Contacts of the strand formed by residues 210 - 214 (chain B) in PDB entry 4UC5
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 HIS 210 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A LYS* 6.2 1.8 - - - -
107A LYS* 6.1 1.2 - - - +
111A ASN* 5.5 9.6 + - - +
119A PHE* 3.4 62.3 - + + +
176B GLU* 3.3 19.9 - - - +
208B SER* 5.1 1.1 + - - -
209B HIS* 1.3 77.3 + - - +
211B PHE* 1.3 65.1 + - - +
222B ILE* 4.0 27.8 - - + -
223B VAL 3.1 6.1 - - - +
224B HIS* 3.3 52.1 + + + +
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Residues in contact with PHE 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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12A ILE* 5.5 1.8 - - + -
111A ASN* 6.2 0.2 - - - -
149B MET* 3.8 22.7 - - + -
173B VAL* 4.3 9.9 - - + -
176B GLU* 3.6 45.1 - - + +
177B LEU* 3.8 24.7 - - + -
180B GLY* 5.1 1.6 - - - -
210B HIS* 1.3 77.8 - - - +
212B LEU* 1.3 76.6 + - - +
213B SER* 3.9 20.4 - - - -
222B ILE* 3.7 3.2 - - - +
223B VAL* 2.9 49.3 + - + +
225B THR* 3.7 20.9 - - + -
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Residues in contact with LEU 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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18A LEU* 3.8 20.6 - - + -
111A ASN* 5.5 2.2 - - - +
121A ILE* 4.3 13.7 - - + -
125A LEU* 5.5 3.4 - - + -
148A ASP* 3.5 17.7 + - - +
150A ILE* 3.6 35.9 - - + +
151A THR* 3.5 31.9 - - + -
154A TYR* 5.6 1.1 - - + -
149B MET* 3.8 12.5 - - - +
173B VAL* 5.6 1.2 - - - +
211B PHE* 1.3 82.0 - - - +
213B SER* 1.3 62.6 + - - +
221B ALA 3.3 12.6 - - - +
222B ILE* 3.8 25.4 - - + -
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Residues in contact with SER 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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150A ILE* 3.6 10.1 - - - +
149B MET 2.7 25.7 + - - -
150B ILE* 4.1 7.8 - - - -
153B GLN* 4.1 9.2 - - - +
211B PHE* 3.9 6.0 + - - -
212B LEU* 1.3 75.8 - - - +
214B VAL* 1.3 68.7 + - - +
220B SER* 3.5 2.8 - - - -
221B ALA* 2.6 40.9 + - - +
223B VAL* 3.7 22.4 - - - -
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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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15A VAL* 4.8 2.4 - - - +
214A VAL* 3.8 28.7 - - + -
220A SER* 4.0 19.1 - - - -
21B PRO* 4.5 11.7 - - + -
150B ILE* 4.0 30.9 - - + +
153B GLN* 2.9 26.6 + - + +
154B TYR* 5.3 0.2 - - + -
213B SER* 1.3 86.0 + - - +
215B THR* 1.3 70.2 + - - +
218B GLY* 3.8 11.9 - - - +
219B HIS 3.1 13.0 - - - +
221B ALA* 4.3 2.2 - - - -
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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