Contacts of the helix formed by residues 88 - 93 (chain L) in PDB entry 2QJK
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 VAL 88 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172E ALA 4.3 3.1 - - - +
84L LEU 3.6 14.4 - - - +
85L GLY 3.6 3.1 + - - +
86L ARG 3.1 7.4 + - - +
87L SER* 1.3 88.3 - - - +
89L GLN* 1.3 76.3 + - - +
90L LEU* 3.2 4.2 + - - -
92L GLN* 3.7 18.4 - - + +
93L LEU* 3.6 22.4 - - + +
110L THR* 6.1 0.9 - - - -
157L ASP* 6.2 0.2 - - + -
161L ARG* 4.1 24.1 + - - +
163L ARG* 3.9 24.7 - - - +
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Residues in contact with GLN 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C GLY 3.6 7.1 + - - -
143C ASP* 2.8 45.6 + - - +
172E ALA 3.8 4.7 - - - +
173E ASN* 2.4 44.8 + - + +
174E GLY* 3.5 3.4 + - - -
87L SER 4.0 1.9 + - - +
88L VAL* 1.3 77.4 - - - +
90L LEU* 1.3 55.3 + - - +
91L GLY* 2.7 7.2 + - - +
92L GLN* 2.6 58.4 + - + +
93L LEU* 3.9 0.3 + - - +
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Residues in contact with LEU 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172E ALA* 3.1 27.7 + - + +
173E ASN* 3.3 23.2 + - - +
88L VAL 3.2 4.6 + - - -
89L GLN* 1.3 70.0 - - - +
91L GLY* 1.3 60.6 + - - +
92L GLN 3.3 0.2 - - - -
93L LEU* 3.7 25.0 + - - +
96L THR* 4.0 28.1 + - + +
108L GLU* 3.3 51.8 - - + +
109L ALA* 3.7 22.0 - - + +
110L THR* 4.5 2.2 - - + -
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Residues in contact with GLY 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173E ASN* 3.0 13.8 + - - -
89L GLN* 2.7 5.5 + - - +
90L LEU* 1.3 75.2 - - - +
92L GLN* 1.3 59.1 + - - +
93L LEU 3.0 15.4 + - - +
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Residues in contact with GLN 92 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C ASP* 3.2 43.2 + - + +
144C PHE* 3.5 24.2 - - - -
164C LYS* 5.7 1.0 - - - +
87L SER 4.7 1.7 - - - +
88L VAL* 3.7 13.6 - - + +
89L GLN* 2.6 43.5 + - + +
91L GLY* 1.3 72.7 - - - +
93L LEU* 1.3 66.0 + - - +
94L VAL* 5.5 0.7 - - - +
163L ARG* 3.7 14.4 + - - +
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Residues in contact with LEU 93 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88L VAL* 3.6 20.4 - - + +
89L GLN 3.9 5.6 - - - +
90L LEU* 3.7 25.4 - - + +
91L GLY 3.0 8.9 - - - +
92L GLN* 1.3 88.1 - - - +
94L VAL* 1.3 62.9 + - - +
95L ASP 3.5 13.7 - - - +
96L THR* 5.5 1.8 + - - -
109L ALA* 3.5 40.4 - - + +
157L ASP* 4.6 0.2 - - - +
161L ARG* 3.8 24.2 - - + +
162L ILE 5.4 0.9 - - - +
163L ARG* 3.7 22.0 - - - +
170L ASN* 5.8 0.4 - - - +
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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