Contacts of the helix formed by residues 82 - 88 (chain Z) 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 THR 82 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37Z TYR* 3.2 20.9 - - - +
80Z PHE* 3.8 11.5 - - - +
81Z MET* 1.3 91.7 - - + +
83Z PHE* 1.3 53.9 + - - +
84Z ASN* 3.0 32.4 + - - +
85Z PHE* 2.7 44.6 + - + +
117Z PRO* 3.6 16.8 - - + -
128Z HIS* 5.0 9.3 - - + +
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Residues in contact with PHE 83 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80Z PHE* 3.9 21.8 - + + -
82Z THR* 1.3 69.6 - - - +
84Z ASN* 1.3 68.5 + - - +
85Z PHE 3.0 0.4 - - - -
86Z SER* 2.7 42.6 + - - -
87Z MET 3.8 1.0 + - - -
114Z PHE* 4.1 15.0 - - + -
115Z ARG 3.9 2.2 - - - -
116Z GLY* 3.5 33.9 - - - -
117Z PRO 3.2 10.4 + - - +
118Z ASN* 3.6 21.7 - - + +
132Z PHE* 3.4 12.0 - - + -
136Z TYR* 3.7 19.7 - + - -
168Z VAL* 3.4 30.7 - - + -
169Z VAL 3.7 7.2 - - - -
170Z LEU* 3.6 19.7 - - + -
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Residues in contact with ASN 84 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1371 ILE* 4.6 2.5 - - + +
912 ASP* 5.4 0.2 - - - +
952 ASN* 4.4 4.5 + - - +
992 LYS* 5.1 1.0 + - - -
82Z THR* 3.0 21.0 + - - +
83Z PHE* 1.3 78.9 - - - +
85Z PHE* 1.3 69.1 + - + +
86Z SER 3.3 0.3 + - - -
87Z MET* 3.7 26.4 + - - +
119Z GLY 4.7 3.8 + - - +
127Z GLN* 3.3 27.3 - - - +
128Z HIS* 2.7 33.2 + - - +
129Z SER* 3.3 1.7 + - - +
130Z GLN* 3.0 35.9 + - - +
132Z PHE* 3.7 9.8 - - - -
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Residues in contact with PHE 85 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1361 GLY 4.4 4.9 - - - -
1371 ILE* 3.8 29.4 - - + -
1381 VAL* 5.8 3.1 - - + -
28Z GLU* 4.6 3.1 - - - -
59Z GLU* 3.3 44.7 - - + +
80Z PHE* 5.0 2.9 - - + -
81Z MET* 3.3 44.2 - - + -
82Z THR* 2.7 26.3 + - + +
84Z ASN* 1.3 79.0 - - + +
86Z SER* 1.3 64.3 + - - +
87Z MET 3.2 0.4 - - - -
88Z GLN* 3.3 19.8 + - - +
128Z HIS* 3.9 30.1 - + - -
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Residues in contact with SER 86 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80Z PHE* 3.4 41.3 - - - -
82Z THR 3.8 1.6 + - - -
83Z PHE* 2.7 26.4 + - - +
85Z PHE* 1.3 79.7 - - - +
87Z MET* 1.3 53.5 + - - +
89Z ALA* 2.6 28.8 + - - +
90Z ILE* 3.0 10.2 + - - +
93Z VAL* 5.6 0.2 - - - +
132Z PHE* 4.9 2.6 - - - -
136Z TYR* 2.5 30.9 + - - -
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Residues in contact with MET 87 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872 MET 3.9 6.6 - - - +
882 GLN 5.3 0.5 - - - +
902 ILE* 3.8 25.2 - - + +
912 ASP* 4.1 22.0 + - + +
942 ILE* 4.1 23.3 - - + -
952 ASN* 2.8 45.3 - - - +
992 LYS* 5.2 0.2 - - - +
84Z ASN* 3.7 15.4 + - + +
86Z SER* 1.3 80.9 + - - +
88Z GLN* 1.3 61.7 + - + +
89Z ALA 3.3 0.3 + - - -
90Z ILE* 3.5 16.6 + - + +
130Z GLN* 4.5 2.5 - - - +
132Z PHE* 3.7 34.1 - - + -
135Z TRP* 4.3 12.1 - - + -
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Residues in contact with GLN 88 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1371 ILE* 3.4 22.0 - - + +
1381 VAL 3.6 2.0 + - - +
1721 GLN* 3.0 28.5 + - - +
1741 GLN* 3.2 15.1 + - - -
602 MET* 3.5 27.5 - - + +
882 GLN* 4.8 2.1 - - - +
912 ASP* 4.0 14.9 - - + +
59Z GLU* 3.2 37.3 + - + +
60Z MET* 3.3 34.1 - - + +
85Z PHE* 3.3 12.7 + - - +
86Z SER 2.9 1.4 + - - -
87Z MET* 1.3 76.4 - - + +
89Z ALA* 1.3 56.8 + - - +
90Z ILE 3.6 0.4 + - - -
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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