Contacts of the strand formed by residues 193 - 198 (chain G) in PDB entry 3EO1
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 TYR 193 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133G VAL* 5.8 6.7 - - + -
149G TRP* 5.7 4.5 - + + -
150G LYS 3.4 9.6 - - - -
151G VAL* 3.8 23.7 - - + +
152G ASP 4.6 0.2 - - - -
180G LEU* 4.8 18.8 - - + -
182G LEU* 5.9 2.9 - - - +
186G ASP* 3.0 27.4 + - - +
187G TYR* 3.4 45.3 + + - -
190G HIS* 4.5 10.3 - - + +
191G LYS 3.6 10.3 + - - -
192G VAL* 1.3 92.4 - - - +
194G ALA* 1.3 60.2 + - - +
209G SER* 3.1 17.3 - - - -
210G PHE* 3.1 47.2 + + + +
212G ARG* 5.2 6.1 - - + -
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Residues in contact with ALA 194 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G ILE* 4.7 2.2 - - - -
149G TRP* 3.3 16.1 - - - +
150G LYS* 3.2 46.5 + - + -
153G ASN* 5.8 0.2 - - - +
192G VAL* 5.6 3.6 - - + -
193G TYR* 1.3 74.1 - - - +
195G CYS* 1.3 61.0 + - - +
196G GLU 3.7 0.9 - - - -
207G THR* 3.4 23.6 - - + -
208G LYS 4.1 0.2 - - - -
209G SER* 3.5 19.1 - - - +
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Residues in contact with CYS 195 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G VAL* 5.5 1.2 - - - +
118G ILE* 3.4 20.4 - - + -
135G CYS* 2.0 51.4 - - + -
137G LEU* 6.1 0.4 - - - -
147G VAL* 4.1 21.3 - - - -
148G GLN 4.7 1.8 - - - -
149G TRP* 4.4 10.1 - - + +
194G ALA* 1.3 73.0 - - - +
196G GLU* 1.3 67.7 - - - +
197G VAL* 3.4 13.5 + - - +
207G THR* 3.8 9.1 - - - +
208G LYS* 3.5 10.9 + - + +
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Residues in contact with GLU 196 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146G LYS 4.6 0.3 - - - +
147G VAL* 3.5 5.2 - - - +
148G GLN* 3.3 47.6 + - + +
150G LYS* 3.8 27.6 - - - +
194G ALA 3.7 1.8 - - - -
195G CYS* 1.3 76.0 - - - +
197G VAL* 1.3 69.3 + - - +
198G THR* 3.8 21.3 + - - +
205G PRO* 3.8 21.7 - - + +
206G VAL 4.6 0.2 - - - +
207G THR* 3.2 27.1 - - - +
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Residues in contact with VAL 197 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114G PRO* 5.3 3.6 - - + -
116G VAL* 3.8 17.7 - - + -
137G LEU* 3.7 24.0 - - + -
145G ALA* 4.4 13.2 - - + -
146G LYS 3.7 7.0 - - - +
147G VAL* 3.9 18.8 - - + -
195G CYS* 3.8 9.4 - - - +
196G GLU* 1.3 80.5 + - - +
198G THR* 1.3 60.9 - - - +
199G HIS* 3.5 8.3 + - + +
204G SER 5.2 0.2 - - - +
205G PRO* 4.0 1.6 - - - +
206G VAL* 3.2 46.1 + - + +
207G THR* 5.3 0.2 - - - -
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Residues in contact with THR 198 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144G GLU 4.6 0.3 - - - +
145G ALA* 3.9 1.0 - - - -
146G LYS* 3.2 65.2 + - + +
196G GLU* 3.8 18.8 + - - +
197G VAL* 1.3 70.9 - - - +
199G HIS* 1.3 63.0 + - - +
205G PRO* 4.1 15.4 - - - +
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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