Contacts of the strand formed by residues 214 - 219 (chain C) in PDB entry 4EN0
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 GLU 214 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C HIS* 4.0 15.2 + - - -
132C ALA* 3.2 27.3 - - + +
133C LEU 3.1 5.6 - - - +
134C VAL* 3.8 23.2 - - + +
167C TYR 3.8 0.2 - - - +
168C LYS* 3.3 6.6 - - - +
169C ARG* 2.9 51.7 + - + +
212C GLY 3.9 9.7 - - - +
213C GLU* 1.3 81.3 - - - +
215C VAL* 1.3 64.6 + - - +
216C VAL* 4.3 0.9 - - - -
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Residues in contact with VAL 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C ALA* 3.5 0.9 - - - -
133C LEU* 2.9 39.6 + - + +
135C VAL* 5.8 0.9 - - + -
143C ILE* 4.3 17.0 - - + -
166C LEU* 4.3 17.0 - - + -
167C TYR 3.3 11.2 - - - +
168C LYS* 4.7 5.8 - - + -
179C LEU* 4.8 2.0 - - + -
209C LEU* 4.1 35.7 - - + -
213C GLU 5.5 0.7 - - - +
214C GLU* 1.3 79.2 - - - +
216C VAL* 1.3 70.0 + - - +
235C PHE* 3.7 29.1 - - + -
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Residues in contact with VAL 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C PRO* 3.9 14.8 - - + -
130C ASP 5.5 0.2 - - - +
131C GLY 3.3 20.9 - - - +
132C ALA* 3.6 17.3 - - + -
166C LEU* 3.4 5.0 - - - -
167C TYR* 2.9 54.7 + - + +
169C ARG* 3.6 37.5 - - - +
215C VAL* 1.3 77.5 - - - +
217C VAL* 1.3 64.7 + - - +
218C ARG* 3.9 18.8 + - + -
235C PHE* 5.0 0.2 - - - -
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Residues in contact with VAL 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C PRO* 3.6 0.2 - - - +
112C LEU* 2.9 39.7 + - + +
114C TRP* 3.5 26.5 - - + +
131C GLY 4.3 4.6 + - - -
145C SER* 3.6 14.8 - - - +
147C VAL* 4.5 0.7 - - + -
164C HIS* 3.9 20.0 - - + +
165C GLY 3.5 4.9 - - - +
166C LEU* 3.5 16.6 - - + -
216C VAL* 1.3 73.4 - - - +
218C ARG* 1.3 64.6 + - - +
235C PHE* 3.3 38.6 - - + -
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Residues in contact with ARG 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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110C GLY* 3.8 24.8 - - - +
111C PRO* 3.8 23.6 - - + +
112C LEU* 4.6 1.6 - - - -
163C THR 3.8 0.9 - - - +
164C HIS* 3.5 0.5 - - - -
165C GLY* 2.9 33.1 + - - -
167C TYR* 3.5 37.5 + - + -
176C GLU* 3.1 38.3 + - - -
216C VAL* 3.9 9.2 - - + -
217C VAL* 1.3 79.4 - - - +
219C VAL* 1.3 66.3 + - - +
220C LEU 4.4 0.2 - - - -
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Residues in contact with VAL 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C GLY 5.1 3.3 + - - +
112C LEU* 3.8 27.1 - - + +
147C VAL* 4.0 10.5 - - + -
149C LEU* 4.5 2.7 - - + -
162C ILE* 4.0 15.3 - - + -
163C THR 3.1 9.0 - - - +
164C HIS* 3.8 25.8 - - + -
217C VAL* 4.6 0.2 - - + -
218C ARG* 1.3 81.5 - - - +
220C LEU* 1.3 77.3 + - - +
221C ASP 3.4 2.8 + - - +
222C GLU* 3.7 14.9 + - + +
225C VAL* 3.6 25.8 - - + -
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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