Contacts of the strand formed by residues 162 - 166 (chain C) in PDB entry 5DST
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 162 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126C SER* 3.6 32.1 - - - +
127C MET* 3.7 28.7 - - + -
130C ALA* 4.0 8.3 - - + -
137C VAL* 3.3 21.8 - - + +
139C GLY 5.1 0.4 - - - +
153C ILE* 3.6 29.1 - - + +
158C LEU* 2.9 23.5 + - + +
159C ASP* 3.1 22.2 - - - +
161C ILE* 1.3 77.0 - - - +
163C THR* 1.3 68.4 + - - +
164C ILE* 4.0 13.4 - - + +
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Residues in contact with THR 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C LYS* 3.8 18.7 + - - -
137C VAL 3.0 9.3 + - - -
138C PHE* 3.4 10.1 - - - -
139C GLY 3.0 22.5 + - - +
159C ASP 4.6 2.4 + - - -
162C ILE* 1.3 76.4 + - - +
164C ILE* 1.3 68.4 + - - +
165C PHE* 3.8 31.8 - - + -
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Residues in contact with ILE 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C SER* 3.7 31.2 - - - +
123C GLY* 5.3 0.7 - - - -
126C SER* 5.0 2.7 - - - +
139C GLY* 3.5 8.1 - - - +
141C GLU* 4.8 1.3 - - + -
146C SER* 4.1 19.5 - - - +
149C SER* 3.6 22.2 - - - +
150C GLU* 3.9 31.0 + - + +
153C ILE* 3.7 29.2 - - + -
162C ILE* 4.0 7.4 - - + -
163C THR* 1.3 84.0 - - - +
165C PHE* 1.3 72.8 + - - +
166C LYS* 3.7 3.8 + - + +
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Residues in contact with PHE 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C PHE* 3.9 26.0 - + + -
139C GLY 2.6 19.8 + - - +
140C ILE* 3.5 13.6 - - + +
141C GLU 3.3 17.0 + - - -
163C THR* 3.8 30.3 - - + -
164C ILE* 1.3 77.8 - - - +
166C LYS* 1.3 58.2 + - - +
167C GLY 3.0 9.5 + - - -
172C VAL* 4.4 13.7 - - + -
173C GLU 4.3 13.5 - - - -
174C LEU* 3.9 18.6 - - + -
175C PRO* 3.8 23.6 - - + -
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Residues in contact with LYS 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C GLU 3.5 4.7 - - - -
142C CYS 4.3 12.9 + - - +
144C SER* 3.9 22.1 - - - +
146C SER* 3.0 30.3 - - - +
147C ASP* 3.1 30.1 + - - +
150C GLU* 6.1 3.8 - - - +
164C ILE* 3.7 5.9 + - + +
165C PHE* 1.3 67.5 - - - +
167C GLY* 1.3 59.3 + - - +
172C VAL* 4.4 4.0 - - - +
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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