Contacts of the strand formed by residues 194 - 199 (chain B) in PDB entry 1CT8
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 194 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B TRP* 3.4 6.1 - - - -
155B ASN* 2.8 43.0 + - - -
192B THR* 3.3 11.3 - - - +
193B VAL* 1.3 72.9 - - - +
195B CYS* 1.3 67.1 + - - +
196B ASN* 3.9 9.8 + - - +
207B ASP* 3.9 17.0 - - + +
208B LYS 3.3 29.6 - - - +
209B LYS* 3.2 29.9 + - - +
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Residues in contact with CYS 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B VAL* 4.3 0.9 - - - -
140B CYS* 2.0 50.3 - - + -
152B VAL* 4.5 3.6 - - + -
153B THR 3.4 6.7 - - - +
154B TRP* 3.5 26.5 - - + -
194B THR* 1.3 74.3 - - - +
196B ASN* 1.3 59.8 + - - +
197B VAL* 4.1 17.3 - - - -
206B VAL 3.7 1.4 - - - +
207B ASP* 3.5 2.9 - - - -
208B LYS* 2.8 40.4 + - - -
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Residues in contact with ASN 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B THR* 3.4 1.0 - - - +
152B VAL* 3.2 7.6 - - - -
153B THR* 2.7 54.7 + - - +
155B ASN* 3.6 1.1 + - - +
156B SER* 2.7 33.8 + - - +
194B THR* 3.9 13.1 + - - +
195B CYS* 1.3 76.6 - - - +
197B VAL* 1.3 62.6 + - - +
198B ALA 4.2 0.4 - - - -
206B VAL 3.4 4.7 - - - -
207B ASP* 3.1 29.8 + - - +
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Residues in contact with VAL 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B PRO* 4.7 5.4 - - + -
121B VAL* 4.0 31.6 - - + -
142B VAL* 3.8 44.2 - - + -
150B VAL* 4.2 12.3 - - + -
151B THR 3.3 7.6 - - - +
152B VAL* 4.4 7.2 - - + -
195B CYS* 4.1 13.0 - - - -
196B ASN* 1.3 79.5 - - - +
198B ALA* 1.3 64.3 + - - +
199B HIS 4.3 0.2 + - - -
204B THR* 3.8 1.4 - - - +
205B LYS* 3.4 3.1 - - - -
206B VAL* 2.9 40.4 + - + +
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Residues in contact with ALA 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B VAL* 3.1 9.3 - - - +
151B THR* 3.0 44.1 + - + +
196B ASN 4.2 0.4 - - - -
197B VAL* 1.3 74.8 - - - +
199B HIS* 1.3 59.9 + - - +
200B PRO* 3.6 9.1 - - + +
204B THR 3.3 7.4 - - - +
205B LYS* 4.4 16.2 - - + +
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Residues in contact with HIS 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B THR 3.6 12.3 + - - -
119B PRO* 3.8 23.4 - - + +
145B TYR* 3.8 5.4 - + - -
146B PHE 3.2 24.5 + - - -
147B PRO* 2.7 24.8 + - - +
149B PRO 3.4 19.7 - - - -
150B VAL* 3.5 14.6 - - + -
197B VAL 4.3 0.4 + - - -
198B ALA* 1.3 74.6 - - - +
200B PRO* 1.3 68.7 - - + +
201B ALA* 4.2 11.1 - - + +
202B SER* 2.5 43.5 + - - +
203B SER 3.1 8.5 + - - -
204B THR* 2.8 18.8 + - - -
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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