Contacts of the strand formed by residues 219 - 229 (chain B) in PDB entry 1RLU
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 GLY 219 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152B ARG* 5.0 13.2 - - - -
155B CYS 5.6 1.1 - - - -
156B ASP 2.8 18.7 + - - -
157B THR* 3.1 7.4 - - - +
158B LEU* 2.9 26.6 + - - -
217B GLY 3.3 3.4 - - - -
218B ALA* 1.3 71.3 - - - +
220B THR* 1.3 63.6 + - - -
221B ALA 3.5 0.3 + - - -
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Residues in contact with THR 220 (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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152B ARG* 3.2 32.1 + - - +
158B LEU* 3.4 6.6 - - - +
160B VAL* 4.0 24.6 - - + +
218B ALA 3.7 1.4 + - - -
219B GLY* 1.3 71.9 - - - -
221B ALA* 1.3 67.8 + - - +
222B LEU* 5.0 7.9 - - + -
309B ALA 4.4 0.2 - - - +
310B ALA* 3.9 1.8 - - - +
311B GLY* 3.8 19.8 + - - +
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Residues in contact with ALA 221 (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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157B THR* 3.6 24.2 - - + -
158B LEU 2.8 10.7 + - - +
159B ILE* 3.4 7.0 - - + -
160B VAL* 3.0 27.7 + - - +
219B GLY 3.5 0.6 + - - -
220B THR* 1.3 74.5 - - - +
222B LEU* 1.3 66.9 + - - +
308B ILE* 4.0 16.6 - - + -
309B ALA 3.2 13.9 - - - +
310B ALA* 3.8 10.3 - - + -
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Residues in contact with LEU 222 (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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159B ILE* 5.0 3.1 - - - -
160B VAL* 3.5 32.1 - - + +
162B PRO* 4.5 4.9 - - + -
220B THR* 5.0 8.3 - - + -
221B ALA* 1.3 80.2 - - - +
223B MET* 1.3 61.2 + - - +
246B LEU 3.8 14.1 - - - +
247B LEU* 3.2 37.4 - - + +
248B GLU* 4.2 20.4 - - + +
250B SER* 3.5 17.5 - - - +
308B ILE* 3.4 5.9 - - - +
309B ALA 2.9 31.7 + - - +
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Residues in contact with MET 223 (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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159B ILE* 4.6 6.3 - - + -
160B VAL 4.8 3.0 + - - -
161B ILE* 4.0 22.9 - - + -
186B VAL* 3.4 23.6 - - + +
189B ASN* 3.8 12.8 - - - +
190B GLY* 3.6 29.8 - - - +
222B LEU* 1.3 75.9 - - - +
224B GLY* 1.3 70.6 + - - +
225B ILE* 4.4 5.6 - - + -
246B LEU* 3.1 50.0 + - + +
247B LEU* 3.5 5.6 - - - -
306B THR* 4.1 11.2 - - + -
307B VAL 3.2 9.9 - - - +
308B ILE* 3.9 14.8 - - + -
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Residues in contact with GLY 224 (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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223B MET* 1.3 75.2 - - - +
225B ILE* 1.3 64.2 + - - +
241B ALA* 3.5 23.2 - - - +
244B SER* 3.6 10.3 - - - -
246B LEU* 4.9 0.2 - - - -
247B LEU* 3.7 6.5 - - - +
306B THR* 3.5 3.6 - - - -
307B VAL* 2.7 35.0 + - - +
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Residues in contact with ILE 225 (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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169B MET* 3.9 30.0 - - + +
186B VAL* 3.9 20.9 - - + -
189B ASN* 3.3 33.9 - - + +
223B MET* 4.4 13.0 - - + -
224B GLY* 1.3 78.1 - - - +
226B GLY* 1.3 59.3 + - - +
240B ILE* 3.6 11.3 - - - +
241B ALA* 3.5 13.5 - - - +
244B SER* 4.0 8.2 + - - +
246B LEU* 5.0 5.4 - - + -
305B VAL 3.1 12.6 - - - +
306B THR* 4.3 3.4 - - - +
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Residues in contact with GLY 226 (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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225B ILE* 1.3 76.4 - - - +
227B SER* 1.3 59.4 + - - -
237B ALA* 3.4 23.0 - - - +
240B ILE* 3.5 14.8 - - - -
241B ALA* 3.7 0.8 - - - +
304B ARG* 3.5 2.3 - - - +
305B VAL* 2.7 33.7 + - - +
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Residues in contact with SER 227 (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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226B GLY* 1.3 72.3 - - - -
228B ALA* 1.3 63.9 + - - +
237B ALA* 3.8 4.0 - - - +
240B ILE* 3.7 16.3 - - - +
302B GLU* 3.3 26.3 + - - -
303B VAL 3.1 9.0 - - - -
304B ARG* 3.5 17.0 + - - +
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Residues in contact with ALA 228 (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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227B SER* 1.3 76.8 - - - +
229B ARG* 1.3 63.8 - - - +
233B ARG* 3.5 29.6 - - - +
236B LYS* 3.8 20.4 - - + -
237B ALA* 3.8 3.7 - - - +
240B ILE* 5.1 2.0 - - + -
302B GLU* 3.5 3.7 - - - +
303B VAL* 2.9 31.7 + - - -
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Residues in contact with ARG 229 (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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228B ALA* 1.3 79.5 - - - +
230B GLY* 1.3 66.4 + - - +
231B GLU 4.2 4.2 - - - +
233B ARG* 3.8 6.2 - - - +
299B LEU 3.9 4.4 + - - -
300B GLY* 4.9 1.2 - - - -
301B ASP* 3.7 24.4 - - + +
302B GLU* 3.7 50.7 + - + +
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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