Contacts of the strand formed by residues 185 - 189 (chain K) in PDB entry 3IT8
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 THR 185 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183K THR 5.2 0.5 + - - -
184K PRO* 1.3 75.2 + - - +
186K VAL* 1.3 64.6 + - - +
187K LYS* 3.3 37.9 - - + +
203K THR 3.4 1.9 - - - +
204K VAL* 3.4 2.6 - - - -
205K ASN* 2.7 45.0 + - - +
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Residues in contact with VAL 186 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184K PRO* 4.3 6.9 + - + +
185K THR* 1.3 83.9 - - - +
187K LYS* 1.3 76.9 + - - +
202K CYS* 4.0 21.3 - - - -
203K THR 3.3 9.0 - - - +
204K VAL* 4.1 19.3 - - + -
283K VAL* 4.2 7.6 - - + -
288K LEU* 6.1 0.2 - - + -
293K TYR* 3.5 66.8 - - + +
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Residues in contact with LYS 187 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185K THR* 3.3 29.9 - - + +
186K VAL* 1.3 83.7 - - - +
188K VAL* 1.3 64.4 + - - +
189K THR* 4.1 4.9 - - - +
201K GLU 3.5 2.3 - - - +
202K CYS* 3.8 0.2 - - - -
203K THR* 3.0 37.6 + - + +
205K ASN* 4.2 15.4 - - - +
293K TYR* 5.8 1.3 - - - -
299K CYS* 6.0 0.7 - - - -
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Residues in contact with VAL 188 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187K LYS* 1.3 75.1 - - - +
189K THR* 1.3 59.4 + - - +
200K LEU* 3.9 18.2 - - + -
201K GLU 3.2 8.1 - - - +
202K CYS* 4.1 5.8 - - - -
216K TRP* 4.1 16.6 - - + -
279K PRO 5.9 1.1 - - - +
280K VAL* 6.3 0.2 - - - -
281K CYS* 3.7 26.5 - - + +
293K TYR* 3.7 21.7 - - + +
294K THR 3.1 20.9 + - - +
295K CYS* 3.2 13.7 - - - +
299K CYS* 2.4 38.5 - - - +
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Residues in contact with THR 189 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187K LYS* 4.9 6.2 + - - +
188K VAL* 1.3 75.6 + - - +
190K GLY* 1.3 63.0 + - - +
191K ASN* 3.2 36.3 + - - +
199K THR 3.5 0.9 - - - +
200K LEU* 3.3 8.2 - - - +
201K GLU* 2.7 48.8 + - - +
203K THR* 5.2 4.5 - - - +
298K GLY* 4.0 18.3 + - - +
299K CYS* 4.6 0.4 - - - +
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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