Contacts of the strand formed by residues 212 - 217 (chain E) in PDB entry 4LOU
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 212 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126E PRO* 3.6 19.7 - - + +
127E PRO* 4.7 3.6 - - + +
206E ALA* 4.4 0.2 - - - +
207E HIS* 2.8 38.1 + - - +
210E SER* 2.7 29.9 + - - -
211E SER* 1.3 77.3 - - - +
213E LYS* 1.3 75.2 + - - +
214E VAL* 4.6 11.0 - - + -
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Residues in contact with LYS 213 (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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205E VAL 3.2 7.9 - - - +
206E ALA* 4.2 19.1 - - + -
211E SER 4.3 1.5 + - - +
212E THR* 1.3 82.6 - - - +
214E VAL* 1.3 67.4 + - - +
215E ASP* 4.2 14.0 + - - +
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Residues in contact with VAL 214 (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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127E PRO* 4.3 15.9 - - + +
129E VAL* 3.9 40.4 - - + +
203E CYS 3.5 1.6 - - - +
204E ASN* 3.5 0.9 - - - -
205E VAL* 2.7 41.9 + - + +
212E THR* 4.6 11.7 - - + -
213E LYS* 1.3 79.1 - - - +
215E ASP* 1.3 62.4 + - - +
216E LYS* 3.7 21.3 - - + +
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Residues in contact with ASP 215 (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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202E THR* 4.8 5.6 - - - +
203E CYS 3.2 5.8 - - - -
204E ASN* 2.9 37.3 + - - +
205E VAL 5.3 0.2 - - - +
213E LYS* 4.9 13.5 - - - +
214E VAL* 1.3 76.1 - - - +
216E LYS* 1.3 61.2 + - - +
217E LYS* 4.0 2.4 + - - +
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Residues in contact with LYS 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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129E VAL* 3.2 31.6 + - + +
131E PRO* 4.1 29.8 - - + -
202E THR* 3.1 2.1 - - - -
203E CYS* 2.6 58.7 + - - -
214E VAL* 3.7 13.0 - - + +
215E ASP* 1.3 74.4 - - - +
217E LYS* 1.3 65.0 + - - +
218E ILE 4.0 0.2 + - - -
122F GLU* 3.3 32.8 + - - +
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Residues in contact with LYS 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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131E PRO* 4.4 7.6 - - - +
200E THR* 4.0 23.0 + - + +
201E VAL 4.1 3.1 - - - +
202E THR* 3.6 25.8 - - + -
215E ASP 4.0 2.2 + - - +
216E LYS* 1.3 81.1 - - - +
218E ILE* 1.3 69.5 + - - +
219E VAL* 3.3 30.1 + - + +
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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