Contacts of the strand formed by residues 205 - 210 (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 ILE 205 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C ILE* 3.8 26.0 - - + -
100C LEU* 4.4 6.5 - - + -
183C ILE* 3.7 23.1 - - + -
184C LEU 3.2 3.4 + - - +
185C VAL* 3.3 18.2 - - + +
186C VAL* 2.7 34.1 + - - +
199C LEU* 4.3 1.8 - - - -
203C ALA* 4.2 2.4 - - - +
204C ASP* 1.3 82.3 - - - +
206C SER* 1.3 60.7 + - - +
225C VAL* 3.6 28.5 - - + -
226C SER 3.8 5.4 - - - +
227C VAL* 3.5 13.5 - - + -
232C LEU* 3.7 21.5 - - + -
236C LEU* 4.5 4.9 - - + -
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Residues in contact with SER 206 (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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79C ASP* 4.1 12.4 + - - +
186C VAL 3.5 4.7 - - - -
188C ASN* 3.8 11.8 + - - +
198C PRO* 3.5 35.9 - - - +
199C LEU* 4.0 17.5 - - - +
205C ILE* 1.3 73.4 - - - +
207C MET* 1.3 60.3 + - - +
208C TYR* 3.9 1.4 + - - +
224C LEU 3.8 1.4 - - - +
225C VAL* 3.9 0.2 - - - -
226C SER* 3.0 38.4 + - - -
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Residues in contact with MET 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C GLY* 3.5 14.8 - - - +
93C ALA* 4.0 16.6 - - + -
94C THR* 3.2 26.5 - - - +
97C ILE* 4.4 15.9 - - + -
155C TRP* 3.5 18.8 - - + -
185C VAL* 4.5 3.1 - - + -
186C VAL 2.9 12.9 + - - +
187C ASP* 3.4 27.9 - - - +
188C ASN* 2.9 24.0 + - - -
205C ILE 4.0 0.8 - - - -
206C SER* 1.3 71.2 + - - +
208C TYR* 1.3 59.8 + - - +
209C SER* 3.5 27.1 - - - -
224C LEU 3.4 9.0 - - - +
225C VAL* 4.1 6.1 - - + +
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Residues in contact with TYR 208 (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* 5.6 2.5 - - + -
79C ASP* 5.1 10.3 - - - +
188C ASN* 3.5 20.9 - - + -
189C THR* 3.7 22.6 + - + +
192C SER* 3.6 25.1 - - - -
193C PRO* 3.9 29.2 - - + -
206C SER* 3.9 2.3 + - - +
207C MET* 1.3 73.2 - - - +
209C SER* 1.3 61.6 + - - +
210C ALA* 4.0 21.8 + - + +
214C MET* 5.9 4.3 - - - +
223C GLY* 3.8 0.5 - - - -
224C LEU* 2.8 61.6 + - + +
259C LEU* 5.4 11.2 - - + -
262C LEU* 4.6 11.5 - - + +
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Residues in contact with SER 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C GLY* 3.1 34.8 + - - -
187C ASP* 5.2 0.4 - - - -
189C THR* 2.9 42.2 + - - +
207C MET* 3.5 12.5 - - - -
208C TYR* 1.3 75.9 - - - +
210C ALA* 1.3 61.1 + - - +
211C THR* 4.1 8.1 + - - +
222C MET 3.6 5.1 + - - -
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Residues in contact with ALA 210 (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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90C GLY 5.5 0.2 + - - -
189C THR* 5.2 0.4 - - - -
208C TYR* 4.0 26.0 + - + +
209C SER* 1.3 75.6 + - - +
211C THR* 1.3 67.6 + - - +
214C MET* 5.9 6.7 - - + -
220C VAL 3.9 1.9 - - - +
221C VAL* 3.6 4.7 - - - +
222C MET* 3.1 39.6 + - + +
224C LEU* 6.2 2.4 - - + +
255C CYS* 5.9 4.7 - - - -
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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