Contacts of the strand formed by residues 35 - 42 (chain B) in PDB entry 5DO7
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 SER 35 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ASP* 4.6 0.5 + - - -
34B ASN* 1.3 86.3 + - - +
36B LEU* 1.3 57.6 + - - +
37B TYR* 5.5 0.4 - - - +
95B VAL 2.7 17.9 - - - -
96B ARG* 2.9 14.0 - - - +
97B SER* 2.5 32.6 + - - -
134B ILE* 3.2 1.6 - - - +
135B ASN* 2.2 45.1 + - - +
233B ILE* 5.1 1.3 - - - -
264B LEU* 4.4 7.2 - - - -
361B TRP* 5.0 7.0 - - - -
365B THR* 5.3 6.9 + - - -
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Residues in contact with LEU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B SER* 1.3 77.1 - - - +
37B TYR* 1.3 64.1 + - - +
38B PHE* 3.8 27.1 - - + -
93B PHE* 3.9 9.1 - - + +
95B VAL* 2.1 73.7 + - + +
118B ILE* 4.9 15.0 - - + -
132B ILE* 4.6 5.2 - - + -
133B TRP 3.5 17.9 - - - +
134B ILE* 4.0 17.9 - - + -
233B ILE* 5.4 4.3 - - + -
235B ILE* 5.9 2.5 - - + -
264B LEU* 4.1 9.9 - - + -
266B LEU* 4.5 19.5 - - + -
361B TRP* 4.0 7.5 + - - +
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Residues in contact with TYR 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B SER 5.5 1.1 - - - +
36B LEU* 1.3 78.8 - - - +
38B PHE* 1.3 75.8 + - - +
39B THR* 5.5 4.5 - - - -
93B PHE 4.1 8.3 - - - -
133B TRP* 2.9 83.5 + + + +
134B ILE 5.7 0.9 - - - -
135B ASN 5.8 4.5 - - - +
358B ASP* 2.9 40.6 + - - -
361B TRP* 3.3 34.1 - + - +
362B LYS* 4.7 15.0 - - + +
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Residues in contact with PHE 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LEU* 3.8 22.7 - - + -
37B TYR* 1.3 96.8 - - - +
39B THR* 1.3 67.2 + - - +
41B SER* 3.9 21.1 - - - -
91B LEU* 4.5 12.6 - - + +
92B SER* 3.9 20.6 - - - +
93B PHE* 3.3 53.0 + + + +
114B LEU* 6.1 0.2 - - + -
118B ILE* 3.7 25.4 - - + -
131B GLN 3.8 6.3 - - - -
132B ILE* 3.3 42.2 - - + -
133B TRP* 5.3 0.7 - - - -
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Residues in contact with THR 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B TYR* 5.5 4.3 - - - -
38B PHE* 1.3 82.9 + - - +
40B TYR* 1.3 95.7 + - + +
41B SER* 3.8 2.0 - - - -
91B LEU 3.6 2.0 - - - -
92B SER* 4.9 1.8 - - - -
130B GLY* 3.4 1.2 - - - -
131B GLN* 3.2 39.4 + - + +
133B TRP* 5.2 4.7 + - - -
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Residues in contact with TYR 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B THR* 1.3 90.5 - - + +
41B SER* 1.3 58.4 + - - +
90B ASN* 3.3 42.2 - - + +
91B LEU 2.8 17.3 + - - -
92B SER* 4.6 10.1 - - - -
129B SER* 3.5 6.8 + - - +
130B GLY* 2.8 24.3 + - - -
354B ARG* 5.6 4.1 + - - -
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Residues in contact with SER 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B PHE* 3.9 25.6 - - - -
39B THR 4.2 2.9 + - - -
40B TYR* 1.3 72.6 - - - +
42B GLY* 1.3 58.2 + - - +
88B ILE* 4.1 17.5 - - - -
89B GLN* 3.6 2.1 - - - -
90B ASN* 2.8 25.8 + - - +
91B LEU* 3.7 18.5 - - - +
127B ILE* 6.3 2.2 - - - -
129B SER* 2.9 12.9 + - - -
130B GLY* 3.8 12.3 - - - -
131B GLN 4.7 1.4 + - - -
132B ILE* 5.4 1.4 - - - +
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Residues in contact with GLY 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B SER* 1.3 78.2 - - - +
43B GLN* 1.3 55.2 - - - +
88B ILE* 3.2 18.7 - - - +
127B ILE* 3.3 4.8 - - - +
128B LYS* 2.3 40.1 + - - -
129B SER* 2.8 17.0 + - - +
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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