Contacts of the strand formed by residues 191 - 196 (chain A) in PDB entry 3C3P
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 PHE 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A LEU* 3.9 23.8 - - + -
146A ASN* 3.6 12.8 - - - -
149A LEU* 4.1 10.5 - - + -
153A ALA 5.0 1.3 - - - -
155A LEU* 4.9 8.5 - - + -
185A LEU* 4.0 19.3 - - + +
186A SER 5.7 0.2 - - - +
188A ARG* 2.9 21.5 + - + +
189A ARG 3.2 0.2 - - - -
190A ASP* 1.3 108.4 - - - +
192A PHE* 1.3 59.7 + - - +
193A THR* 4.0 15.0 + - - +
205A GLY* 3.8 17.3 - - - -
206A TYR 3.3 18.8 - - - -
207A ARG* 3.6 36.3 - - + -
208A LEU* 4.1 2.9 - - - -
218A EDO 3.0 20.6 + - - -
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Residues in contact with PHE 192 (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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191A PHE* 1.3 73.4 - - - +
193A THR* 1.3 70.7 + - - +
194A THR* 5.0 2.0 - - - -
204A LEU 3.8 1.0 - - - +
205A GLY* 3.5 0.7 - - - -
206A TYR* 2.9 41.3 + - + +
208A LEU* 4.1 19.0 - - + +
218A EDO 3.7 15.7 - - - -
45B ARG* 3.4 71.6 - - + -
48B TYR* 3.7 27.1 - + + -
49B LEU* 4.2 17.5 - - + +
216B PEG 3.7 30.1 - - - -
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Residues in contact with THR 193 (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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185A LEU* 3.3 40.8 + - + +
186A SER* 4.6 11.9 - - - +
191A PHE* 4.0 5.1 + - - +
192A PHE* 1.3 82.8 + - - +
194A THR* 1.3 68.6 + - - +
195A ILE* 5.2 0.4 - - + -
203A LEU* 2.9 37.9 - - + -
204A LEU 3.1 9.7 + - - +
205A GLY* 4.0 2.1 - - - -
218A EDO 4.7 1.6 - - - -
45B ARG* 2.9 32.3 + - - +
49B LEU* 6.2 0.2 - - - -
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Residues in contact with THR 194 (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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192A PHE* 5.0 2.0 - - - -
193A THR* 1.3 79.8 - - - +
195A ILE* 1.3 68.4 + - - +
196A VAL* 4.4 12.1 - - + +
202A VAL 3.9 0.2 - - - +
203A LEU* 3.7 1.0 - - - -
204A LEU* 2.8 39.5 + - + +
42B GLN* 3.9 21.7 + - - -
45B ARG* 4.5 16.7 + - - +
46B LEU* 4.6 11.3 - - + +
49B LEU* 3.6 30.3 - - + +
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Residues in contact with ILE 195 (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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160A ALA* 4.7 2.7 - - + -
161A LEU* 4.0 31.2 - - + -
182A ASN* 3.6 28.7 - - + +
193A THR* 5.2 0.4 - - + -
194A THR* 1.3 79.9 + - - +
196A VAL* 1.3 69.4 + - - +
197A PRO* 3.7 6.8 - - - +
202A VAL 3.3 14.8 - - - +
203A LEU* 3.5 25.1 - - + +
13B LEU* 3.7 24.7 - - + +
16B LEU* 3.6 31.4 - - + -
42B GLN* 5.3 3.7 + - - +
198B VAL* 5.8 1.9 - - - +
215B PEG 5.1 1.9 + - - -
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Residues in contact with VAL 196 (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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46A LEU* 3.6 31.9 - - + -
194A THR* 4.1 6.5 - - + +
195A ILE* 1.3 77.6 - - - +
197A PRO* 1.3 65.0 - - + +
198A VAL* 2.8 14.9 + - + +
201A GLY* 3.6 0.5 - - - -
202A VAL* 2.9 42.8 + - + +
204A LEU* 4.3 14.4 - - + -
46B LEU* 4.2 31.4 - - + -
196B VAL* 5.0 14.4 - - + -
197B PRO* 5.8 0.2 - - + -
198B VAL* 5.1 7.9 - - + -
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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