Contacts of the strand formed by residues 94 - 97 (chain Z) in PDB entry 3EHW
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 ILE 94 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114X PHE* 4.5 1.0 - - - -
58Z ILE* 5.8 2.0 - - + -
84Z PRO* 4.6 3.9 - - + +
85Z ARG 4.9 0.2 - - - +
88Z LEU* 3.1 32.8 + - + +
89Z ALA* 3.3 25.0 + - - +
92Z HIS* 3.1 16.4 - - + +
93Z PHE* 1.3 77.9 - - - +
95Z ASP* 1.3 65.4 + - - +
96Z VAL* 5.7 1.3 - - + -
113Z LEU* 4.0 30.7 - - + -
114Z PHE 3.5 2.5 - - - +
115Z ASN* 3.6 37.5 - - + +
121Z PHE* 3.7 36.6 - - + -
129Z ILE 5.2 0.4 - - - +
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Residues in contact with ASP 95 (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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96X VAL 5.2 0.7 - - - +
97X GLY* 4.6 5.3 - - - -
114X PHE* 3.9 20.6 - - + -
778X MG 2.6 28.5 - - - -
95Y ASP* 4.3 1.0 - - - +
84Z PRO* 3.8 18.1 - - - +
94Z ILE* 1.3 76.7 - - - +
96Z VAL* 1.3 82.4 + - - +
113Z LEU* 3.5 8.8 - - - +
114Z PHE* 2.8 34.1 + - + +
116Z PHE* 3.7 31.0 - - + -
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Residues in contact with VAL 96 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95Y ASP* 5.1 2.9 - - - +
82Z VAL* 3.6 37.9 - - + +
83Z ALA 3.9 4.0 - - - +
84Z PRO* 3.5 37.9 - - + +
94Z ILE* 5.7 0.9 - - + -
95Z ASP* 1.3 95.6 + - - +
97Z GLY* 1.3 73.2 + - - +
98Z ALA 5.1 0.3 - - - +
111Z VAL* 4.7 2.2 - - + -
112Z VAL 3.3 7.9 - - - +
113Z LEU* 4.0 17.3 - - + -
114Z PHE* 4.6 1.3 - - - -
129Z ILE 4.6 1.1 - - - +
130Z ALA* 4.2 8.7 - - + -
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Residues in contact with GLY 97 (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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777X DUP 4.1 1.2 - - - +
84Y PRO* 4.6 0.4 - - - -
95Y ASP* 4.5 5.2 - - - -
95Z ASP 4.1 0.4 - - - -
96Z VAL* 1.3 87.2 - - - +
98Z ALA* 1.3 73.8 + - - +
99Z GLY* 3.1 3.6 + - - -
112Z VAL* 2.7 20.3 + - - +
114Z PHE* 3.5 32.1 - - - -
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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