Contacts of the strand formed by residues 141 - 147 (chain D) in PDB entry 6DBU
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 THR 141 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76D ALA* 3.9 4.9 - - - -
77D ILE 5.7 0.2 - - - -
139D GLY 4.5 3.6 - - - +
140D HIS* 1.3 79.8 - - - +
142D LEU* 1.3 61.3 + - - +
154D VAL 3.7 0.9 - - - +
155D LEU* 3.2 6.9 - - - +
156D PHE* 2.9 32.3 + - - -
206D PHE 5.6 0.4 - - - -
207D HIS* 2.9 50.0 + - + +
208D VAL* 4.7 1.1 - - - -
209D ALA* 4.1 22.0 - - - +
218D PHE* 4.8 5.4 - - - -
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Residues in contact with LEU 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D ALA* 3.9 15.0 - - + +
77D ILE 3.5 18.9 + - - +
78D ALA* 3.6 25.0 - - + +
91D LEU* 3.7 32.5 - - + +
93D HIS* 5.5 3.4 - - + +
106D LEU* 4.1 15.3 - - + -
141D THR* 1.3 74.8 - - - +
143D SER* 1.3 70.9 + - - +
153D CYS* 3.6 22.4 - - + -
154D VAL 3.2 17.0 - - - +
155D LEU* 3.6 28.0 - - + -
185D ILE* 4.2 7.0 - - + -
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Residues in contact with SER 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D ALA* 4.4 4.9 - - - +
142D LEU* 1.3 84.5 + - - +
144D VAL* 1.3 63.4 + - - +
153D CYS* 3.4 2.8 - - - -
154D VAL* 2.9 45.3 + - - +
209D ALA* 3.7 24.8 - - - +
211D ALA* 3.7 23.7 + - - -
216D VAL* 4.6 3.6 - - - -
218D PHE* 5.7 0.7 - - - -
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Residues in contact with VAL 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D ALA* 4.5 9.6 - - + -
79D HIS 3.5 27.6 - - - +
80D PHE* 3.6 26.0 - - + +
81D GLU* 4.9 4.7 - - + +
83D GLN* 4.9 4.0 - - - +
91D LEU* 5.0 0.7 - - + -
143D SER* 1.3 75.3 - - - +
145D ILE* 1.3 71.5 + - - +
146D ASN* 5.3 2.4 - - - +
151D THR* 3.7 22.4 - - + -
152D ALA 3.5 12.8 - - - +
153D CYS* 4.3 13.7 - - - +
211D ALA* 3.3 16.0 - - - +
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Residues in contact with ILE 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D SER 4.8 0.2 - - - +
144D VAL* 1.3 81.7 - - - +
146D ASN* 1.3 69.4 + - - +
147D SER* 4.3 9.2 - - - +
151D THR* 3.2 8.1 - - - +
152D ALA* 2.9 59.9 + - + +
153D CYS* 4.4 3.8 - - - +
154D VAL* 4.5 12.3 - - + +
184D LEU* 6.1 3.8 - - + -
211D ALA* 4.1 4.7 - - + -
212D ARG 5.5 0.7 - - - +
213D GLN 6.2 0.2 - - - +
214D ASP* 4.3 17.5 - - - +
215D CYS 4.9 0.4 - - - +
216D VAL* 3.7 29.6 - - + -
238D VAL* 3.6 28.3 - - + -
240D LEU* 4.4 6.7 - - + -
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Residues in contact with ASN 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D GLN* 4.7 11.1 + - - +
144D VAL* 5.3 2.6 - - - +
145D ILE* 1.3 82.9 - - - +
147D SER* 1.3 60.7 + - - +
149D GLY 4.7 4.9 - - - +
150D LYS 3.2 7.0 - - - +
151D THR* 3.7 16.4 - - - +
213D GLN* 4.3 28.3 + - - +
214D ASP* 3.2 19.2 - - - +
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Residues in contact with SER 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D ILE* 4.3 4.7 - - - +
146D ASN* 1.3 75.9 - - - +
148D ARG* 1.3 73.4 + - - +
149D GLY* 3.4 2.9 - - - -
150D LYS* 2.9 17.1 + - - +
214D ASP* 3.4 29.0 - - - +
238D VAL* 4.0 11.0 + - - +
239D GLU* 4.7 6.7 - - - -
240D LEU* 3.0 36.1 + - - +
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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