Contacts of the strand formed by residues 117 - 120 (chain Y) in PDB entry 3AOI
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 MET 117 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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977I ALA* 4.9 13.5 - - + -
982I PHE* 3.9 24.9 - - + -
983I LEU* 5.2 2.0 - - - -
100Y LEU* 5.0 9.0 - - + -
101Y SER 3.7 18.2 + - - +
102Y VAL* 3.3 9.5 - - + +
103Y GLN* 2.7 32.4 + - - -
111Y ASN 4.1 1.1 - - - -
112Y VAL* 3.7 44.6 - - + +
114Y ASP 4.1 5.6 - - - -
115Y THR 3.4 5.8 + - - +
116Y PRO* 1.3 70.9 - - - +
118Y LYS* 1.3 56.1 + - - +
119Y ILE* 3.7 25.0 + - + -
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Residues in contact with LYS 118 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Y THR* 4.6 4.9 + - - -
10Y ALA* 4.8 7.3 - - - +
11Y GLY* 4.6 8.9 - - - +
14Y ARG* 4.6 10.1 - - - +
103Y GLN* 3.2 42.1 + - - +
105Y VAL* 3.6 18.2 - - + -
109Y GLU* 3.7 27.8 + - + +
110Y ALA* 3.7 6.3 - - - +
111Y ASN* 3.1 39.3 + - + +
112Y VAL* 5.1 1.7 - - - +
114Y ASP* 4.4 23.8 + - + -
116Y PRO* 3.0 17.2 + - - +
117Y MET* 1.3 73.7 - - - +
119Y ILE* 1.3 65.1 + - - +
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Residues in contact with ILE 119 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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982I PHE* 3.8 13.7 - - + +
983I LEU* 5.4 4.3 - - + -
987I GLU* 5.3 1.3 - - - +
102Y VAL* 3.5 34.1 - - + -
103Y GLN 3.1 4.0 + - - -
104Y VAL* 3.2 9.3 - - + -
105Y VAL* 2.9 22.7 + - - -
117Y MET* 3.7 35.7 - - + +
118Y LYS* 1.3 79.6 - - - +
120Y SER* 1.3 68.4 + - - +
123Y SER* 2.9 31.2 - - - +
125Y MET* 3.9 12.8 - - + -
126Y GLY* 4.0 9.4 - - - +
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Residues in contact with SER 120 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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987I GLU* 3.3 36.0 + - - +
105Y VAL 3.3 6.3 - - - -
107Y PRO* 3.8 22.4 + - - +
110Y ALA* 3.3 25.6 - - - +
119Y ILE* 1.3 79.0 - - - +
121Y ASP* 1.3 66.4 + - - +
122Y ALA* 4.2 2.5 - - - -
123Y SER* 2.9 19.4 - - - -
126Y GLY* 3.5 8.1 - - - -
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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