Contacts of the helix formed by residues 82 - 92 (chain Z) in PDB entry 2W4V
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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80Z GLN* 4.3 9.4 - - - +
81Z GLY* 1.3 73.4 - - - -
83Z PHE* 1.3 57.4 + - - +
84Z ALA* 3.4 11.4 + - - +
85Z ASP* 2.5 36.3 + - - +
86Z TYR* 2.3 38.8 + - - -
149Z MET* 4.6 3.1 - - - -
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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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82Z THR* 1.3 72.9 - - - +
84Z ALA* 1.3 63.1 + - - +
86Z TYR* 3.3 5.9 + - + -
87Z MET* 2.4 96.3 + - + +
142Z GLU* 4.2 4.7 - - + -
145Z VAL* 3.5 24.2 - - + -
146Z LYS* 4.6 11.4 - - + -
149Z MET* 4.6 22.3 - - + +
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Residues in contact with ALA 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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725C PRO* 6.0 6.3 - - + -
82Z THR* 3.5 10.3 - - - +
83Z PHE* 1.3 80.2 - - - +
85Z ASP* 1.3 53.9 + - - +
87Z MET* 3.0 8.3 + - - +
88Z GLU* 2.7 44.3 + - + +
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Residues in contact with ASP 85 (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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725C PRO* 4.8 16.0 - - - +
781C ILE* 3.9 25.8 - - + +
80Z GLN 5.2 0.5 - - - +
81Z GLY* 4.6 5.4 - - - -
82Z THR* 2.5 41.2 + - - +
84Z ALA* 1.3 80.9 - - - +
86Z TYR* 1.3 65.9 + - + +
88Z GLU* 3.3 8.3 + - - +
89Z ALA* 3.2 25.6 + - - +
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Residues in contact with TYR 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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781C ILE* 4.0 11.4 - - + -
784C MET* 2.7 33.7 + - + +
785C PHE* 2.6 65.3 - + + -
788C HIS* 4.0 8.6 - - + +
80Z GLN* 4.5 3.3 + - - -
81Z GLY* 2.6 38.4 + - - -
82Z THR 2.3 26.6 + - - -
83Z PHE* 3.3 7.6 + - + +
85Z ASP* 1.3 77.7 - - + +
87Z MET* 1.3 62.0 + - - +
89Z ALA* 4.3 1.4 - - - +
90Z PHE* 3.4 23.7 + - - +
141Z TYR* 3.5 11.4 + - - +
145Z VAL* 4.6 10.8 - - + -
149Z MET* 4.2 12.6 - - - -
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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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83Z PHE* 2.4 86.5 + - + +
84Z ALA* 3.3 5.8 - - - +
86Z TYR* 1.3 76.5 - - - +
88Z GLU* 1.3 70.9 + - + +
90Z PHE* 3.4 5.0 + - - +
91Z LYS* 3.1 20.7 + - - +
141Z TYR* 5.0 0.2 - - - -
142Z GLU* 2.3 50.2 - - - +
145Z VAL* 3.9 9.0 - - - -
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Residues in contact with GLU 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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721C SER* 4.5 11.6 - - - -
722C ILE* 3.6 35.1 + - + +
725C PRO* 5.9 4.4 - - + +
778C LEU* 5.1 0.9 - - + -
84Z ALA* 2.7 37.1 + - + +
85Z ASP* 3.5 9.6 - - - +
87Z MET* 1.3 74.1 - - - +
89Z ALA* 1.3 59.4 + - - +
91Z LYS* 2.8 35.6 + - - +
92Z THR* 3.5 8.8 + - - +
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Residues in contact with ALA 89 (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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778C LEU* 3.5 19.6 - - + +
781C ILE* 2.4 48.9 - - + -
782C ILE* 3.7 11.0 - - + +
85Z ASP 3.2 4.5 + - - +
86Z TYR 4.3 1.3 - - - +
88Z GLU* 1.3 78.6 - - - +
90Z PHE* 1.3 58.4 + - - +
92Z THR* 2.5 27.0 + - - -
93Z PHE* 4.3 1.6 + - - +
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Residues in contact with PHE 90 (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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86Z TYR 3.4 7.8 + - - +
87Z MET 3.8 4.0 - - - +
88Z GLU 3.2 1.0 - - - -
89Z ALA* 1.3 77.3 - - - +
91Z LYS* 1.3 59.7 + - - +
93Z PHE* 3.3 13.1 + - + +
94Z ASP* 2.6 40.7 - - - +
99Z GLY* 4.5 7.6 - - - -
100Z PHE 3.4 7.2 - - - -
101Z ILE* 2.9 52.9 - - + -
106Z LEU* 3.4 3.1 - - + -
109Z VAL* 6.3 0.9 - - + -
141Z TYR* 2.4 82.6 - + + -
142Z GLU* 4.8 6.5 - - - -
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Residues in contact with LYS 91 (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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718C GLN* 3.9 29.6 - - - +
87Z MET 3.1 11.6 + - - +
88Z GLU* 2.8 22.6 + - - +
90Z PHE* 1.3 75.1 - - - +
92Z THR* 1.3 51.8 + - + +
93Z PHE 2.8 6.2 + - - -
94Z ASP* 2.8 43.1 + - + +
97Z GLY* 4.5 20.4 + - - -
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Residues in contact with THR 92 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718C GLN* 6.2 3.6 - - - +
722C ILE* 6.2 3.6 - - + -
778C LEU* 3.9 29.9 - - + +
88Z GLU 3.8 10.1 - - - +
89Z ALA* 2.5 23.8 + - - +
91Z LYS* 1.3 74.3 - - + +
93Z PHE* 1.3 58.0 + - - +
94Z ASP 5.3 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