Contacts of the strand formed by residues 209 - 218 (chain B) in PDB entry 1SOX
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 ILE 209 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B LEU* 3.4 16.4 - - + +
136B PHE* 3.5 4.6 - - - -
182B THR* 3.4 26.5 - - + -
183B LEU 3.2 10.3 - - - +
184B GLN* 3.8 25.8 - - + +
188B ASN* 3.9 4.3 - - - +
206B ILE 3.7 11.7 - - - +
207B GLY 2.9 5.6 + - - +
208B ALA* 1.3 79.2 - - - +
210B SER* 1.3 72.9 + - - +
348B GLN* 5.3 0.9 - - + -
370B TYR* 3.7 48.7 - - + +
372B TRP* 4.7 10.5 - - + -
410B TRP* 4.2 10.8 - - + -
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Residues in contact with SER 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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119B PRO* 4.4 4.3 - - - +
124B LEU* 4.7 0.3 - - - +
130B THR* 3.7 14.8 - - - +
135B PHE* 3.4 43.2 - - - -
136B PHE* 3.0 21.7 + - - +
182B THR* 3.4 1.2 - - - -
183B LEU 2.8 31.7 + - - +
209B ILE* 1.3 82.9 + - - +
211B THR* 1.3 66.8 + - - +
410B TRP* 4.4 4.5 - - - -
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Residues in contact with THR 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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128B PHE* 3.6 24.2 - - + +
129B LEU* 3.7 2.8 - - + -
130B THR* 2.8 38.6 + - - +
135B PHE* 3.6 1.7 - - - -
180B THR* 4.0 21.8 - - + -
181B ALA 3.7 9.9 - - - +
182B THR* 2.5 28.5 + - - +
210B SER* 1.3 74.6 - - - +
212B ALA* 1.3 68.8 + - - +
409B ALA* 4.3 3.6 - - + -
410B TRP* 3.1 25.1 - - + +
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Residues in contact with ALA 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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129B LEU* 4.2 8.7 - - - -
135B PHE* 3.8 7.8 - - + -
180B THR* 3.4 1.1 - - - -
181B ALA 2.9 30.1 + - - -
211B THR* 1.3 79.1 - - - +
213B ARG* 1.3 61.5 + - - +
214B TRP* 3.3 32.5 - - + -
274B MET* 4.1 11.4 - - + -
275B ASN* 3.3 20.6 - - - +
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Residues in contact with ARG 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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129B LEU* 4.1 14.6 - - + +
178B GLU* 3.4 55.9 + - + +
179B VAL* 3.7 1.5 - - - +
180B THR* 3.0 41.3 + - - +
212B ALA* 1.3 72.0 - - - +
214B TRP* 1.3 61.5 + - - +
215B GLY 4.1 0.2 + - - -
273B GLU 4.1 0.3 - - - +
274B MET* 3.7 0.9 - - - -
275B ASN* 2.7 46.9 + - - +
276B GLY 4.5 1.8 + - - +
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Residues in contact with TRP 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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135B PHE* 3.6 24.7 - + - -
178B GLU* 3.2 6.1 - - - +
179B VAL* 2.7 45.3 + - + +
181B ALA* 3.2 26.9 + - + +
183B LEU* 3.9 12.0 - - + +
212B ALA* 3.3 20.1 + - + -
213B ARG* 1.3 74.1 - - - +
215B GLY* 1.3 58.2 + - - +
269B LEU* 3.6 15.2 - - + +
271B ALA* 4.3 3.6 - - + -
273B GLU 3.4 14.4 - - - -
274B MET* 3.5 41.3 - - + -
279B LEU* 4.3 5.8 - - + -
283B HIS 5.1 0.2 - - - -
288B ARG* 3.8 34.1 - - - -
290B VAL* 3.7 37.2 - - + +
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Residues in contact with GLY 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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176B LYS* 4.6 4.9 - - - -
177B HIS 3.5 7.2 - - - -
178B GLU* 4.2 11.4 - - - -
213B ARG 4.1 0.2 + - - -
214B TRP* 1.3 75.4 - - - +
216B GLY* 1.3 57.9 + - - -
269B LEU* 4.3 0.4 - - - -
271B ALA* 3.4 3.4 - - - -
272B TYR* 2.8 28.0 + - - -
273B GLU* 2.8 33.7 + - - +
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Residues in contact with GLY 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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176B LYS* 3.7 4.6 - - - +
177B HIS* 2.9 35.8 + - - +
215B GLY* 1.3 75.5 - - - -
217B ALA* 1.3 64.9 + - - -
269B LEU* 3.9 5.9 - - - +
270B LEU 3.3 13.2 - - - -
271B ALA* 4.0 1.6 - - - -
272B TYR* 3.5 20.9 - - - -
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Residues in contact with ALA 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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170B LEU* 4.1 31.9 - - + +
174B PHE* 3.8 27.8 - - + -
175B PRO 4.7 3.4 - - - -
176B LYS* 5.3 0.2 - - - +
216B GLY* 1.3 73.6 - - - -
218B ARG* 1.3 59.7 + - - +
222B VAL* 4.1 9.2 - - + -
269B LEU* 3.4 4.3 - - - -
270B LEU* 2.7 39.8 + - + +
272B TYR* 3.7 3.7 - - - -
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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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174B PHE* 5.2 0.2 - - - +
175B PRO 4.9 4.0 + - - +
177B HIS* 3.2 54.1 + - + +
216B GLY 4.0 0.2 + - - -
217B ALA* 1.3 73.4 - - - +
219B LEU* 1.3 64.7 + - - +
220B ARG* 4.1 12.5 - - + +
221B ASP* 3.0 45.5 + - - +
222B VAL* 3.3 14.7 + - - +
264B PRO* 3.2 33.5 + - - +
267B ASP* 3.8 13.1 + - - +
268B VAL 3.6 8.7 - - - +
269B LEU* 4.0 3.1 - - + -
406B ARG* 4.3 5.7 - - - +
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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