Contacts of the strand formed by residues 211 - 219 (chain B) 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 211 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ALA 3.3 10.1 - - - +
48B GLU* 4.7 0.4 - - - -
49B ARG* 3.9 12.5 + - - -
194B ILE* 5.7 3.1 - - + -
197B LEU* 3.6 29.4 - - + -
201B MET* 4.0 5.6 - - - -
206B LEU* 3.7 24.0 - - + -
207B SER 4.0 8.1 - - - +
208B ALA 3.2 14.5 + - - +
209B GLU 3.6 0.2 - - - -
210B LYS* 1.4 83.4 - - - +
212B GLU* 1.3 61.9 + - - +
213B ILE* 4.8 10.1 - - + -
233B VAL* 3.5 32.8 - - + +
237B ILE* 4.9 3.8 - - + -
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Residues in contact with GLU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LEU 3.9 0.5 - - - +
46B ALA* 3.1 4.3 - - - -
47B ALA* 2.8 41.0 + - + +
49B ARG* 4.3 20.6 + - + +
61B PHE 5.6 0.2 - - - +
62B SER* 3.1 17.0 - - - -
63B GLU* 2.4 39.5 + - - +
64B LYS* 3.1 26.7 + - - +
65B ILE* 3.7 18.5 + - + +
211B VAL* 1.3 77.8 - - - +
213B ILE* 1.3 64.1 + - - +
227B VAL* 5.0 8.1 - - + -
233B VAL* 5.8 0.9 - - - -
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Residues in contact with ILE 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 4.9 1.1 - - + -
45B LEU 3.3 9.6 - - - +
46B ALA* 3.8 17.3 - - + -
65B ILE* 5.1 1.6 - - - -
190B LEU* 3.6 27.8 - - + -
193B ALA* 5.4 3.1 - - + -
194B ILE* 4.2 28.7 - - + -
197B LEU* 5.7 1.6 - - + -
211B VAL* 4.8 5.8 - - + -
212B GLU* 1.3 83.4 - - - +
214B ALA* 1.3 69.1 + - - +
215B THR* 4.6 0.4 - - + -
227B VAL* 3.5 8.2 - - - +
228B LEU* 2.9 44.4 + - + +
233B VAL* 4.5 20.6 - - + +
236B LEU* 4.4 11.9 - - + -
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Residues in contact with ALA 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 3.3 5.9 - - - +
45B LEU* 2.9 36.6 + - + +
65B ILE* 3.7 37.6 - - + +
73B ALA* 6.0 0.4 - - + -
137B ILE* 4.6 4.7 - - + +
213B ILE* 1.3 76.0 - - - +
215B THR* 1.3 64.3 + - - +
225B ILE* 5.4 5.4 - - + -
226B ARG 3.2 14.4 - - - +
227B VAL* 4.5 3.8 - - + -
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Residues in contact with THR 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL 3.6 5.6 - - - -
44B LEU* 4.4 1.1 - - + -
137B ILE* 4.8 2.2 - - - -
186B LEU* 4.1 33.2 - - + +
190B LEU* 4.3 20.9 - - + -
213B ILE* 4.6 0.2 - - + -
214B ALA* 1.3 78.6 - - - +
216B LEU* 1.3 61.9 + - - +
217B THR* 4.1 4.6 + - - +
224B VAL 3.8 0.9 - - - +
225B ILE* 3.4 5.0 - - - +
226B ARG* 2.9 47.4 + - - +
228B LEU* 3.9 23.8 - - + +
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Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLY* 3.2 5.9 - - - -
43B VAL* 2.9 32.8 + - + +
71B ASP 3.5 21.5 - - - +
72B MET* 4.1 0.9 - - - -
73B ALA* 4.4 0.4 - - + +
137B ILE* 3.8 27.6 - - + +
138B GLY* 3.7 31.6 - - - +
139B TRP* 4.0 2.0 - - + +
145B PHE* 4.0 17.3 - - + -
215B THR* 1.3 74.2 - - - +
217B THR* 1.3 63.0 + - - +
223B THR* 3.7 22.9 - - + -
224B VAL 3.4 3.4 - - - -
225B ILE* 3.7 23.6 - - + -
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Residues in contact with THR 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ASP* 3.6 19.3 - - - +
42B GLY* 4.4 0.2 - - - -
145B PHE* 4.1 7.4 - - - -
186B LEU* 3.7 27.4 - - + -
215B THR* 4.9 4.7 + - - +
216B LEU* 1.3 77.9 - - - +
218B ARG* 1.3 64.5 + - - +
219B GLU* 3.5 21.4 + - - -
223B THR* 3.4 7.3 - - - +
224B VAL* 2.7 45.3 + - - +
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Residues in contact with ARG 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ASP 4.9 0.8 + - - -
71B ASP* 4.1 4.0 + - - -
139B TRP* 3.3 61.4 - - + +
145B PHE* 3.4 29.4 - - + -
217B THR* 1.3 76.8 - - - +
219B GLU* 1.3 66.5 + - - +
221B GLY* 3.3 33.8 + - - +
222B LYS* 3.3 4.6 - - - +
223B THR* 2.9 41.7 + - - +
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Residues in contact with GLU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B THR* 3.5 18.0 + - - +
218B ARG* 1.3 77.7 - - - +
220B ASN* 1.3 79.6 + - - +
221B GLY 3.3 0.9 - - - +
222B LYS* 2.8 28.6 + - - +
224B VAL* 3.8 27.9 - - + +
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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