Contacts of the strand formed by residues 210 - 216 (chain E) in PDB entry 5LF4
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 VAL 210 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47E VAL* 4.4 3.1 - - + -
48E ALA 3.5 2.9 - - - -
49E LEU* 4.6 0.4 - - + -
50E LYS* 3.9 10.8 + - - -
192E LEU* 3.7 26.2 - - + -
195E LEU* 4.5 4.9 - - + -
205E LEU* 3.6 35.4 - - + -
206E THR 3.3 12.3 + - - +
207E THR 4.1 6.1 - - - +
208E LYS 3.7 0.6 - - - -
209E ASN* 1.3 90.7 + - - +
211E SER* 1.3 65.5 + - - +
212E ILE* 3.9 18.6 - - + -
225E ASP* 4.1 0.7 - - - +
226E ASP 4.6 0.5 + - - -
229E VAL* 3.6 23.2 - - + +
233E LEU* 4.6 3.8 - - + -
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Residues in contact with SER 211 (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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47E VAL* 3.4 4.3 - - - +
48E ALA* 2.8 35.9 + - - -
50E LYS* 3.9 17.4 - - - +
62E LYS* 5.4 2.1 + - - -
63E ILE* 3.5 23.8 + - - +
209E ASN 4.2 0.2 + - - -
210E VAL* 1.3 73.2 - - - +
212E ILE* 1.3 63.9 + - - +
223E ILE* 4.1 4.9 - - - +
224E TYR 3.6 5.0 + - - -
225E ASP* 2.6 29.5 + - - -
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Residues in contact with ILE 212 (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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45E VAL* 4.4 3.1 - - + -
46E LEU 3.4 10.5 - - - +
47E VAL* 4.4 7.6 - - + -
63E ILE* 3.7 4.5 - - - -
188E VAL* 4.0 16.8 - - + -
192E LEU* 4.3 5.2 - - + -
210E VAL* 3.9 15.3 - - + -
211E SER* 1.3 81.3 + - - +
213E GLY* 1.3 61.5 + - - +
214E ILE* 3.8 27.8 - - + -
223E ILE* 3.4 5.4 - - - +
224E TYR* 2.7 46.9 + - + +
229E VAL* 4.2 14.8 - - + -
232E PHE* 3.8 39.0 - - + -
233E LEU* 5.9 0.2 - - + -
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Residues in contact with GLY 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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45E VAL* 3.3 4.5 - - - +
46E LEU* 2.7 40.0 + - - +
63E ILE* 3.7 9.1 - - - +
212E ILE* 1.3 72.9 - - - +
214E ILE* 1.3 63.2 + - - +
221E PHE* 3.8 21.8 - - - -
222E THR 3.2 8.5 - - - -
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Residues in contact with ILE 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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43E HIS* 4.2 5.8 - - + -
44E ALA 3.6 7.9 - - - +
45E VAL* 4.1 7.2 - - + -
184E LEU* 3.7 29.6 - - + -
188E VAL* 4.0 16.8 - - + -
212E ILE* 3.8 10.5 - - + -
213E GLY* 1.3 79.3 - - - +
215E VAL* 1.3 65.5 + - - +
219E LEU* 3.6 21.9 - - + +
220E GLU 3.5 3.5 - - - +
221E PHE* 3.3 5.9 - - - -
222E THR* 3.0 31.8 + - - -
224E TYR* 3.6 28.0 - - + +
232E PHE* 3.9 22.2 - - + -
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Residues in contact with VAL 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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43E HIS* 3.4 7.6 - - - +
44E ALA* 2.8 45.0 + - + +
68E ASN 4.2 0.4 - - - +
69E HIS* 3.9 22.4 - - + +
135E ALA* 4.0 7.9 - - + +
136E GLY* 3.9 33.2 - - - +
137E TYR* 4.0 11.6 - - + +
214E ILE* 1.3 77.3 - - - +
216E GLY* 1.3 59.9 + - - +
219E LEU* 3.4 15.3 - - - +
220E GLU* 4.5 0.2 - - - -
221E PHE* 3.8 24.0 - - + +
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Residues in contact with GLY 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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42E THR 3.2 14.6 - - - -
43E HIS* 3.7 10.3 - - - -
137E TYR* 3.9 19.3 - - - +
215E VAL* 1.3 78.0 - - - +
217E LYS* 1.3 66.7 - - - +
218E ASP* 3.3 3.1 - - - -
219E LEU* 3.0 23.0 + - - +
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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