Contacts of the strand formed by residues 108 - 113 (chain Z) in PDB entry 3SDI
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 GLY 108 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7Z ALA* 3.6 14.3 - - - +
8Z GLY 3.3 6.6 + - - +
9Z GLU 3.2 11.3 + - - -
11Z PHE 3.2 28.7 - - - +
103Z GLY 3.6 6.3 - - - -
104Z LEU* 4.2 2.7 - - - -
106Z GLY 3.8 1.2 - - - -
107Z LYS* 1.3 73.6 - - - +
109Z ALA* 1.3 57.0 + - - -
121Z ARG* 3.0 15.4 + - - -
123Z GLN* 5.5 1.6 + - - +
145Z TYR* 6.0 0.9 - - - -
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Residues in contact with ALA 109 (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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7Z ALA* 3.8 4.0 - - - +
12Z ALA* 3.9 1.5 - - - +
76Z ILE* 4.0 25.5 - - + +
102Z ALA* 3.1 7.8 - - - +
103Z GLY 2.8 38.0 + - - +
105Z ASP 4.2 4.5 - - - +
108Z GLY* 1.3 74.3 - - - -
110Z VAL* 1.3 64.6 + - - +
111Z TYR* 4.3 6.3 - - + -
121Z ARG* 3.4 27.1 - - - +
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Residues in contact with VAL 110 (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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5Z GLY* 3.9 12.6 - - - +
6Z ILE 3.9 15.7 - - - +
7Z ALA* 3.9 25.1 - - + +
12Z ALA* 4.7 0.4 - - + -
100Z ILE* 3.9 22.7 - - + -
101Z ILE 3.3 2.7 - - - -
102Z ALA* 4.3 12.3 - - + -
109Z ALA* 1.3 80.5 - - - +
111Z TYR* 1.3 64.1 + - - +
121Z ARG* 3.3 6.8 - - - +
122Z GLU* 2.8 49.1 + - + +
123Z GLN 4.7 0.9 - - - +
124Z CYS 4.8 1.1 - - - -
125Z ARG* 4.3 14.6 - - + +
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Residues in contact with TYR 111 (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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76Z ILE* 4.0 41.2 - - + +
77Z ASN* 3.6 25.7 - - + +
80Z ALA* 3.6 20.2 - - + -
100Z ILE* 3.4 3.8 - - - +
101Z ILE* 2.9 45.4 + - + +
105Z ASP* 5.9 0.3 - - - +
109Z ALA* 4.3 4.0 - - + -
110Z VAL* 1.3 80.4 - - - +
112Z SER* 1.3 62.0 + - - +
113Z PHE* 3.9 10.5 - - + -
119Z TYR* 3.8 20.0 - + + -
120Z GLU 3.4 4.7 - - - +
121Z ARG* 3.6 48.2 + - + +
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Residues in contact with SER 112 (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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302Y 3SD 3.4 13.4 - - - +
99Z THR 3.3 10.5 - - - -
100Z ILE* 3.9 4.0 - - - -
111Z TYR* 1.3 74.4 - - - +
113Z PHE* 1.3 65.2 + - - +
119Z TYR* 3.2 22.2 - - - +
120Z GLU 3.1 10.4 + - - -
122Z GLU* 2.7 27.5 + - - -
125Z ARG* 3.2 32.9 + - - -
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Residues in contact with PHE 113 (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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302Y 3SD 4.5 5.9 - - - +
80Z ALA* 3.3 43.5 - - + -
83Z ILE* 3.4 28.7 - - + -
84Z GLN 3.9 5.2 - - - -
87Z LEU* 3.7 16.4 - - + -
98Z HIS* 4.1 8.5 + - - +
99Z THR* 2.8 43.3 + - + +
101Z ILE* 4.2 17.5 - - + -
111Z TYR* 3.9 18.2 - - + -
112Z SER* 1.3 76.5 - - - +
114Z ASP* 1.3 71.2 + - - +
117Z GLY 4.4 2.9 - - - -
118Z SER 3.1 7.4 - - - +
119Z TYR* 3.2 27.8 - + + -
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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