Contacts of the helix formed by residues 217 - 229 (chain D) in PDB entry 4F2N
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 ASP 217 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113D LYS 4.0 6.2 - - - +
114D CYS 2.8 23.5 + - - +
115D LEU 4.1 1.4 - - - +
116D SER* 4.0 16.8 - - - -
120D LYS* 3.4 39.2 + - - +
215D ILE 3.3 2.8 + - - -
216D VAL* 1.3 69.2 - - - +
218D TRP* 1.3 62.3 + - - +
219D GLU* 3.0 15.3 + - - +
220D PHE* 3.0 26.3 + - - +
221D VAL* 3.3 13.9 + - - +
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Residues in contact with TRP 218 (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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120D LYS 3.2 25.9 + - - +
121D PRO* 4.7 0.7 - - + -
122D MET* 3.5 62.8 - - + +
123D PRO* 3.6 4.2 - - + +
126D LEU* 3.7 15.4 - - + +
130D ILE* 4.5 5.8 - - + -
140D PHE* 4.2 12.3 - + - -
141D MET* 3.9 11.9 - - + +
159D LEU* 5.3 1.8 - - + -
188D PHE* 4.9 6.5 - + + -
213D TRP* 3.5 48.0 + + - -
216D VAL* 3.1 30.3 + - + +
217D ASP* 1.3 70.5 + - - +
219D GLU* 1.3 59.9 + - - +
221D VAL* 3.7 24.0 - - + +
222D CYS* 2.9 29.8 + - - +
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Residues in contact with GLU 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D LYS* 3.4 32.5 - - + +
121D PRO* 4.0 23.1 + - - +
123D PRO* 4.3 15.5 - - + -
217D ASP* 3.0 7.5 + - - +
218D TRP* 1.3 76.2 - - - +
220D PHE* 1.3 59.2 + - - +
222D CYS* 3.4 1.9 + - - +
223D HIS* 3.0 28.6 + - - +
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Residues in contact with PHE 220 (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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26D LEU* 4.5 6.7 - - + -
28D HIS* 6.2 0.7 - + - -
110D PHE* 3.7 25.4 - + - -
113D LYS* 3.3 64.4 - - + +
114D CYS* 4.0 13.7 - - - -
187D ILE 4.6 0.4 - - - -
217D ASP* 3.0 20.2 + - - +
219D GLU* 1.3 74.5 - - - +
221D VAL* 1.3 67.4 + - - +
223D HIS* 3.2 16.1 + + + +
224D MET* 2.9 58.0 + - + +
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Residues in contact with VAL 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D CYS* 4.9 1.8 - - + -
126D LEU* 3.7 15.3 - - + -
159D LEU* 4.9 1.1 - - + -
187D ILE* 3.3 46.2 - - + +
188D PHE* 3.9 24.9 - - + -
216D VAL* 4.2 2.0 - - + -
217D ASP 3.3 15.1 + - - +
218D TRP* 3.7 29.2 - - + +
220D PHE* 1.3 79.8 - - + +
222D CYS* 1.3 58.8 + - - +
224D MET* 3.2 4.0 + - - +
225D TYR* 2.8 26.0 + - - +
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Residues in contact with CYS 222 (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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123D PRO* 3.8 25.6 - - + -
125D THR* 4.1 8.1 - - - -
126D LEU* 3.8 34.7 - - + +
218D TRP 2.9 18.1 + - - +
219D GLU 3.8 3.6 - - - +
221D VAL* 1.3 74.4 - - - +
223D HIS* 1.3 66.0 + - - +
225D TYR* 3.1 7.2 + - - +
226D GLU* 2.9 51.6 + - - +
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Residues in contact with HIS 223 (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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219D GLU 3.0 15.1 + - - +
220D PHE* 3.4 19.1 - + - +
222D CYS* 1.3 75.9 - - - +
224D MET* 1.3 74.2 + - - +
226D GLU* 3.3 12.3 + - - +
227D ARG* 3.2 43.0 + - + +
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Residues in contact with MET 224 (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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23D TYR* 3.4 25.6 + - - +
25D THR* 3.5 32.5 - - + +
26D LEU* 5.3 0.7 - - - -
110D PHE* 4.3 5.2 - - + -
186D PRO 3.8 7.2 - - - +
187D ILE* 3.8 17.9 - - + +
220D PHE* 2.9 54.8 + - + +
221D VAL 3.5 8.1 - - - +
223D HIS* 1.3 79.8 - - - +
225D TYR* 1.3 62.4 + - - +
227D ARG* 3.4 25.0 + - - +
228D ALA* 2.9 26.7 + - - +
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Residues in contact with TYR 225 (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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125D THR* 4.4 18.4 - - + -
126D LEU* 4.2 14.1 - - + -
129D ALA* 3.4 33.6 - - + +
132D LYS* 5.6 4.5 + - - -
161D VAL* 3.9 9.6 - - + -
166D LYS* 5.0 6.1 + - - +
168D LEU* 3.9 22.9 - - + -
187D ILE* 3.7 18.8 - - + +
221D VAL 2.8 17.4 + - - +
222D CYS* 3.1 8.5 + - - +
224D MET* 1.3 74.0 - - - +
226D GLU* 1.3 72.1 + - + +
228D ALA* 3.8 1.0 - - - -
229D THR* 2.9 59.1 + - + +
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Residues in contact with GLU 226 (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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125D THR* 3.9 22.7 + - + +
222D CYS* 2.9 40.7 + - - +
223D HIS* 3.8 9.6 + - - +
224D MET 3.3 0.2 - - - -
225D TYR* 1.3 80.1 - - + +
227D ARG* 1.3 61.2 + - - +
229D THR* 3.5 6.4 + - - -
230D LYS* 3.4 19.6 + - - +
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Residues in contact with ARG 227 (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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23D TYR* 3.2 42.1 + - + +
24D HIS 2.9 31.3 + - - +
25D THR 3.2 17.7 + - - -
27D PRO* 3.8 19.1 - - - +
185D ARG* 4.1 2.8 + - - -
223D HIS* 3.2 37.8 + - + +
224D MET* 3.5 17.8 - - - +
226D GLU* 1.3 77.4 - - - +
228D ALA* 1.3 66.0 + - - +
229D THR 3.4 0.3 + - - -
230D LYS* 3.4 19.6 + - - +
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Residues in contact with ALA 228 (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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23D TYR* 3.6 21.3 - - - +
161D VAL* 3.8 23.1 - - + +
163D PRO* 4.5 4.0 - - - +
166D LYS* 5.2 0.5 + - - -
185D ARG* 2.9 42.8 + - + +
187D ILE* 4.3 4.3 - - + -
224D MET 2.9 20.2 + - - +
225D TYR 3.9 2.9 - - - +
227D ARG* 1.3 79.3 - - - +
229D THR* 1.3 59.4 + - - +
230D LYS* 3.3 0.4 - - - +
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Residues in contact with THR 229 (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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161D VAL* 3.7 22.4 - - + -
166D LYS* 3.0 36.9 + - + +
225D TYR* 2.9 57.4 + - + +
226D GLU* 3.5 6.8 + - - -
227D ARG 3.3 0.2 - - - -
228D ALA* 1.3 75.0 - - - +
230D LYS* 1.3 67.1 + - - +
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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