Contacts of the strand formed by residues 213 - 217 (chain E) in PDB entry 2SEC
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 THR 213 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39E HIS* 2.8 19.4 + - - -
209E TYR* 2.8 33.3 + - + +
210E PRO 3.5 19.5 - - - +
211E THR 3.9 6.3 - - - +
212E ASN* 1.3 80.0 - - - +
214E TYR* 1.3 89.2 + - - +
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Residues in contact with TYR 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E HIS* 3.4 24.2 - + - -
40E PRO* 4.9 4.6 - - + +
41E ASP* 3.8 7.9 + - - +
79E THR* 4.2 8.2 + - - +
80E GLY* 3.1 37.3 + - - -
81E VAL* 4.0 10.3 - - + -
206E TYR* 3.3 31.4 - - + +
207E SER 3.2 20.2 - - - +
208E THR* 3.9 13.5 - - + -
209E TYR* 3.8 3.4 - - - -
212E ASN 4.4 5.4 - - - -
213E THR* 1.3 104.0 + - - +
215E ALA* 1.3 65.6 + - - +
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Residues in contact with ALA 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E HIS* 2.9 19.6 + - + -
206E TYR* 3.9 6.7 - - - -
207E SER 2.9 18.7 + - - -
209E TYR* 3.5 37.6 - - + +
214E TYR* 1.3 77.2 - - - +
216E THR* 1.3 67.6 + - - +
217E LEU* 5.2 2.5 - - + -
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Residues in contact with THR 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E GLY* 3.2 45.1 - - - +
205E VAL 3.2 4.7 - - - +
206E TYR* 3.4 20.6 - - - +
215E ALA* 1.3 75.3 - - - +
217E LEU* 1.3 70.4 + - - +
218E ASN* 4.8 6.2 + - - +
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Residues in contact with LEU 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E HIS* 4.8 3.4 - - - -
67E HIS* 3.6 37.2 + - + -
202E GLY 4.3 0.2 - - - +
204E GLY 3.6 1.0 + - - -
205E VAL* 3.0 30.9 + - - +
209E TYR* 4.3 12.8 - - + +
215E ALA* 5.2 2.5 - - + -
216E THR* 1.3 82.6 - - - +
218E ASN* 1.3 68.8 - - - +
222E MET* 3.7 28.5 - - + +
60I ASP* 4.0 19.5 - - + +
61I LEU 5.1 7.2 - - - +
62I ARG* 4.1 26.5 - - + +
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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