Contacts of the strand formed by residues 287 - 293 (chain C) in PDB entry 1K4R
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 287 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24C VAL* 4.5 17.3 - - + -
25C LEU 3.1 14.6 - - - +
26C GLU* 4.2 10.1 - - + +
45C LEU* 3.9 5.6 - - - -
48C ILE* 4.1 2.2 - - - +
139C TYR* 3.7 4.7 - - - -
190C SER 3.6 20.3 + - - -
191C GLY* 3.2 20.6 + - - -
192C VAL* 3.8 21.7 + - + +
286C GLY* 1.3 76.5 - - - +
288C VAL* 1.3 66.2 + - - +
289C THR* 5.4 2.7 - - + -
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Residues in contact with VAL 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C VAL* 3.6 1.8 - - - -
25C LEU* 2.9 35.3 + - + +
45C LEU* 4.1 17.0 - - + -
139C TYR* 3.7 31.2 - - + -
141C VAL* 4.9 3.1 - - + -
186C CYS* 4.4 7.0 - - + -
187C ARG 3.3 34.8 - - - +
188C VAL* 4.3 2.7 - - + +
190C SER* 3.7 4.5 - - - +
191C GLY* 4.6 1.1 - - - +
287C HIS* 1.3 79.8 - - - +
289C THR* 1.3 66.8 + - - +
290C CYS* 4.0 17.3 - - - -
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Residues in contact with THR 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C THR* 5.0 10.3 - - - +
23C LEU 3.1 7.9 - - - -
24C VAL* 3.4 30.3 - - + -
185C LEU 4.0 0.3 - - - +
186C CYS* 3.5 1.9 - - - -
187C ARG* 3.3 29.6 + - - +
190C SER* 3.1 29.2 + - - +
287C HIS* 5.4 2.5 - - + -
288C VAL* 1.3 75.6 - - - +
290C CYS* 1.3 61.1 + - - +
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Residues in contact with CYS 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C VAL 3.8 0.5 - - - +
22C THR* 3.3 5.5 - - - +
23C LEU* 2.9 33.9 + - + +
25C LEU* 3.8 29.8 - - + -
141C VAL* 4.4 0.7 - - - -
184C LEU* 4.5 9.0 - - + -
185C LEU 3.1 5.6 - - - +
186C CYS* 2.0 48.2 - - - -
288C VAL* 4.0 9.4 - - - -
289C THR* 1.3 76.5 - - - +
291C GLU* 1.3 65.3 + - - +
292C VAL* 4.1 4.3 - - + -
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Residues in contact with GLU 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ARG* 2.9 48.6 + - + +
21C VAL 3.3 5.6 - - - +
22C THR* 3.9 20.8 + - + +
183C SER* 3.5 1.9 + - - +
184C LEU* 3.5 5.0 - - - +
185C LEU* 2.8 42.7 + - + +
187C ARG* 3.2 34.4 + - - +
290C CYS* 1.3 75.2 - - - +
292C VAL* 1.3 61.0 + - - +
293C GLY 4.1 0.2 - - - -
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Residues in contact with VAL 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ARG* 3.4 7.1 - - - +
21C VAL* 2.7 42.4 + - + +
23C LEU* 3.8 29.8 - - + -
33C ILE* 4.2 14.6 - - + -
41C MET* 6.4 0.9 - - + -
43C VAL* 5.2 6.1 - - + -
182C VAL* 3.6 25.6 - - + -
183C SER 3.4 3.8 - - - +
184C LEU* 3.8 19.1 - - + -
290C CYS* 4.9 2.2 - - + +
291C GLU* 1.3 76.8 - - - +
293C GLY* 1.3 62.6 + - - +
294C LEU* 3.7 18.0 + - + +
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Residues in contact with GLY 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C THR 3.9 1.6 - - - -
20C ARG* 4.7 8.7 - - - +
181C ASP 4.5 0.9 - - - +
182C VAL* 3.4 13.0 - - - +
183C SER* 2.9 45.0 + - - -
291C GLU 4.1 0.6 + - - -
292C VAL* 1.3 71.6 - - - +
294C LEU* 1.3 62.5 + - - -
295C GLU* 3.5 18.4 - - - +
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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