Contacts of the strand formed by residues 162 - 166 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126N SER* 3.4 44.2 - - - +
127N MET* 3.7 22.4 - - + -
130N ALA* 3.9 12.6 - - + -
137N VAL* 3.2 16.6 - - + +
139N GLY 5.0 0.4 - - - +
153N ILE* 3.7 30.1 - - + +
158N LEU* 2.9 22.7 + - + +
159N ASP* 2.9 22.3 - - - +
161N ILE* 1.3 78.9 - - - +
163N THR* 1.3 65.7 + - - +
164N ILE* 3.9 14.3 - - + +
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Residues in contact with THR 163 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136N LYS* 3.7 19.2 + - - -
137N VAL 2.9 6.5 + - - -
138N PHE* 3.3 13.4 - - - -
139N GLY 2.9 22.9 + - - +
159N ASP 4.7 1.7 + - - -
162N ILE* 1.3 75.9 + - - +
164N ILE* 1.3 70.2 + - - +
165N PHE* 3.9 29.3 - - + -
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Residues in contact with ILE 164 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120N SER* 3.9 23.6 - - - +
123N GLY* 5.4 0.7 - - - -
126N SER* 5.0 2.9 - - - +
139N GLY* 3.4 15.0 - - - +
141N GLU* 5.0 0.9 - - + -
146N SER* 4.2 17.0 - - - +
149N SER* 3.6 23.8 - - - +
150N GLU* 3.8 31.5 + - + +
153N ILE* 3.7 29.6 - - + -
162N ILE* 3.9 8.7 - - + -
163N THR* 1.3 86.0 - - - +
165N PHE* 1.3 72.4 + - - +
166N LYS* 3.9 3.0 + - + +
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Residues in contact with PHE 165 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138N PHE* 3.9 21.8 - + + -
139N GLY 2.7 16.1 + - - +
140N ILE* 3.5 5.4 - - + +
141N GLU 3.2 24.8 + - - -
163N THR* 3.9 26.7 - - + -
164N ILE* 1.3 76.4 - - - +
166N LYS* 1.3 60.5 + - - +
167N GLY* 3.2 3.7 + - - -
172N VAL* 4.3 23.6 - - + -
173N GLU 4.2 17.7 - - - -
174N LEU* 3.9 22.9 - - + -
175N PRO* 3.6 25.8 - - + -
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Residues in contact with LYS 166 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141N GLU 3.6 3.8 - - - -
142N CYS 4.5 9.2 + - - +
143N SER 4.3 4.0 - - - +
144N SER* 3.9 20.9 - - - +
146N SER* 2.9 30.7 - - - +
147N ASP* 3.3 31.0 + - - +
150N GLU* 6.1 2.7 - - - +
164N ILE* 3.9 4.7 + - + +
165N PHE* 1.3 68.0 - - - +
167N GLY* 1.3 57.4 + - - +
172N VAL* 4.5 4.2 - - - +
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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
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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