Contacts of the strand formed by residues 219 - 224 (chain B) in PDB entry 1SHJ
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 PHE 219 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B THR* 3.7 25.1 - - - -
166B PHE* 3.4 28.3 - - + -
167B ARG* 4.3 6.5 - - + -
179B LYS* 3.5 17.0 - - + -
181B PHE* 3.5 34.1 - + - -
214B PRO* 5.8 4.5 - - + -
216B GLU* 3.4 47.4 + - + +
217B ALA 3.2 8.2 - - - -
218B ASP* 1.3 79.9 - - - +
220B LEU* 1.3 62.2 + - - +
221B PHE* 4.1 16.2 - + + -
292B VAL 4.8 0.4 - - - -
294B MET* 3.0 39.3 + - + -
295B LEU* 3.4 5.6 + - - +
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Residues in contact with LEU 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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179B LYS 3.1 9.5 + - - +
180B LEU* 4.5 17.9 - - + -
181B PHE* 2.9 28.8 + - - +
182B PHE* 5.3 4.3 - - + -
219B PHE* 1.3 77.2 - - - +
221B PHE* 1.3 78.9 + - - +
222B ALA* 4.4 3.6 - - + +
258B ILE* 3.8 31.9 - - + -
259B MET* 4.3 13.0 - - - -
262B LEU* 3.9 22.4 - - + -
291B VAL* 4.2 3.1 - - + -
292B VAL 3.3 11.9 - - - +
293B SER* 4.1 9.6 - - - +
295B LEU* 3.8 19.3 - - + -
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Residues in contact with PHE 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B THR* 3.8 24.9 - - + -
181B PHE* 3.4 19.5 - + + -
183B ILE* 3.9 12.3 - - + -
213B ILE* 4.5 9.0 - - + -
214B PRO* 4.0 15.0 - - + -
219B PHE* 4.1 31.0 - + + -
220B LEU* 1.3 79.3 - - - +
222B ALA* 1.3 60.6 + - - +
223B TYR 3.9 1.6 - - - +
290B CYS 3.8 0.4 - - - +
291B VAL* 3.4 7.4 - - - +
292B VAL* 2.8 40.0 + - + +
294B MET* 4.3 13.0 - - + -
401B NXN 3.7 58.1 - + + -
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Residues in contact with ALA 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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181B PHE 2.9 9.6 + - - +
182B PHE* 3.6 26.0 - - + -
183B ILE* 2.9 28.6 + - - +
220B LEU* 4.6 1.8 - - + -
221B PHE* 1.3 74.4 - - - +
223B TYR* 1.3 60.4 + - - +
224B SER 3.8 0.3 + - - -
241B PHE* 3.8 18.0 - - + -
262B LEU* 4.3 21.1 - - + -
289B PRO* 5.8 0.7 - - + -
290B CYS 3.8 5.4 - - - +
291B VAL* 4.7 4.5 - - + +
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Residues in contact with TYR 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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146B GLU 3.1 24.1 + - - -
147B GLU 3.6 2.8 + - - -
159B ILE* 3.9 19.5 - - + +
183B ILE* 3.5 30.5 - - + -
185B ALA* 3.7 16.6 - - + +
187B ARG* 3.1 23.5 + - - -
221B PHE 3.9 0.2 - - - -
222B ALA* 1.3 72.6 - - - +
224B SER* 1.3 71.6 + - - +
225B THR* 3.9 9.2 + - + -
288B ILE 4.9 0.5 - - - +
289B PRO* 3.5 2.3 - - - +
290B CYS* 3.1 44.4 + - - -
401B NXN 3.5 57.7 - + + -
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Residues in contact with SER 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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183B ILE 3.0 7.9 + - - +
184B GLN* 2.9 20.5 + - - +
185B ALA 3.4 25.3 + - - +
222B ALA 3.8 0.6 + - - -
223B TYR* 1.3 80.5 - - - +
225B THR* 1.3 63.2 + - - +
226B VAL* 3.8 8.6 + - - +
241B PHE* 3.3 42.7 - - - +
289B PRO* 3.9 12.3 - - - -
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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