Contacts of the strand formed by residues 185 - 189 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183F THR 5.2 0.5 + - - -
184F PRO* 1.3 74.9 + - - +
186F VAL* 1.3 63.1 + - - +
187F LYS* 3.3 38.4 - - + +
203F THR 3.4 1.7 - - - +
204F VAL* 3.4 3.1 - - - -
205F ASN* 2.7 43.8 + - - +
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Residues in contact with VAL 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184F PRO* 4.6 7.0 - - + +
185F THR* 1.3 84.1 - - - +
187F LYS* 1.3 77.1 + - - +
202F CYS* 4.0 21.3 - - - -
203F THR 3.3 8.7 - - - +
204F VAL* 4.2 19.3 - - + -
283F VAL* 4.2 7.2 - - + -
288F LEU* 6.2 0.2 - - + -
293F TYR* 3.5 66.5 - - + +
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Residues in contact with LYS 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185F THR* 3.3 29.5 - - + +
186F VAL* 1.3 83.3 - - - +
188F VAL* 1.3 65.6 + - - +
189F THR* 5.0 4.5 - - - +
201F GLU 3.6 1.7 - - - +
202F CYS* 3.8 0.2 - - - -
203F THR* 3.0 38.2 + - + +
205F ASN* 4.2 15.4 - - - +
293F TYR* 5.8 1.1 - - - -
299F CYS* 6.2 0.7 - - - -
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Residues in contact with VAL 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187F LYS* 1.3 77.8 - - - +
189F THR* 1.3 59.5 + - - +
200F LEU* 3.9 18.6 - - + -
201F GLU 3.2 7.9 - - - +
202F CYS* 4.1 5.6 - - - -
216F TRP* 4.1 16.8 - - + -
279F PRO 6.0 0.7 - - - +
280F VAL* 6.3 0.2 - - - -
281F CYS* 3.7 26.9 - - + +
293F TYR* 3.7 19.7 - - + +
294F THR* 3.2 21.9 + - - +
295F CYS 3.2 12.8 - - - +
299F CYS* 2.5 38.4 - - - +
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Residues in contact with THR 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187F LYS* 4.1 6.4 + - - +
188F VAL* 1.3 74.9 + - - +
190F GLY* 1.3 63.7 + - - +
191F ASN* 3.2 36.6 + - - +
199F THR 3.5 1.0 - - - +
200F LEU* 3.3 8.4 - - - +
201F GLU* 2.7 48.9 + - - +
203F THR* 5.2 4.7 - - - +
295F CYS 4.6 0.2 - - - -
298F GLY* 4.0 18.3 + - - +
299F CYS* 5.8 0.3 - - - +
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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