Contacts of the helix formed by residues 218 - 228 (chain C) in PDB entry 3FUB
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 218 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A SER* 4.0 7.4 - - - -
317A ASN* 3.2 33.1 - - - +
150C LYS* 5.8 2.4 - - - +
152C ASN* 4.8 6.9 + - - +
216C CYS* 4.5 0.2 - - - +
217C ARG* 1.3 84.5 + - + +
219C ILE* 1.3 63.9 + - - +
220C ALA* 4.0 15.4 + - - +
221C CYS* 3.2 23.2 + - - +
222C THR* 3.1 21.9 + - - +
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Residues in contact with ILE 219 (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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239A GLU* 5.2 6.5 - - + +
240A ARG 5.7 7.9 - - - +
314A ASP* 5.4 3.6 - - - +
316A SER* 4.2 9.8 - - - -
317A ASN* 3.2 22.7 - - - +
218C ASP* 1.3 70.0 - - - +
220C ALA* 1.3 58.6 + - - +
222C THR* 3.1 13.8 + - - +
223C GLU* 2.7 53.9 + - - +
304C SER* 3.8 17.0 - - - +
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Residues in contact with ALA 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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150C LYS* 4.6 20.0 - - + -
152C ASN* 4.4 4.9 + - - +
218C ASP* 3.3 15.3 - - - +
219C ILE* 1.3 78.0 - - - +
221C CYS* 1.3 62.7 + - - +
223C GLU* 4.2 6.8 - - - +
224C ARG* 3.3 23.2 + - - +
118D LEU* 5.3 2.3 - - - +
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Residues in contact with CYS 221 (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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152C ASN* 3.8 28.6 - - + +
154C CYS* 3.4 20.3 - - - -
215C SER 3.7 4.7 - - - -
216C CYS* 2.0 54.2 - - + -
217C ARG 4.5 0.7 - - - +
218C ASP* 3.2 20.4 + - - +
219C ILE 3.1 0.2 - - - -
220C ALA* 1.3 79.1 - - - +
222C THR* 1.3 57.2 + - - +
224C ARG* 3.4 4.9 + - - +
225C ARG* 3.0 23.4 + - - +
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Residues in contact with THR 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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316A SER* 4.9 6.1 - - - +
216C CYS* 3.8 15.9 - - + -
218C ASP 3.1 12.1 + - - +
219C ILE* 3.1 20.8 + - - +
221C CYS* 1.3 72.4 - - - +
223C GLU* 1.3 60.5 + - - +
225C ARG* 3.3 28.4 + - - +
226C ARG* 3.0 31.5 + - - +
304C SER* 2.9 36.6 + - - +
305C SER 4.8 7.0 - - - +
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Residues in contact with GLU 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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239A GLU* 4.6 14.6 - - - +
219C ILE* 2.7 41.1 + - + +
220C ALA* 4.3 5.0 - - - +
222C THR* 1.3 71.8 + - - +
224C ARG* 1.3 60.2 + - - +
226C ARG* 3.8 4.2 + - - +
227C GLN* 3.3 28.1 + - - +
304C SER* 3.9 23.1 - - - +
118D LEU* 3.5 35.1 - - + +
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Residues in contact with ARG 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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152C ASN* 4.3 6.2 - - - +
154C CYS* 3.7 34.8 - - + +
155C LEU* 4.0 17.9 - - - +
158C ALA* 3.5 18.0 - - - +
171C ARG* 4.2 4.4 - - - +
220C ALA 3.3 19.7 + - - +
221C CYS 3.5 3.8 - - - +
222C THR 3.2 0.2 - - - -
223C GLU* 1.3 75.9 - - - +
225C ARG* 1.3 66.3 + - - +
227C GLN* 3.0 17.8 + - - +
228C THR* 3.4 6.5 + - - +
59D THR* 4.6 2.2 + - - -
60D LYS* 5.3 3.2 - - - +
61D GLU* 3.0 31.4 + - - +
114D LEU* 3.1 49.4 + - + +
115D ASP 4.9 3.6 + - - -
116D ASP* 5.8 1.6 + - - -
118D LEU* 4.1 4.6 - - + +
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Residues in contact with ARG 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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154C CYS* 3.7 9.6 - - - -
211C MET 4.2 2.5 - - - +
212C LEU* 3.6 27.4 - - - +
213C PHE 4.8 0.2 - - - -
214C CYS* 2.8 45.5 + - - +
215C SER* 4.4 1.2 - - - +
216C CYS* 3.7 20.4 - - - +
221C CYS 3.0 16.8 + - - +
222C THR* 3.6 24.8 + - - +
224C ARG* 1.3 77.2 - - - +
226C ARG* 1.3 61.7 + - - +
228C THR* 2.6 27.4 + - - -
300C ASN* 5.1 0.5 - - - +
301C TYR* 3.7 27.3 - - + +
304C SER 6.0 0.4 - - - -
305C SER 5.1 1.8 + - - +
306C SER 3.8 12.7 + - - -
307C LEU* 3.4 32.9 - - - +
342C ILE* 5.9 1.8 - - - +
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Residues in contact with ARG 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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239A GLU* 4.7 7.9 + - - -
222C THR 3.0 17.9 + - - +
223C GLU* 4.2 5.2 - - - +
225C ARG* 1.3 76.4 - - - +
227C GLN* 1.3 70.7 + - - +
228C THR 3.4 0.4 + - - -
229C ILE 4.5 1.0 + - - -
231C PRO* 3.5 9.8 - - + +
235C TYR* 6.1 2.4 - - - -
300C ASN* 3.1 28.9 + - - +
301C TYR* 3.5 34.0 + - + -
302C VAL 3.4 23.0 + - - -
303C ASP* 3.6 21.7 + - - +
304C SER* 3.2 28.6 + - - +
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Residues in contact with GLN 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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223C GLU 3.3 14.7 + - - +
224C ARG 3.0 11.7 + - - +
226C ARG* 1.3 82.4 + - - +
228C THR* 1.3 66.3 + - - +
229C ILE 3.2 2.9 - - - -
230C VAL* 2.7 23.8 + - - +
231C PRO* 3.5 29.5 - - - +
232C VAL* 5.3 8.4 + - - +
114D LEU* 3.7 21.3 - - + -
118D LEU* 4.4 27.5 - - + +
120D TYR* 3.0 19.2 + - + +
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Residues in contact with THR 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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174C TYR* 2.8 37.7 + - - +
199C PHE* 5.7 1.3 - - + -
200C PHE* 5.3 6.7 - - + -
211C MET* 3.4 50.3 + - + +
212C LEU* 4.5 17.0 - - + +
224C ARG* 3.4 4.8 + - - +
225C ARG* 2.6 26.4 + - - -
227C GLN* 1.3 77.2 - - - +
229C ILE* 1.3 60.7 + - + +
230C VAL* 3.4 2.8 + - - +
120D TYR* 3.6 11.9 + - - -
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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
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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