Contacts of the strand formed by residues 153 - 158 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B GLY 2.8 12.9 + - - +
123B TYR* 3.4 21.3 - - + -
124B LYS 3.2 23.9 + - - +
151B ASN 3.5 4.9 + - - +
152B LEU* 1.3 75.3 - - - +
154B LEU* 1.3 59.1 + - - +
155B GLN* 2.8 25.8 + - - -
187B GLU* 3.3 28.7 + - - +
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Residues in contact with LEU 154 (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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116B ILE* 4.4 8.3 - - + -
117B VAL* 4.5 6.3 - - + -
120B SER* 4.4 7.6 - - - +
124B LYS* 3.3 32.5 - - + +
126B VAL* 4.4 8.1 - - + -
141B ARG* 2.8 35.6 + - - +
144B PHE* 3.7 52.9 - - + -
152B LEU* 3.9 40.2 + - + +
153B ASN* 1.3 76.0 + - - +
155B GLN* 1.3 60.8 + - - +
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Residues in contact with GLN 155 (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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123B TYR* 3.8 28.3 - - + +
124B LYS 2.9 9.9 + - - +
125B ILE* 3.5 5.4 - - + +
126B VAL* 2.6 35.2 + - - +
141B ARG* 4.2 5.2 + - - +
153B ASN* 2.8 28.7 + - - +
154B LEU* 1.3 80.0 + - - +
156B VAL* 1.3 62.1 + - - +
157B LEU* 4.0 0.4 + - + -
183B ASP* 5.7 0.9 - - - +
185B THR* 5.3 0.3 + - - -
187B GLU* 3.7 37.8 + - - +
188B GLY* 3.9 6.6 + - - -
191B ALA* 3.8 22.2 - - + -
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Residues in contact with VAL 156 (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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126B VAL* 3.2 7.9 - - + +
128B GLU* 5.1 0.7 - - + -
137B ALA* 4.0 35.2 - - + +
140B ILE* 4.0 18.6 - - + -
141B ARG* 4.0 26.3 - - + +
144B PHE* 3.7 33.4 - - + -
155B GLN* 1.3 78.2 + - - +
157B LEU* 1.3 75.6 + - - +
182B GLY* 4.4 6.6 - - - -
183B ASP* 4.9 6.2 + - - +
213B THR* 4.6 4.9 + - - +
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Residues in contact with LEU 157 (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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125B ILE* 3.6 23.8 - - + -
126B VAL 2.9 6.4 + - - +
127B THR* 3.3 17.9 - - + +
128B GLU* 3.0 29.6 + - - +
156B VAL* 1.3 85.2 - - - +
158B SER* 1.3 61.8 + - - +
180B ILE* 4.4 2.9 - - + -
181B GLY 3.3 15.0 - - - +
182B GLY* 3.7 5.2 - - - -
188B GLY* 4.3 3.6 - - - +
191B ALA* 3.6 35.7 - - + +
192B VAL* 3.6 26.0 - - + +
195B LEU* 4.0 18.8 - - + -
213B THR* 5.0 3.6 - - - -
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Residues in contact with SER 158 (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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127B THR* 4.3 0.4 - - - -
128B GLU* 3.6 23.7 + - - +
157B LEU* 1.3 74.3 - - - +
159B ASN* 1.3 61.6 + - - +
160B PRO* 3.5 9.2 - - - +
179B LEU 3.7 0.3 - - - +
180B ILE* 3.3 6.9 - - - +
181B GLY 2.8 36.1 + - - +
213B THR* 4.0 17.7 - - - +
216B SER* 2.8 28.7 + - - -
217B GLU* 3.9 6.5 + - - +
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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