Contacts of the strand formed by residues 222 - 227 (chain C) in PDB entry 3ELP
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 MET 222 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71C LEU* 3.6 16.4 - - + -
86C ALA* 4.1 3.8 - - - -
87C PHE 3.8 1.8 - - - +
88C ALA 3.6 5.8 - - - -
89C SER* 3.9 5.4 - - - -
90C GLY 3.6 6.4 + - - -
208C TYR 4.8 0.2 - - - -
210C ALA* 3.1 38.1 + - + +
220C VAL* 4.4 2.9 - - + -
221C VAL* 1.3 78.7 - - - +
223C GLY* 1.3 60.3 + - - +
224C LEU* 3.8 24.7 - - + -
247C PRO* 3.3 32.8 - - + -
251C ASP* 3.3 43.7 - - + +
252C CYS* 3.7 2.2 - - - +
255C CYS* 3.3 26.0 - - + -
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Residues in contact with GLY 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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85C LEU 3.8 1.0 - - - +
86C ALA* 3.3 2.8 - - - -
87C PHE* 2.6 41.1 + - - +
89C SER 3.6 21.5 - - - -
90C GLY* 3.6 8.3 - - - -
93C ALA* 4.3 7.2 - - - -
207C MET* 5.3 0.2 - - - -
208C TYR 3.9 2.7 - - - -
222C MET* 1.3 75.1 - - - +
224C LEU* 1.3 62.7 + - - +
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Residues in contact with LEU 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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71C LEU* 4.1 11.0 - - + +
72C GLU* 5.6 0.7 - - + -
75C VAL* 3.7 32.1 - - + -
79C ASP* 5.5 0.2 - - - +
84C CYS* 4.1 17.9 - - - -
85C LEU 3.7 0.9 - - - -
86C ALA* 3.6 28.7 - - + -
93C ALA* 4.9 0.2 - - - +
206C SER 3.8 0.9 - - - +
207C MET* 3.4 4.7 - - - +
208C TYR* 2.8 66.6 + - + +
210C ALA* 6.2 2.5 - - + +
222C MET* 3.8 20.0 - - + -
223C GLY* 1.3 72.6 - - - -
225C VAL* 1.3 62.7 + - - +
226C SER 4.0 1.1 + - - -
255C CYS* 4.3 12.6 - - - -
259C LEU* 5.4 2.5 - - + -
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Residues in contact with VAL 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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84C CYS* 3.2 2.9 - - - -
85C LEU* 2.8 42.5 + - + +
87C PHE* 3.7 19.3 - - + -
93C ALA* 3.5 30.3 - - + +
97C ILE* 4.1 13.2 - - + -
205C ILE* 3.6 28.7 - - + -
206C SER 3.9 2.7 - - - +
207C MET* 4.1 7.4 - - + -
224C LEU* 1.3 77.7 - - - +
226C SER* 1.3 58.7 + - - +
236C LEU* 4.2 20.9 - - + -
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Residues in contact with SER 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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75C VAL 3.8 3.1 + - - -
76C ALA* 4.0 0.5 - - - -
79C ASP* 2.5 44.4 + - - +
81C ALA* 3.9 5.6 - - - -
83C TYR 3.2 10.4 + - - -
84C CYS* 3.5 19.5 - - - +
199C LEU* 4.2 5.2 - - - +
205C ILE* 3.8 1.9 - - - +
206C SER* 3.0 31.4 + - - +
224C LEU 4.0 0.4 - - - -
225C VAL* 1.3 72.4 - - - +
227C VAL* 1.3 67.1 + - - +
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Residues in contact with VAL 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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81C ALA* 3.6 2.1 - - - +
82C LYS 3.4 3.3 + - - -
83C TYR* 3.0 35.5 + - + +
85C LEU* 5.3 2.5 - - + -
199C LEU* 4.2 2.7 - - - -
204C ASP 3.2 24.0 - - - +
205C ILE* 3.5 22.7 - - + -
225C VAL 4.0 2.2 + - - +
226C SER* 1.3 77.8 - - - +
228C ASN* 1.3 64.7 + - - +
229C CYS 3.6 21.5 - - - +
232C LEU* 3.5 15.0 - - + -
233C HIS* 3.7 27.1 - - + +
236C LEU* 4.6 8.1 - - + -
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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