Contacts of the strand formed by residues 208 - 215 (chain B) in PDB entry 5LPE
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 208 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B LEU* 4.6 0.9 - - - -
122B GLN* 3.3 28.7 - - + +
123B LEU 4.4 0.2 - - - +
124B PRO* 4.3 10.7 - - - +
125B TYR* 3.6 35.1 - - + +
200B VAL* 3.4 5.6 - - - +
201B CYS* 2.9 39.7 + - - +
202B ASP* 4.6 4.4 - - + +
207B GLU* 1.3 85.5 - - - +
209B LEU* 1.3 62.6 + - - +
210B GLN* 3.4 17.0 + - - -
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Residues in contact with LEU 209 (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 VAL* 3.5 25.4 - - + -
47B VAL* 4.1 25.6 - - + -
53B LEU* 4.1 10.8 - - + -
121B LEU* 3.5 26.8 - - + +
122B GLN 2.9 16.4 + - - +
123B LEU* 4.2 7.0 - - + -
124B PRO* 3.2 29.1 - - + +
198B PRO* 3.7 11.9 - - + -
199B LEU 3.9 4.3 - - - +
200B VAL* 4.6 0.2 - - - +
208B THR* 1.3 69.8 - - - +
210B GLN* 1.3 61.0 + - - +
211B GLY 3.9 16.6 - - - +
212B ILE* 4.3 3.4 - - + -
231B ILE* 4.1 24.5 - - + +
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Residues in contact with GLN 210 (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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124B PRO* 3.5 12.7 - - - +
128B ARG* 2.9 28.2 + - - +
130B ALA* 3.4 38.6 + - + +
181B ILE* 3.9 16.3 - - + +
199B LEU* 2.8 13.7 + - + -
201B CYS* 3.6 31.2 - - + -
208B THR* 3.4 16.9 + - - +
209B LEU* 1.3 75.0 + - - +
211B GLY* 1.3 57.0 + - - +
229B THR 3.9 0.5 - - - +
230B GLN* 4.0 4.3 + - - +
231B ILE* 3.5 20.4 + - - -
232B CYS* 4.0 15.2 + - - +
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Residues in contact with GLY 211 (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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198B PRO* 3.4 4.5 - - - +
199B LEU* 2.6 39.9 + - - -
209B LEU* 3.6 5.0 - - - +
210B GLN* 1.3 81.7 - - - +
212B ILE* 1.3 61.4 + - - +
228B TYR* 3.7 11.7 - - - -
229B THR 3.3 11.2 - - - -
231B ILE* 3.6 7.4 - - - +
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Residues in contact with ILE 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 VAL* 3.6 23.8 - - + -
53B LEU* 3.5 41.5 - - + +
54B THR* 4.0 14.8 - - - -
55B ALA 4.1 4.0 - - - +
102B ASP 4.1 7.2 - - - +
103B LEU* 3.6 26.5 - - + -
196B GLY* 3.2 22.0 - - - +
197B GLY 3.5 2.9 - - - +
209B LEU* 4.3 5.8 - - + -
211B GLY* 1.3 75.9 - - - +
213B LEU* 1.3 68.6 + - - +
214B SER 3.1 0.3 + - - -
228B TYR* 3.3 4.3 - - - -
229B THR* 2.7 35.1 + - - -
231B ILE* 4.0 3.1 - - + +
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Residues in contact with LEU 213 (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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55B ALA* 3.8 4.7 - - - +
57B HIS* 3.8 7.6 - - - -
193B SER* 5.1 4.7 - - - -
194B ASP 3.7 22.4 - - - +
195B SER* 4.3 9.6 - - - +
196B GLY 3.3 18.6 + - - +
197B GLY* 3.3 9.5 + - - +
212B ILE* 1.3 74.3 - - - +
214B SER* 1.3 65.4 + - - +
215B TRP* 3.6 15.5 - - - +
217B VAL* 3.4 29.2 - - + -
226B ALA* 3.5 18.4 - - + -
227B VAL 3.8 4.5 - - - +
228B TYR* 3.3 43.0 - - + +
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Residues in contact with SER 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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55B ALA* 5.1 0.2 - - - -
57B HIS* 3.0 24.8 + - - -
99B ASP 3.6 2.4 + - - -
102B ASP* 3.0 28.9 + - - +
180B MET* 3.6 19.6 - - - +
195B SER* 5.2 0.5 + - - -
212B ILE 3.1 2.8 + - - -
213B LEU* 1.3 75.3 - - - +
215B TRP* 1.3 78.9 + - - +
227B VAL 2.9 17.2 + - - -
229B THR* 4.0 12.3 - - - -
304B ZN 3.6 2.8 - - - -
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Residues in contact with TRP 215 (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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218A TYR* 5.9 2.5 - + + -
98B THR* 2.9 39.2 + - + +
99B ASP* 5.1 1.1 - - + -
172B TYR* 3.6 33.4 - + + -
175B VAL* 3.5 33.4 - - + -
180B MET* 4.3 7.0 - - - +
213B LEU* 3.6 11.7 - - - +
214B SER* 1.3 97.6 + - - +
216B GLY* 1.3 65.1 + - - +
217B VAL* 3.6 2.5 - - - -
226B ALA 3.8 0.3 - - - -
227B VAL* 2.8 64.7 + - + +
301B SO4 2.6 34.8 - - - +
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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