Contacts of the strand formed by residues 193 - 197 (chain D) in PDB entry 1OIK
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 GLU 193 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D VAL* 4.0 19.7 - - + +
162D HIS 3.2 5.6 - - - +
163D SER* 3.8 18.9 + - - +
165D ARG* 5.7 1.0 - - - +
192D TYR* 1.3 78.7 - - - +
194D THR* 1.3 56.9 + - - +
217D LYS* 5.4 3.1 - - - +
218D ARG* 5.7 1.7 + - - -
297D THR* 3.6 3.1 - - - +
298D THR* 2.8 40.3 + - - +
299D ARG* 3.2 28.8 + - + +
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Residues in contact with THR 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D THR 4.3 0.2 - - - -
113D PHE 2.7 31.0 + - - -
114D VAL* 3.5 2.1 - - - -
115D GLU* 3.9 13.0 - - + -
160D ALA 3.6 0.5 - - - +
161D VAL* 3.5 2.7 - - - -
162D HIS* 2.7 41.8 + - - +
193D GLU* 1.3 72.5 - - - +
195D GLU* 1.3 70.0 + - - +
196D HIS* 3.5 30.3 + - + +
296D ARG 3.8 17.5 - - - +
297D THR* 3.1 17.8 + - - +
298D THR 4.4 0.2 - - - +
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Residues in contact with GLU 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D TRP* 3.5 17.5 - - + -
160D ALA 3.4 6.1 - - - +
161D VAL* 4.2 21.4 - - + +
194D THR* 1.3 73.0 - - - +
196D HIS* 1.3 60.7 + - - +
218D ARG* 5.9 0.7 + - - -
220D LYS* 5.4 8.8 - - + +
295D SER* 3.2 8.5 - - - -
296D ARG* 3.0 53.4 + - + +
298D THR* 3.8 26.9 + - + +
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Residues in contact with HIS 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D THR* 2.8 31.1 + - - -
114D VAL 3.0 11.2 + - - -
115D GLU 3.4 25.4 - - - -
117D TYR* 3.7 17.4 - + - -
159D TRP* 3.4 7.8 - - - -
160D ALA* 2.8 30.6 + - - +
162D HIS* 3.6 31.0 - + - +
194D THR* 3.5 14.0 - - + +
195D GLU* 1.3 72.3 - - - +
197D PRO* 1.3 73.0 - - + +
211D GLN* 4.0 6.9 + - - +
287D PRO* 3.7 6.4 - - + +
295D SER* 2.7 26.5 + - - -
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Residues in contact with PRO 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D ASP 6.0 1.6 - - - +
158D LEU 3.6 9.0 - - - +
159D TRP* 3.6 32.5 - - + +
196D HIS* 1.3 87.5 - - - +
198D VAL* 1.3 64.1 + - - +
199D VAL 3.6 18.4 - - - +
211D GLN* 2.8 39.8 + - - +
287D PRO* 4.6 1.8 - - + +
288D VAL 4.4 3.8 - - - -
289D GLY* 3.9 22.7 - - - +
295D SER* 3.5 17.7 - - - +
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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