Contacts of the helix formed by residues 84 - 88 (chain 2) 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 ASN 84 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822 THR* 2.9 25.5 + - - +
832 PHE* 1.3 77.2 - - - +
852 PHE* 1.3 68.7 + - + +
872 MET* 3.2 29.2 + - + +
882 GLN* 4.9 0.3 + - - +
1182 ASN* 6.3 0.6 - - - +
1192 GLY 5.3 1.8 + - - +
1272 GLN 3.3 22.6 - - - +
1282 HIS* 3.0 27.8 + - - +
1292 SER* 3.2 2.1 + - - +
1302 GLN* 3.1 38.1 + - - +
1322 PHE* 3.7 10.0 - - - -
137Y ILE* 4.8 3.2 - - + +
91Z ASP* 5.9 0.2 - - - +
95Z ASN* 4.6 3.0 + - - -
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Residues in contact with PHE 85 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282 GLU* 5.2 1.3 - - - -
592 GLU* 3.6 41.1 - - + +
802 PHE* 4.5 0.9 - - + -
812 MET* 3.5 35.2 - - + +
822 THR* 2.7 44.5 + - + +
842 ASN* 1.3 72.6 - - + +
862 SER* 1.3 55.0 + - - +
872 MET 2.9 11.2 + - - -
882 GLN* 3.3 16.1 + - - +
1282 HIS* 3.6 36.8 - + - -
136Y GLY 4.6 3.1 - - - -
137Y ILE* 3.7 28.7 - - + -
138Y VAL* 5.7 3.6 - - + -
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Residues in contact with SER 86 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802 PHE* 3.6 45.6 - - - -
822 THR 3.6 2.8 + - - -
832 PHE* 2.9 25.0 + - - -
852 PHE* 1.3 76.8 - - - +
872 MET* 1.3 58.6 + - - +
882 GLN 3.3 0.4 - - - -
892 ALA 3.6 2.9 - - - +
902 ILE* 3.1 27.1 + - - +
932 VAL* 5.8 0.4 - - - -
1322 PHE* 5.6 0.5 - - - -
1362 TYR* 2.8 22.4 + - - -
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Residues in contact with MET 87 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832 PHE 4.7 0.2 - - - +
842 ASN* 3.2 14.7 + - + +
852 PHE 2.9 2.8 + - - -
862 SER* 1.3 74.7 - - - +
882 GLN* 1.3 64.6 + - - +
892 ALA 2.9 5.3 + - - -
902 ILE* 3.3 22.7 + - + +
1302 GLN* 3.4 22.2 - - - +
1322 PHE* 3.7 30.7 - - + -
1352 TRP* 4.0 11.7 - - + -
87Z MET 3.9 8.8 - - - +
88Z GLN 5.1 0.5 - - - +
90Z ILE* 3.7 30.7 - - + +
91Z ASP* 4.1 14.1 + - + -
94Z ILE* 4.0 15.9 - - + -
95Z ASN* 3.1 33.9 - - - +
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Residues in contact with GLN 88 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1771 GLU* 4.6 2.8 + - - -
592 GLU* 3.0 24.1 + - + +
602 MET* 3.4 38.2 - - + +
842 ASN 5.9 0.2 - - - +
852 PHE* 3.8 12.6 - - - +
872 MET* 1.3 78.6 - - + +
892 ALA* 1.3 55.3 + - - +
912 ASP 5.1 0.4 + - - -
137Y ILE* 4.0 12.0 - - + +
138Y VAL 3.4 9.7 - - - +
172Y GLN* 2.9 44.4 + - - +
174Y GLN* 3.5 11.0 + - - +
60Z MET* 3.7 25.4 - - + +
87Z MET 5.3 1.0 - - - +
88Z GLN 4.8 1.4 - - - +
91Z ASP* 4.3 11.2 - - + +
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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