Contacts of the strand formed by residues 187 - 193 (chain B) in PDB entry 4H3K
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 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292A SER* 3.6 9.3 + - - -
137B VAL* 3.8 19.3 - - + -
138B ASN 3.2 15.5 - - - +
139B VAL* 3.4 24.7 - - + -
154B LEU* 3.8 30.5 - - + -
155B ILE* 6.3 0.9 - - + -
158B LEU* 4.4 13.5 - - + -
176B LEU* 4.3 26.0 - - + +
179B PHE* 4.0 20.9 - + + -
180B GLU* 3.0 33.3 + - + +
183B SER* 3.7 13.0 - - - -
185B ARG* 3.3 24.7 - - + -
186B THR* 1.3 71.8 + - - +
188B LEU* 1.3 65.8 + - - +
189B HIS* 3.6 6.6 + - - +
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Residues in contact with LEU 188 (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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292A SER* 3.6 13.7 - - - +
295A SER* 3.7 20.4 - - - -
296A SER* 3.5 17.9 - - - +
299A LYS* 4.2 4.9 - - + -
113B GLU* 3.8 37.7 - - + +
116B TYR* 3.7 31.6 - - + -
137B VAL* 3.2 7.3 - - - +
138B ASN* 3.0 41.9 + - + +
186B THR* 4.0 13.1 - - - +
187B PHE* 1.3 73.9 - - - +
189B HIS* 1.3 59.1 + - - +
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Residues in contact with HIS 189 (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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250A SER* 4.3 5.6 + - - +
251A ILE* 3.4 24.2 - - + +
254A THR* 5.2 1.2 - - - +
293A GLN* 6.1 3.1 - - + -
296A SER* 3.0 26.6 + - - +
116B TYR* 3.6 1.3 + - - -
135B HIS* 2.8 45.4 - + + -
136B VAL 3.4 8.3 + - - -
137B VAL* 3.6 5.5 - - - +
172B ILE* 3.6 14.6 - - + +
173B ASP* 2.7 37.1 + - - +
176B LEU* 3.6 22.2 - - + -
187B PHE 3.6 3.3 + - - +
188B LEU* 1.3 76.7 - - - +
190B THR* 1.3 75.3 + - - +
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Residues in contact with THR 190 (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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251A ILE* 3.7 10.5 - - - -
254A THR* 3.5 7.4 + - - -
296A SER* 5.2 0.4 - - - -
300A ASN* 2.9 31.3 + - - +
116B TYR* 3.1 28.5 - - + +
120B VAL* 3.7 22.6 - - + +
135B HIS* 3.5 3.1 - - - -
136B VAL* 2.9 39.8 + - + +
189B HIS* 1.3 80.3 + - - +
191B VAL* 1.3 73.8 + - - +
192B CYS* 4.9 1.3 - - - -
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Residues in contact with VAL 191 (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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181A THR* 5.0 0.9 - - + -
251A ILE* 3.7 19.0 - - + +
254A THR* 3.9 12.2 + - - +
255A THR* 3.4 25.8 - - - +
133B PRO* 4.4 5.8 - - + -
134B VAL 3.2 7.2 - - - +
135B HIS* 3.4 46.9 - - + +
136B VAL 4.7 0.2 - - - +
169B GLU* 5.0 0.2 - - - +
190B THR* 1.3 85.0 + - - +
192B CYS* 1.3 69.8 + - - +
193B PHE* 3.8 17.8 - - + -
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Residues in contact with CYS 192 (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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120B VAL* 4.3 34.5 - - - -
123B LEU* 3.7 46.4 - - + -
124B ASN* 4.8 5.4 - - - +
133B PRO* 3.3 4.7 - - - +
134B VAL* 2.7 39.2 + - + +
136B VAL* 4.3 5.8 - - + -
190B THR* 4.9 1.3 - - - -
191B VAL* 1.3 77.6 - - - +
193B PHE* 1.3 67.1 + - - +
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Residues in contact with PHE 193 (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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181A THR* 4.0 7.2 - - + -
185A LYS* 3.7 33.9 - - + -
254A THR 5.8 0.2 - - - -
255A THR* 3.5 39.3 - - + -
258A GLY* 6.5 1.3 - - - -
123B LEU* 4.6 12.3 + - - +
126B ARG* 5.1 3.8 - - - +
127B GLU 5.2 0.7 - - - +
128B GLN* 3.9 24.6 - - + +
131B CYS* 3.4 21.8 - - - -
132B GLN 3.5 1.1 - - - +
133B PRO* 3.7 23.6 - - + -
191B VAL* 3.8 26.2 - - + -
192B CYS* 1.3 80.5 - - - +
194B TYR* 1.3 70.3 + - - +
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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