Contacts of the strand formed by residues 198 - 202 (chain A) in PDB entry 3THW
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 198 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ARG* 4.0 5.7 + - - -
124A SER* 2.9 31.7 + - - -
125A PRO* 3.5 6.2 - - - +
126A GLY* 2.9 17.8 + - - +
146A GLY 3.2 1.9 + - - +
147A VAL* 3.4 20.0 - - + +
148A VAL* 3.1 25.6 + - - +
196A PRO* 3.5 0.8 - - - +
197A LYS* 1.3 81.0 - - - +
199A CYS* 1.3 62.4 + - - +
200A VAL* 5.4 0.2 - - + -
222A ILE* 3.8 4.5 - - - -
223A LEU* 3.6 18.4 - - + -
225A THR* 2.8 29.9 + - - +
276A PHE* 3.3 21.4 - - + -
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Residues in contact with CYS 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A VAL* 3.3 25.4 - - + -
150A VAL* 3.9 9.2 - - - -
191A LEU* 5.6 0.4 - - - -
198A GLU* 1.3 76.4 - - - +
200A VAL* 1.3 66.6 + - - +
201A LEU* 3.7 17.6 + - + -
217A ILE* 3.5 46.2 - - + -
222A ILE* 3.7 3.6 - - + +
223A LEU 3.2 9.9 + - - +
224A ILE* 3.7 3.5 - - + +
225A THR* 2.8 27.5 + - - -
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Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A VAL* 4.9 5.8 - - + -
148A VAL 3.0 14.6 + - - +
149A GLY* 3.8 9.0 - - - -
150A VAL 3.5 12.5 + - - -
198A GLU* 5.4 0.2 - - + -
199A CYS* 1.3 72.7 - - - +
201A LEU* 1.3 68.5 + - - +
225A THR* 3.3 33.7 - - + +
227A ARG* 3.9 12.1 - - + -
232A PHE* 3.8 6.0 - - - -
272A ALA* 4.7 15.0 - - + +
273A VAL* 4.1 16.8 - - + +
276A PHE* 3.9 28.9 - - + -
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Residues in contact with LEU 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A VAL* 3.3 29.8 - - + +
199A CYS* 3.7 23.3 + - + +
200A VAL* 1.3 79.0 - - - +
202A PRO* 1.3 77.4 - - + +
210A MET* 3.8 24.0 - - + -
213A LEU* 5.0 5.8 - - + -
214A ARG* 4.0 33.4 - - + +
217A ILE* 4.3 14.6 - - + -
224A ILE* 4.1 14.1 - - + -
225A THR 3.2 7.0 + - - +
226A GLU* 3.8 2.9 - - - +
227A ARG* 3.1 21.7 + - - +
232A PHE* 3.8 4.3 - - - -
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Residues in contact with PRO 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A VAL 3.8 11.4 - - - +
151A LYS* 4.7 15.0 - - + -
201A LEU* 1.3 89.5 - - + +
203A GLY* 1.3 55.7 + - - +
204A GLY* 2.7 26.6 + - - +
210A MET* 4.3 17.2 - - + +
214A ARG* 4.0 7.8 + - - -
226A GLU* 3.8 5.1 - - - +
227A ARG 4.1 2.7 - - - +
229A LYS* 4.5 12.8 - - + -
232A PHE* 3.4 34.7 - - + -
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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