Contacts of the helix formed by residues 119 - 128 (chain A) in PDB entry 5K9S
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 GLY 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A ILE 2.9 14.3 + - - -
117A ARG 3.0 3.4 + - - -
118A ALA* 1.3 77.9 - - - +
120A LEU* 1.3 62.9 + - - +
121A ILE 3.4 3.1 - - - -
122A PRO* 3.3 18.0 - - - +
123A LYS* 4.2 15.1 - - - +
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A VAL* 4.9 0.9 - - + -
81A ILE* 3.9 22.9 - - + -
82A VAL* 4.1 22.7 - - + -
85A ILE* 3.6 24.2 - - + -
115A ILE* 3.6 38.1 + - + +
116A ILE 4.3 0.2 + - - -
118A ALA* 4.0 19.1 - - + +
119A GLY* 1.3 77.2 - - - +
121A ILE* 1.3 66.4 + - - +
122A PRO 3.4 0.2 - - - -
123A LYS* 3.2 22.5 + - + +
124A PHE* 2.9 41.8 + - + -
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Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ILE* 5.5 0.9 - - + +
116A ILE* 3.9 28.7 + - + +
119A GLY 3.4 0.2 - - - -
120A LEU* 1.3 76.1 - - - +
122A PRO* 1.3 72.3 - - + +
124A PHE* 3.0 10.8 + - + +
125A VAL* 2.9 24.9 + - + +
144A LEU* 4.3 15.7 - - + -
147A ILE* 4.4 11.0 - - + -
157A ALA* 3.4 51.4 - - + +
158A VAL* 3.8 18.2 - - + +
161A GLY* 4.0 14.8 - - - -
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Residues in contact with PRO 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A GLY* 3.3 21.5 - - - +
120A LEU 3.5 0.2 - - - -
121A ILE* 1.3 98.9 - - + +
123A LYS* 1.3 57.0 + - + +
125A VAL* 3.3 9.2 + - + +
126A SER* 3.0 27.4 + - - -
161A GLY* 4.5 11.7 - - - +
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Residues in contact with LYS 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A VAL* 4.7 3.6 + - - +
85A ILE* 3.5 31.5 - - + +
86A ASN* 2.3 42.7 + - - +
118A ALA 5.1 3.4 + - - -
119A GLY 4.2 17.6 + - - +
120A LEU* 3.2 18.8 + - + +
122A PRO* 1.3 75.3 - - + +
124A PHE* 1.3 66.7 + - + +
126A SER* 3.2 7.7 + - - -
127A PHE* 3.0 33.1 + - + -
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Residues in contact with PHE 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ILE* 3.8 21.8 - - + -
97A THR* 3.9 20.9 - - + -
100A ALA* 3.8 24.2 - - + -
104A LEU* 5.0 0.2 - - + -
115A ILE* 4.0 15.5 - - + -
120A LEU* 2.9 41.9 + - + -
121A ILE* 3.0 6.7 + - - +
123A LYS* 1.3 77.5 - - - +
125A VAL* 1.3 61.7 + - - +
127A PHE* 3.2 9.8 + + - +
128A LEU* 3.1 23.0 + - - +
140A SER* 3.6 21.8 - - - -
143A ALA* 4.3 14.1 - - + -
144A LEU* 3.7 32.8 - - + -
147A ILE* 4.4 4.3 - - + -
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Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ILE* 2.9 21.1 + - + +
122A PRO 3.3 8.3 + - - +
124A PHE* 1.3 76.7 - - - +
126A SER* 1.3 63.6 + - - +
128A LEU* 3.2 23.1 + - + +
129A GLY 3.9 1.9 + - - -
144A LEU* 4.0 8.3 - - + -
161A GLY 3.3 29.8 - - - +
162A GLY* 3.8 15.7 - - - +
163A ALA* 3.8 24.9 - - + -
166A ALA* 4.2 13.2 - - + +
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Residues in contact with SER 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A PRO 3.0 13.6 + - - -
123A LYS* 3.6 11.0 - - - -
124A PHE 3.2 0.4 - - - -
125A VAL* 1.3 76.4 - - - +
127A PHE* 1.3 68.4 + - - +
129A GLY* 2.9 16.6 + - - -
130A LYS* 3.7 9.2 + - - +
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Residues in contact with PHE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ILE* 4.1 23.6 - - + -
93A GLN* 3.7 39.3 - - + -
97A THR* 3.7 18.6 - - - -
123A LYS* 3.0 25.6 + - + -
124A PHE* 3.2 7.6 + + - +
126A SER* 1.3 78.3 - - - +
128A LEU* 1.3 61.2 + - - +
130A LYS* 3.0 41.8 + - + +
136A ILE* 3.8 30.5 - - + +
137A GLN* 3.4 13.7 - - - +
140A SER* 3.1 27.6 - - - +
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Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A PHE 3.1 15.5 + - - +
125A VAL* 3.3 14.6 - - + +
126A SER 3.1 1.2 - - - -
127A PHE* 1.3 76.0 - - - +
129A GLY* 1.3 56.1 + - - +
130A LYS 3.4 0.2 - - - -
137A GLN* 3.0 31.1 + - - +
140A SER* 3.9 3.8 - - - -
141A ALA* 3.5 37.0 - - + +
144A LEU* 3.9 15.3 - - + -
163A ALA 4.6 0.9 - - - +
166A ALA* 3.6 29.2 - - + +
167A PHE* 3.8 25.8 - - + +
170A LEU* 3.5 29.4 - - + +
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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