Contacts of the strand formed by residues 116 - 119 (chain Q) in PDB entry 3K9Q
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 LYS 116 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91Q ASP 3.2 12.8 + - - +
92Q VAL* 3.2 16.9 - - + -
93Q VAL* 2.8 24.3 + - - +
110Q ILE* 4.0 1.6 - - - -
114Q ALA* 3.4 3.7 - - - +
115Q LYS* 1.3 88.1 - - + +
117Q VAL* 1.3 68.0 + - - +
141Q GLY* 3.2 31.3 + - - -
143Q GLU 3.2 24.2 + - - +
144Q THR* 3.2 9.6 - - + +
331Q LEU* 3.9 35.2 + - + +
332Q ALA* 5.1 1.3 - - - +
335Q SER* 3.1 28.9 + - - -
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Residues in contact with VAL 117 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92Q VAL* 4.3 1.8 - - - -
93Q VAL* 3.4 7.2 - - + +
95Q GLU* 3.8 26.9 - - + -
106Q ALA* 3.7 20.6 - - + +
109Q HIS* 3.4 35.7 - - + -
110Q ILE* 4.0 12.3 - - + -
114Q ALA* 5.2 0.4 - - + -
116Q LYS* 1.3 80.3 - - - +
118Q LEU* 1.3 64.0 + - - +
119Q ILE* 3.9 13.0 - - + -
144Q THR 2.7 12.5 + - - +
145Q VAL* 3.4 9.5 - - + -
146Q VAL* 3.0 27.0 + - - +
331Q LEU* 4.8 2.1 - - - +
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Residues in contact with LEU 118 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92Q VAL* 4.0 10.0 - - + +
93Q VAL 2.7 9.8 + - - +
94Q LEU* 3.4 26.1 - - + +
95Q GLU 2.7 30.9 + - - -
117Q VAL* 1.3 74.1 - - - +
119Q ILE* 1.3 57.4 + - - +
146Q VAL* 3.4 31.0 - - + +
147Q SER 4.0 0.2 - - - -
148Q GLY* 3.7 21.1 - - - +
324Q LEU* 3.5 33.4 - - + +
327Q THR* 4.1 11.2 - - + -
328Q LEU* 3.7 22.7 - - + +
331Q LEU* 4.3 7.6 - - + -
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Residues in contact with ILE 119 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95Q GLU* 3.5 19.3 - - + +
100Q TYR 3.7 15.3 - - - +
101Q THR* 4.3 24.9 - - + -
102Q ASP 4.4 1.8 - - - +
106Q ALA* 3.9 5.2 - - + -
117Q VAL* 3.9 14.1 - - + -
118Q LEU* 1.3 74.9 - - - +
120Q SER* 1.3 63.3 + - - +
121Q ALA* 3.0 20.7 + - + +
123Q ALA* 4.0 19.3 - - + -
127Q LEU* 4.4 3.4 - - + -
145Q VAL* 3.7 25.4 - - + -
146Q VAL 2.9 14.5 + - - +
147Q SER* 4.3 1.3 - - - -
148Q GLY* 2.8 30.7 + - - -
324Q LEU* 3.9 2.8 - - - +
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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
------------------------------------------------------------
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