Contacts of the strand formed by residues 159 - 164 (chain D) in PDB entry 3C6M
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 GLY 159 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330B GLU* 4.5 9.6 + - - -
154D HIS* 4.0 11.2 - - - -
155D SER* 2.8 39.0 + - - -
156D LYS 4.3 1.4 + - - -
157D GLN 3.5 2.4 + - - -
158D PHE* 1.3 79.1 - - - +
160D ASN* 1.3 64.4 + - - -
161D ILE* 3.6 0.9 + - - +
172D GLU* 3.8 9.9 - - - -
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Residues in contact with ASN 160 (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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334B ARG* 3.3 14.6 + - - +
140D VAL* 3.5 15.8 - - - +
152D ILE* 3.9 11.2 - - + -
153D LEU 3.6 0.8 + - - -
154D HIS* 3.3 36.2 + - - +
158D PHE 3.9 0.2 + - - -
159D GLY* 1.3 71.7 - - - -
161D ILE* 1.3 60.1 + - - +
171D ALA* 3.3 0.5 - - - -
172D GLU* 2.9 36.8 + - - +
232D TYR* 2.8 35.4 - - - +
233D MET* 3.3 16.8 - - - +
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Residues in contact with ILE 161 (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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134D TYR* 4.1 21.3 - - + -
136D ILE* 4.0 15.0 - - + -
151D LYS 3.5 0.9 - - - +
152D ILE* 3.3 5.0 - - - -
153D LEU 2.7 36.6 + - - +
155D SER* 3.7 23.3 - - - -
158D PHE* 4.2 8.1 - - + -
159D GLY 3.8 7.9 - - - +
160D ASN* 1.3 76.5 - - - +
162D LEU* 1.3 70.9 + - - +
163D ILE* 3.6 17.0 + - + +
168D VAL* 3.8 23.1 - - + -
170D LEU 3.5 11.4 - - - +
171D ALA* 3.7 14.6 - - + -
233D MET* 4.5 1.1 - - - -
350D SER* 4.5 2.2 - - - -
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Residues in contact with LEU 162 (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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150D ILE* 3.9 23.6 - - + -
151D LYS 3.4 3.8 - - - +
152D ILE* 3.8 21.8 - - + -
160D ASN 4.1 1.0 + - - -
161D ILE* 1.3 72.2 - - - +
163D ILE* 1.3 61.5 + - - +
164D LEU* 3.9 14.1 - - + -
169D ASN* 2.8 30.0 + - + -
170D LEU 2.7 20.7 + - - +
201D ASP* 4.1 10.5 - - + +
225D VAL* 4.4 6.7 - - + +
229D CYS* 3.9 26.9 - - - -
233D MET* 4.1 13.6 - - + -
401D MTA 3.8 29.6 - - + -
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Residues in contact with ILE 163 (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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124D TRP* 3.8 44.6 - - + +
136D ILE* 5.8 1.6 - - + -
149D ASN* 3.9 1.7 - - - +
150D ILE* 3.9 0.5 - - - -
151D LYS* 2.8 42.2 + - + +
153D LEU* 3.9 24.2 - - + -
161D ILE* 4.0 18.4 - - + +
162D LEU* 1.3 78.5 - - - +
164D LEU* 1.3 61.8 + - - +
165D SER 4.1 0.2 + - - -
166D GLY* 3.5 38.5 + - - +
167D ASP 3.4 7.9 - - - +
168D VAL* 4.1 11.4 - - + +
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Residues in contact with LEU 164 (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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148D GLN* 3.7 17.5 - - - +
149D ASN 3.5 2.2 - - - +
150D ILE* 3.8 34.8 - - + -
162D LEU* 3.9 15.9 - - + -
163D ILE* 1.3 71.3 - - - +
165D SER* 1.3 70.9 + - - +
166D GLY 3.1 0.9 - - - -
167D ASP* 3.0 24.6 + - - +
169D ASN* 3.5 20.2 + - - +
225D VAL* 4.0 11.4 - - + -
278D THR* 3.7 7.4 - - + +
401D MTA 3.5 50.3 - - + +
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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