Contacts of the helix formed by residues 217 - 229 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113C LYS 3.9 7.1 - - - +
114C CYS 2.8 23.9 + - - +
115C LEU 4.0 2.3 - - - +
116C SER* 4.0 15.5 - - - -
120C LYS* 3.5 32.7 - - - +
215C ILE 3.4 2.2 + - - -
216C VAL* 1.3 70.6 - - - +
218C TRP* 1.3 61.5 + - - +
219C GLU* 3.0 13.3 + - - +
220C PHE* 3.0 27.0 + - - +
221C VAL* 3.2 20.8 + - - +
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Residues in contact with TRP 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C LYS 3.2 24.8 + - - +
121C PRO* 4.6 1.3 - - + -
122C MET* 3.5 58.5 - - + +
123C PRO* 3.6 3.6 - - + +
126C LEU* 3.7 19.9 - - + +
130C ILE* 4.5 6.3 - - + -
140C PHE* 4.2 11.7 - + - -
141C MET* 3.9 12.0 - - + +
159C LEU* 5.2 1.6 - - + -
188C PHE* 5.0 6.7 - + + -
213C TRP* 3.5 49.1 + + - -
216C VAL* 3.2 26.3 + - + +
217C ASP* 1.3 69.4 + - - +
219C GLU* 1.3 59.3 + - - +
220C PHE 3.3 0.2 - - - -
221C VAL* 3.7 25.3 - - + +
222C CYS* 2.9 30.1 + - - +
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Residues in contact with GLU 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C LYS* 3.4 35.1 - - + +
121C PRO* 4.0 19.7 - - - +
123C PRO* 4.4 13.9 - - + -
217C ASP* 3.0 7.5 + - - +
218C TRP* 1.3 75.8 - - - +
220C PHE* 1.3 59.6 + - - +
222C CYS* 3.4 2.1 + - - +
223C HIS* 2.9 28.6 + - - +
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Residues in contact with PHE 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C LEU* 4.5 4.5 - - + -
110C PHE* 3.6 25.4 - + - -
113C LYS* 3.4 71.6 - - + +
114C CYS* 3.9 11.9 - - - -
187C ILE 4.7 0.2 - - - -
217C ASP* 3.0 20.0 + - - +
219C GLU* 1.3 73.9 - - - +
221C VAL* 1.3 62.3 + - - +
223C HIS* 3.1 15.7 + + - +
224C MET* 2.8 65.7 + - + +
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Residues in contact with VAL 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C CYS* 4.8 5.8 - - + -
126C LEU* 3.7 15.9 - - + -
159C LEU* 4.8 1.3 - - + -
187C ILE* 3.3 45.5 - - + +
188C PHE* 3.9 26.0 - - + -
216C VAL* 4.1 2.7 - - + -
217C ASP 3.2 13.3 + - - +
218C TRP* 3.7 29.2 - - + +
219C GLU 3.3 0.4 - - - -
220C PHE* 1.3 77.3 - - + +
222C CYS* 1.3 56.7 + - - +
224C MET* 3.3 3.8 + - - +
225C TYR* 2.8 25.6 + - - +
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Residues in contact with CYS 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C PRO* 3.7 30.7 - - + -
125C THR* 4.2 6.5 - - - -
126C LEU* 3.9 28.9 - - + +
218C TRP 2.9 17.7 + - - +
219C GLU 3.8 2.9 - - - +
221C VAL* 1.3 73.4 - - - +
223C HIS* 1.3 60.5 + - - +
225C TYR* 3.1 7.9 + - - +
226C GLU* 2.8 58.0 + - - +
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Residues in contact with HIS 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C GLU 2.9 17.4 + - - +
220C PHE* 3.5 18.6 - + - +
222C CYS* 1.3 77.4 - - - +
224C MET* 1.3 79.0 + - - +
226C GLU* 3.4 13.4 + - - +
227C ARG* 3.0 44.3 + - + +
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Residues in contact with MET 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C TYR* 3.7 20.0 - - - +
25C THR* 3.6 41.5 - - + +
26C LEU* 5.4 0.2 - - - -
110C PHE* 4.1 5.2 - - + -
186C PRO 3.9 7.2 - - - +
187C ILE* 3.7 17.9 - - + +
220C PHE* 2.8 57.3 + - + +
221C VAL 3.5 7.6 - - - +
223C HIS* 1.3 86.9 - - - +
225C TYR* 1.3 57.3 + - - +
227C ARG* 3.3 10.8 + - - +
228C ALA* 2.9 32.7 + - - +
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Residues in contact with TYR 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C THR* 4.5 17.9 - - + -
126C LEU* 4.1 16.6 - - + -
129C ALA* 3.4 25.8 - - + +
161C VAL* 3.9 6.3 - - + -
166C LYS 4.6 8.0 + - - -
168C LEU* 3.8 38.6 - - + -
187C ILE* 3.7 15.9 - - + +
221C VAL 2.8 14.2 + - - +
222C CYS* 3.1 8.5 + - - +
224C MET* 1.3 77.2 - - - +
226C GLU* 1.3 71.1 + - + +
228C ALA* 3.4 0.7 + - - -
229C THR* 2.9 54.5 + - + +
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Residues in contact with GLU 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C THR* 4.1 18.0 + - + +
222C CYS* 2.8 42.8 + - - +
223C HIS* 3.8 12.9 + - - +
225C TYR* 1.3 79.2 - - + +
227C ARG* 1.3 62.4 + - - +
229C THR* 3.4 7.1 + - - -
230C LYS* 3.4 32.2 + - - +
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Residues in contact with ARG 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C TYR* 3.3 30.9 + - + +
24C HIS* 2.7 33.1 + - - +
25C THR 3.7 11.3 + - - -
27C PRO* 3.8 25.9 - - - +
185C ARG* 4.7 0.5 + - - -
223C HIS* 3.0 41.8 + - + +
224C MET* 3.7 11.2 - - - +
225C TYR 3.2 0.2 - - - -
226C GLU* 1.3 78.6 - - - +
228C ALA* 1.3 61.9 + - - +
229C THR 3.3 0.7 + - - -
230C LYS* 3.4 24.8 + - + +
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Residues in contact with ALA 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C TYR* 3.6 22.6 + - - +
161C VAL* 3.9 25.6 - - + +
163C PRO* 5.1 2.4 - - - +
185C ARG* 2.9 46.4 + - + +
186C PRO 5.6 0.2 - - - +
187C ILE* 4.5 3.6 - - + -
224C MET 2.9 17.4 + - - +
225C TYR 3.4 0.4 + - - +
227C ARG* 1.3 76.7 - - - +
229C THR* 1.3 59.6 + - - +
230C LYS 3.4 0.2 - - - -
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Residues in contact with THR 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C VAL* 3.8 20.6 - - + -
166C LYS* 4.3 21.7 - - + +
225C TYR* 2.9 54.9 + - + +
226C GLU* 3.4 10.4 + - - -
228C ALA* 1.3 75.2 - - - +
230C LYS* 1.3 65.3 + - - +
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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