Contacts of the strand formed by residues 162 - 165 (chain O) 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 ALA 162 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39O GLY 3.2 13.2 - - - +
40O ILE* 4.2 8.3 - - + -
148O LEU* 4.2 1.3 - - - -
160O TRP* 3.3 7.5 - - - -
161O LYS* 1.3 81.6 - - - +
163O THR* 1.3 67.0 + - - +
176O LEU* 4.1 17.7 - - + -
180O TRP* 4.2 15.5 - - + -
58P LEU* 3.5 37.0 + - + +
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Residues in contact with THR 163 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38O LEU* 3.3 6.6 - - - +
39O GLY 3.1 29.5 + - - +
137O LEU* 3.9 26.2 - - + -
148O LEU* 4.7 5.6 - - + -
150O GLN* 3.9 10.5 + - - +
160O TRP* 3.6 40.5 - - + -
162O ALA* 1.3 77.1 - - - +
164O ALA* 1.3 72.7 + - - +
173O LYS* 3.7 19.0 + - - +
176O LEU* 3.7 9.5 - - - +
58P LEU* 5.3 1.1 - - - -
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Residues in contact with ALA 164 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36O THR* 4.5 4.5 - - + -
37O SER 3.2 13.0 - - - +
38O LEU* 4.0 9.0 - - + +
137O LEU* 4.8 0.2 - - - -
163O THR* 1.3 87.6 + - - +
165O ILE* 1.3 69.9 + - - +
169O SER* 3.4 20.7 - - - +
172O ALA* 3.7 29.4 - - + -
173O LYS* 4.1 15.3 + - - +
176O LEU* 4.6 2.0 - - + -
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Residues in contact with ILE 165 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31O VAL* 5.0 2.7 - - + -
36O THR* 3.2 8.7 - - - +
37O SER* 2.8 51.6 + - - +
78O TYR* 4.1 1.6 - - - -
79O SER* 3.4 13.2 + - - +
135O SER* 3.4 40.2 - - - +
137O LEU* 3.8 24.0 - - + -
150O GLN* 3.7 33.4 - - + +
164O ALA* 1.3 79.5 - - - +
166O GLY* 1.3 61.9 + - - +
169O SER* 3.8 5.6 - - - -
173O LYS* 6.1 0.2 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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