Contacts of the strand formed by residues 210 - 214 (chain B) in PDB entry 4HOO
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 LYS 210 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B TYR* 4.2 8.3 + - - -
181B TYR* 5.5 1.2 - - - +
189B PHE* 3.5 30.1 - - + -
202B ASN* 4.4 8.7 + - - +
204B LEU* 4.0 5.2 - - + +
209B PRO* 1.3 74.8 - - - +
211B THR* 1.3 62.6 + - - +
212B TRP* 3.4 36.2 - - + +
265B THR* 3.4 1.3 - - - -
266B GLN* 2.6 53.3 + - - +
283B PHE 3.6 8.5 - - - +
284B ASN* 2.8 37.4 + - - +
285B HIS* 4.3 1.1 - - - -
288B ASN* 4.2 6.1 + - - +
290B ALA* 4.0 23.0 - - - +
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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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118B PHE* 3.4 10.0 - - + -
189B PHE* 3.8 5.0 - - - -
210B LYS* 1.3 72.5 - - - +
212B TRP* 1.3 65.0 + - - +
213B TYR* 3.7 28.7 - - + +
263B ARG* 3.9 19.3 - - + -
264B ILE 3.6 3.4 - - - +
265B THR* 3.1 14.0 + - - +
282B GLY* 3.0 24.4 - - - -
283B PHE* 3.0 29.4 + - + +
285B HIS* 2.8 25.4 + - - -
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Residues in contact with TRP 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 3.9 33.4 - - + -
189B PHE* 4.0 18.2 - + - -
200B SER* 5.3 2.9 - - - -
202B ASN* 3.8 30.7 - - + -
210B LYS* 3.4 30.5 - - + +
211B THR* 1.3 78.8 - - - +
213B TYR* 1.3 63.8 + - - +
214B VAL* 5.5 0.4 - - - -
262B ASN 3.9 0.2 - - - +
263B ARG* 3.2 9.2 - - - +
264B ILE* 2.7 41.4 + - + +
266B GLN* 2.9 37.8 + - + +
272B MET* 3.6 19.8 - - + +
274B THR* 3.8 24.0 - - + -
280B HIS* 3.9 21.8 - + + -
281B ALA 3.5 4.5 - - - -
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Residues in contact with TYR 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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122B GLU* 2.7 35.1 + - - +
126B TRP* 3.2 32.3 + + - -
191B TRP* 3.7 25.1 - + + -
211B THR* 3.7 18.5 - - + +
212B TRP* 1.3 75.1 - - - +
214B VAL* 1.3 62.1 + - - +
249B ILE 5.9 0.2 - - - -
251B PRO* 3.8 20.6 - - + -
254B LEU* 5.7 0.4 - - + -
261B PHE* 4.4 16.6 - + + -
262B ASN 3.4 4.9 - - - +
263B ARG* 3.9 20.6 - - + -
280B HIS* 3.1 9.0 - - - +
281B ALA* 2.7 39.2 + - + +
282B GLY* 4.1 5.4 - - - -
283B PHE* 3.5 19.9 - + - -
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Residues in contact with VAL 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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18B ILE* 3.5 28.3 - - + -
46B ALA 3.2 26.2 - - - +
47B GLY* 3.8 18.4 - - - +
48B LEU* 3.9 17.0 - - + -
191B TRP* 4.3 0.8 - - - -
212B TRP 5.3 0.7 - - - +
213B TYR* 1.3 76.7 - - - +
215B VAL* 1.3 70.7 + - - +
216B PRO* 4.0 1.7 - - - +
261B PHE* 3.3 4.7 - - - +
262B ASN* 2.9 42.1 + - + +
278B GLY 4.9 2.5 - - - +
279B TYR 3.4 10.5 - - - +
280B HIS* 4.6 4.7 - - + -
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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
------------------------------------------------------------
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