + - - +
216A ALA* 3.3 13.2 - - - +
218A LEU* 1.3 78.2 - - - +
220A GLU* 1.3 65.0 + - + +
222A TYR* 3.1 14.2 + - - +
223A ASP* 2.9 57.0 + - - +
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Residues in contact with GLU 220 (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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216A ALA* 3.2 17.4 + - - +
217A HIS* 3.2 27.9 + - + +
219A GLN* 1.3 76.6 - - + +
221A GLU* 1.3 57.7 + - - +
223A ASP* 3.3 11.3 + - - +
224A ASP* 2.9 38.9 + - - +
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Residues in contact with GLU 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A TYR* 5.4 0.7 - - - -
200A CYS* 3.5 7.0 - - - -
201A TRP* 5.7 4.5 - - + -
202A ARG* 2.8 48.5 + - + +
203A CYS* 3.2 16.1 + - - +
217A HIS* 2.9 29.6 + - + +
218A LEU* 3.6 10.3 - - + +
219A GLN 3.2 0.2 - - - -
220A GLU* 1.3 76.2 - - - +
222A TYR* 1.3 58.5 + - - +
224A ASP* 3.4 8.0 + - - +
225A TRP* 2.9 29.8 + - - +
601A ZN 2.0 40.0 - - - -
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Residues in contact with TYR 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LYS* 3.5 35.5 - - + +
120A LEU* 3.5 48.7 + - + +
132A TYR* 3.6 21.8 - + - -
154A ASP* 3.9 11.2 - - + -
156A VAL* 3.8 12.8 - - + -
218A LEU 2.9 14.2 + - - +
219A GLN* 3.1 12.1 + - - +
221A GLU* 1.3 74.1 - - - +
223A ASP* 1.3 78.3 + - - +
225A TRP* 3.1 14.6 + + - -
226A LEU* 2.8 53.3 + - + +
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Residues in contact with ASP 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A GLN* 2.9 46.6 + - - +
220A GLU* 3.5 10.6 - - - +
222A TYR* 1.3 83.5 - - - +
224A ASP* 1.3 66.4 + - - +
226A LEU* 3.5 6.5 + - - +
227A ASP* 3.1 24.6 + - - +
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Residues in contact with ASP 224 (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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202A ARG* 3.9 12.5 + - - +
220A GLU* 2.9 24.7 + - - +
221A GLU* 3.6 10.9 - - - +
223A ASP* 1.3 79.5 - - - +
225A TRP* 1.3 63.3 + - - +
227A ASP* 3.3 7.2 + - - +
228A LYS* 3.1 24.1 + - - +
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Residues in contact with TRP 225 (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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120A LEU* 4.0 6.5 - - + -
124A LEU* 3.7 41.3 - - + -
128A ALA* 4.1 12.1 + - + -
129A LEU* 4.7 3.6 - - + -
131A ASN 5.7 0.6 + - - -
132A TYR* 3.3 71.3 - + + +
202A ARG* 3.8 16.7 - - - +
221A GLU 2.9 18.3 + - - +
222A TYR* 3.7 13.9 - + - +
224A ASP* 1.3 76.2 - - - +
226A LEU* 1.3 76.8 + - + +
228A LYS* 3.3 20.2 + - - +
229A SER* 2.7 50.3 + - - -
701A SO4 3.7 25.3 + - - -
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Residues in contact with LEU 226 (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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120A LEU 5.5 0.7 - - - +
121A SER* 3.9 28.7 - - - -
124A LEU* 4.1 13.7 - - + -
222A TYR* 2.8 45.6 + - + +
223A ASP* 3.7 6.5 - - - +
225A TRP* 1.3 87.1 - - + +
227A ASP* 1.3 64.9 + - - +
229A SER* 3.1 0.7 + - - -
230A VAL* 3.0 43.0 + - + +
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Residues in contact with ASP 227 (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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223A ASP 3.1 15.5 + - - +
224A ASP* 3.7 5.8 - - - +
226A LEU* 1.3 80.6 - - - +
228A LYS* 1.3 57.4 + - - +
230A VAL* 3.5 9.2 - - - +
231A SER* 2.7 40.5 + - - -
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Residues in contact with LYS 228 (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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202A ARG* 3.3 15.5 - - - +
224A ASP 3.1 14.9 + - - +
225A TRP* 3.6 21.9 - - - +
227A ASP* 1.3 77.1 - - - +
229A SER* 1.3 67.6 + - - +
231A SER* 3.7 14.9 + - - -
232A MET 3.8 11.1 + - - +
701A SO4 3.0 39.2 + - - +
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Residues in contact with SER 229 (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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123A GLN 5.4 0.5 - - - +
124A LEU* 3.6 26.0 - - - +
128A ALA* 4.7 11.7 - - - +
225A TRP* 2.7 49.5 + - - -
226A LEU 3.1 2.4 + - - -
228A LYS* 1.3 83.9 + - - +
230A VAL* 1.3 64.1 + - - +
232A MET* 3.2 17.8 + - - +
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Residues in contact with VAL 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A SER* 4.6 1.1 - - - +
123A GLN* 3.7 45.1 - - + +
124A LEU* 4.1 8.1 - - + -
226A LEU* 3.0 38.7 + - + +
227A ASP* 3.5 14.4 - - - +
229A SER* 1.3 72.6 - - - +
231A SER* 1.3 63.2 + - - +
232A MET* 2.8 21.4 + - - +
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Residues in contact with SER 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ASP* 2.7 30.0 + - - -
228A LYS* 3.7 9.6 - - - -
229A SER 3.2 0.4 - - - -
230A VAL* 1.3 79.4 - - - +
232A MET* 1.3 70.9 + - - +
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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