Contacts of the strand formed by residues 219 - 224 (chain B) in PDB entry 4HXG
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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200B TRP* 3.6 11.2 - - - +
202B ILE* 3.5 6.2 - - + +
214B PHE* 4.0 22.4 - + - -
217B VAL* 3.3 39.2 - - + +
218B SER* 1.3 80.2 - - - +
220B TYR* 1.3 60.6 + - - +
231B LEU* 3.3 41.1 - - + -
232B TYR 3.2 27.1 - - - +
233B GLY* 3.5 3.6 - - - -
234B LYS 3.7 9.4 - - - +
235B PRO* 4.1 18.6 - - + -
247B TYR* 3.7 20.2 - + - -
253B VAL* 4.2 15.0 - - + -
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Residues in contact with TYR 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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175B SER* 4.5 14.4 - - - -
186B SER* 3.6 18.4 - - - -
197B PHE* 6.1 2.8 - + - -
200B TRP* 3.3 47.1 - + + -
202B ILE* 3.8 7.4 - - - -
219B PHE* 1.3 74.9 - - - +
221B ALA* 1.3 66.9 + - - +
222B ILE* 3.5 20.1 + - + +
231B LEU* 3.5 6.7 - - - -
232B TYR* 2.9 60.4 + + - +
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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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175B SER* 5.2 2.9 + - - -
176B GLY* 6.0 0.2 - - - -
177B ILE* 3.7 19.3 - - + +
184B VAL* 3.4 32.9 - - + +
186B SER* 3.1 13.1 + - - +
202B ILE* 4.2 2.6 - - + +
220B TYR* 1.3 79.8 - - - +
222B ILE* 1.3 60.5 + - - +
223B ASP 3.6 0.4 - - - -
229B ILE* 3.7 19.3 - - + -
230B LEU 3.6 5.4 - - - -
231B LEU* 3.8 6.5 - - + +
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Residues in contact with ILE 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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177B ILE* 4.1 12.3 - - - +
220B TYR* 3.5 25.1 + - + +
221B ALA* 1.3 73.7 - - - +
223B ASP* 1.3 62.6 + - - +
230B LEU* 3.0 34.2 + - + +
232B TYR* 3.5 40.6 - - + -
246B ILE* 4.6 1.1 - - + -
267B ALA* 3.8 33.4 - - + +
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Residues in contact with ASP 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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110B GLU* 5.2 5.2 - - - +
177B ILE* 3.6 15.9 - - - +
222B ILE* 1.3 83.8 - - + +
224B SER* 1.3 86.4 + - - +
229B ILE* 3.6 2.8 - - - -
230B LEU* 2.9 37.4 + - + -
267B ALA 4.6 1.6 - - - +
268B LYS* 3.4 11.4 - - - +
269B ILE* 2.9 36.6 + - + +
270B ARG* 3.5 23.6 + - - -
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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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110B GLU* 6.0 0.2 + - - -
177B ILE* 4.3 4.6 - - - +
178B TRP 3.3 25.1 + - - +
179B HIS* 2.8 24.8 + - - -
223B ASP* 1.3 91.3 + - - +
225B ASP* 1.3 57.0 + - - +
226B GLY* 2.7 25.8 + - - -
228B ARG 3.3 8.9 + - - -
229B ILE* 4.8 1.8 - - - -
269B ILE* 3.9 11.9 - - - +
270B ARG* 5.0 3.5 + - - -
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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