Contacts of the strand formed by residues 153 - 158 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F GLY 2.8 13.1 + - - +
123F TYR* 3.4 28.2 - - + -
124F LYS 3.3 20.1 + - - +
151F ASN 3.4 4.7 + - - +
152F LEU* 1.3 75.6 - - - +
154F LEU* 1.3 58.6 + - - +
155F GLN* 2.7 26.2 + - - -
187F GLU* 3.7 24.5 + - - +
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Residues in contact with LEU 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F ILE* 4.3 7.4 - - + -
117F VAL* 4.5 5.8 - - + -
120F SER* 4.4 7.2 - - - +
124F LYS* 3.4 34.8 - - + +
126F VAL* 4.3 8.7 - - + -
141F ARG* 2.8 36.2 + - - +
144F PHE* 3.7 53.4 - - + -
152F LEU* 3.8 40.9 - - + +
153F ASN* 1.3 72.9 + - - +
155F GLN* 1.3 61.3 + - - +
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Residues in contact with GLN 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F TYR* 3.8 28.5 - - + +
124F LYS 2.9 10.1 + - - +
125F ILE* 3.5 5.6 - - - +
126F VAL* 2.7 34.4 + - - +
141F ARG* 4.2 4.9 + - - +
153F ASN* 2.7 29.3 + - - +
154F LEU* 1.3 79.8 + - - +
156F VAL* 1.3 60.6 + - - +
157F LEU* 4.0 0.6 + - + -
185F THR* 5.3 0.3 + - - -
187F GLU* 3.6 38.1 - - - +
188F GLY* 3.9 5.8 + - - -
191F ALA* 3.9 21.5 - - + -
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Residues in contact with VAL 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F VAL* 3.2 7.9 - - + +
128F GLU* 5.2 0.4 - - + -
137F ALA* 3.9 35.2 - - + +
140F ILE* 4.0 18.4 - - + -
141F ARG* 3.9 25.5 - - + +
144F PHE* 3.7 34.3 - - + -
155F GLN* 1.3 77.1 + - - +
157F LEU* 1.3 75.7 + - - +
182F GLY* 4.4 6.8 - - - -
183F ASP* 4.9 5.7 + - - +
213F THR* 4.5 4.9 + - - -
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Residues in contact with LEU 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125F ILE* 3.7 24.7 - - + -
126F VAL 2.8 7.3 + - - +
127F THR* 3.3 17.4 - - + +
128F GLU* 3.0 29.7 + - - +
155F GLN* 5.6 0.2 - - + -
156F VAL* 1.3 85.9 - - - +
158F SER* 1.3 62.0 + - - +
180F ILE* 4.3 3.1 - - + -
181F GLY 3.3 14.1 - - - +
182F GLY* 3.7 5.4 - - - -
183F ASP 5.2 0.2 - - - +
188F GLY* 4.2 2.9 - - - +
191F ALA* 3.6 37.0 - - + +
192F VAL* 3.6 25.6 - - + +
195F LEU* 4.0 17.9 - - + -
213F THR* 4.9 3.1 - - - -
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Residues in contact with SER 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127F THR* 4.3 0.2 - - - -
128F GLU* 3.6 22.6 + - - +
132F VAL* 5.7 0.5 - - - +
157F LEU* 1.3 75.2 - - - +
159F ASN* 1.3 63.2 + - - +
160F PRO* 3.4 9.4 - - - +
180F ILE* 3.3 6.2 - - - +
181F GLY 2.7 35.4 + - - +
213F THR* 4.0 15.9 - - - +
216F SER* 3.0 28.3 + - - -
217F GLU* 3.9 7.1 + - - +
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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