Contacts of the strand formed by residues 189 - 195 (chain I) in PDB entry 3EXG
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 CYS 189 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146I ALA* 4.2 6.5 - - - -
149I ALA* 3.6 23.1 - - + -
161I CYS 3.6 3.1 - - - -
163I THR* 3.7 19.7 - - - -
182I ALA* 4.9 1.3 - - + -
187I LEU* 2.6 18.4 + - + +
188I PRO* 1.3 72.7 - - - +
190I ILE* 1.3 63.9 + - - +
191I PHE* 3.4 44.4 + - + -
244I CYS* 4.0 2.1 - - - -
250I PRO* 3.3 3.9 - - + +
251I ILE 3.2 22.2 + - - -
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Residues in contact with ILE 190 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160I VAL* 4.5 7.4 - - + -
161I CYS 2.7 14.4 + - - +
162I LEU* 3.6 26.8 - - + -
163I THR* 2.9 28.1 + - - -
188I PRO 5.2 0.4 - - - +
189I CYS* 1.3 70.5 - - - +
191I PHE* 1.3 61.1 + - - +
192I ILE* 3.5 22.4 + - + +
237I THR* 5.2 2.9 - - + +
240I ALA* 4.1 11.4 - - + -
241I ALA* 4.0 31.2 - - + +
244I CYS* 3.7 20.4 - - + -
251I ILE* 3.5 20.2 - - + +
253I MET* 4.5 11.7 - - + -
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Residues in contact with PHE 191 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142I VAL* 3.7 38.8 - - + -
146I ALA* 4.5 4.0 - - + -
163I THR* 3.6 6.7 - - - -
165I TYR* 4.4 6.5 - + + -
178I ALA* 3.8 15.9 - - + -
179I TYR* 3.9 32.3 - + + -
182I ALA* 3.6 32.5 - - + -
189I CYS* 3.4 34.3 - - - -
190I ILE* 1.3 70.9 - - - +
192I ILE* 1.3 60.3 + - - +
193I CYS 4.2 0.2 + - - -
220I ILE* 4.5 1.6 - - + -
250I PRO* 3.9 13.2 - - + -
251I ILE 2.9 11.1 + - - +
252I LEU* 3.0 15.2 - - + +
253I MET 2.8 23.9 + - - -
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Residues in contact with ILE 192 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75I LEU* 3.6 25.6 - - + -
162I LEU* 4.0 26.0 - - + -
163I THR 3.0 7.0 + - - +
164I LEU* 3.2 25.2 - - + -
165I TYR* 3.0 30.3 + - - +
190I ILE* 3.9 12.8 - - + +
191I PHE* 1.3 75.9 - - - +
193I CYS* 1.3 67.4 + - - +
194I GLU 4.2 0.4 - - - +
253I MET* 3.2 30.7 - - + +
255I LEU* 3.6 26.9 - - + -
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Residues in contact with CYS 193 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165I TYR* 3.1 35.0 - - + +
167I ASP* 4.0 24.0 - - - -
191I PHE 4.2 1.2 + - - -
192I ILE* 1.3 73.5 - - - +
194I GLU* 1.3 59.8 + - - +
195I ASN* 2.8 14.6 + - - -
213I TYR* 3.9 38.8 - - + +
252I LEU* 5.8 2.0 - - + +
253I MET 3.0 11.6 + - - +
254I GLU* 3.7 5.9 - - + +
255I LEU 3.1 19.0 + - - -
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Residues in contact with GLU 194 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65I CYS* 6.0 1.4 - - - +
68I GLN* 3.6 25.7 - - - +
71I CYS* 4.4 13.7 - - - +
87I THR* 4.2 9.7 + - - -
90I ARG* 5.5 10.7 - - - +
94I PHE* 3.9 16.7 - - - -
164I LEU* 3.5 32.2 - - + +
165I TYR 2.8 15.6 + - - +
166I GLY* 3.4 6.6 + - - -
167I ASP 3.3 15.8 + - - -
192I ILE 3.8 2.0 + - - -
193I CYS* 1.3 66.4 - - - +
195I ASN* 1.3 59.8 + - - +
196I ASN* 3.3 11.1 + - - +
255I LEU* 3.7 21.5 - - + -
257I THR* 4.5 3.6 - - + -
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Residues in contact with ASN 195 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167I ASP* 3.8 17.7 - - + +
193I CYS* 2.8 13.3 + - - +
194I GLU* 1.3 69.4 - - - +
196I ASN* 1.3 58.4 + - - +
197I ARG* 2.8 29.1 + - - +
204I VAL* 3.9 5.3 - - - +
211I THR* 5.1 1.2 + - - -
213I TYR* 4.0 27.0 - - + -
254I GLU* 3.4 24.8 + - + -
255I LEU 2.9 10.6 + - - +
256I GLN* 3.4 13.9 - - - +
257I THR* 3.1 19.2 + - - +
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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