Contacts of the strand formed by residues 153 - 158 (chain D) in PDB entry 3KHU
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 ASN 153 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122D GLY 2.7 12.5 + - - +
123D TYR* 3.3 27.4 - - + -
124D LYS 3.2 23.2 + - - +
151D ASN 3.5 4.7 + - - +
152D LEU* 1.3 74.9 - - - +
154D LEU* 1.3 60.9 + - - +
155D GLN* 2.7 29.8 + - - +
187D GLU* 4.0 18.4 + - - +
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Residues in contact with LEU 154 (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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116D ILE* 4.4 7.2 - - + -
117D VAL* 4.5 6.1 - - + -
120D SER* 4.3 8.5 - - - +
124D LYS* 3.4 32.8 - - + +
126D VAL* 4.4 9.0 - - + -
141D ARG* 2.8 34.6 + - - +
144D PHE* 3.6 53.6 - - + -
152D LEU* 3.9 39.6 + - + +
153D ASN* 1.3 74.8 + - - +
155D GLN* 1.3 62.3 + - - +
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Residues in contact with GLN 155 (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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123D TYR* 3.8 28.7 - - + +
124D LYS 2.9 10.5 + - - +
125D ILE* 3.5 4.8 - - + +
126D VAL* 2.6 35.2 + - - +
141D ARG* 4.1 5.2 + - - +
153D ASN* 2.7 31.9 + - - +
154D LEU* 1.3 78.7 + - - +
156D VAL* 1.3 58.9 + - - +
157D LEU* 4.0 0.8 + - + -
183D ASP* 5.7 0.7 - - - +
185D THR* 5.2 0.7 + - - -
187D GLU* 3.8 35.5 - - - +
188D GLY* 3.9 6.3 + - - -
191D ALA* 3.9 21.5 - - + -
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Residues in contact with VAL 156 (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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126D VAL* 3.2 8.1 - - + +
128D GLU* 5.2 0.4 - - + -
137D ALA* 4.0 36.6 - - + +
140D ILE* 4.0 17.3 - - + -
141D ARG* 3.9 27.4 - - + +
144D PHE* 3.8 34.3 - - + -
155D GLN* 1.3 77.5 + - - +
157D LEU* 1.3 73.5 + - - +
182D GLY* 4.4 6.8 - - - -
183D ASP* 4.9 6.2 + - - +
213D THR* 4.6 5.4 + - - +
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Residues in contact with LEU 157 (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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125D ILE* 3.7 24.0 - - + -
126D VAL 2.8 6.2 + - - +
127D THR* 3.3 17.2 - - + +
128D GLU* 3.0 29.1 + - - +
155D GLN* 5.1 0.4 - - + +
156D VAL* 1.3 83.1 - - - +
158D SER* 1.3 63.1 + - - +
180D ILE* 4.3 2.9 - - + -
181D GLY 3.2 14.4 - - - +
182D GLY* 3.7 7.6 - - - -
183D ASP 5.2 0.7 - - - +
188D GLY* 4.2 2.9 - - - +
191D ALA* 3.7 36.1 - - + +
192D VAL* 3.6 25.4 - - + +
195D LEU* 4.0 18.4 - - + -
213D THR* 4.9 3.6 - - - -
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Residues in contact with SER 158 (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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127D THR* 4.2 0.7 - - - -
128D GLU* 3.6 23.2 + - - +
132D VAL* 5.9 0.2 - - - +
157D LEU* 1.3 73.6 - - - +
159D ASN* 1.3 61.6 + - - +
160D PRO* 3.4 9.6 - - - +
180D ILE* 3.3 6.4 - - - +
181D GLY 2.7 34.3 + - - +
213D THR* 4.0 17.8 - - - +
216D SER* 2.8 29.5 + - - -
217D GLU* 3.9 6.4 + - - +
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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