Contacts of the helix formed by residues 114 - 123 (chain A) in PDB entry 1KSV
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 ASP 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A PRO* 4.3 10.8 - - + +
62A TYR* 2.6 31.5 + - + +
96A HIS* 4.5 1.1 - - - -
112A THR* 3.1 16.6 + - - +
113A ASP* 1.3 76.7 - - - +
115A GLY* 1.3 61.7 + - - +
116A GLN* 3.2 11.1 + - - +
117A TRP* 2.8 32.6 + - + +
118A SER* 2.9 22.5 + - - -
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Residues in contact with GLY 115 (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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96A HIS* 4.4 8.9 - - - -
113A ASP 3.7 5.1 + - - -
114A ASP* 1.3 72.9 + - - +
116A GLN* 1.3 62.4 + - - +
118A SER* 3.4 5.5 + - - -
119A HIS* 3.0 27.1 + - - +
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Residues in contact with GLN 116 (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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114A ASP* 3.2 6.8 + - - +
115A GLY* 1.3 76.2 - - - +
117A TRP* 1.3 66.5 + - - +
119A HIS* 3.5 4.9 + - - +
120A ARG* 3.3 31.2 + - - +
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Residues in contact with TRP 117 (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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62A TYR* 3.7 19.3 - + + -
98A ALA* 4.4 1.6 - - + -
110A LEU* 3.8 28.0 - - + -
111A MSE 5.4 0.4 - - - -
112A THR* 3.6 41.3 - - + -
114A ASP* 2.8 32.3 + - - +
116A GLN* 1.3 75.5 - - - +
118A SER* 1.3 69.1 + - - +
120A ARG* 3.2 27.5 + - - +
121A ILE* 3.5 33.1 + - + +
208A ILE* 4.4 2.7 - - + -
222A LEU* 3.6 31.6 - - + -
227A ILE* 3.3 31.6 + - + +
230A VAL* 3.8 16.6 - - + +
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Residues in contact with SER 118 (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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96A HIS* 2.8 34.3 + - - -
98A ALA* 3.5 23.2 - - - +
112A THR* 3.9 8.3 - - - -
114A ASP 2.9 14.6 + - - -
115A GLY* 3.6 4.0 - - - -
117A TRP* 1.3 80.0 - - - +
119A HIS* 1.3 64.4 + - - +
121A ILE* 2.9 16.7 + - - +
122A THR* 3.0 19.1 + - - +
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Residues in contact with HIS 119 (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 GLY 3.0 18.2 + - - +
116A GLN* 3.9 5.4 + - - +
118A SER* 1.3 75.8 - - - +
120A ARG* 1.3 60.5 + - - +
122A THR* 3.4 10.8 - - - -
123A SER* 2.7 60.3 + - - -
124A PRO* 5.5 2.0 - - + +
126A HIS* 4.6 8.8 - + - -
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Residues in contact with ARG 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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116A GLN* 3.3 22.1 + - - +
117A TRP* 3.2 25.2 + - - +
118A SER 3.2 1.0 + - - -
119A HIS* 1.3 79.1 + - - +
121A ILE* 1.3 59.7 + - + +
126A HIS* 3.2 36.8 + - + +
128A CYS* 5.4 2.1 - - - +
231A VAL* 4.0 26.2 - - - +
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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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98A ALA* 4.2 16.8 - - + +
110A LEU* 4.0 9.9 - - + -
117A TRP* 3.7 52.5 - - + +
118A SER* 2.9 7.7 + - - +
120A ARG* 1.3 82.1 - - + +
122A THR* 1.3 59.9 + - + +
123A SER 3.7 1.9 - - - +
126A HIS* 5.4 0.8 - - - +
128A CYS* 3.7 28.6 - - - +
130A LYS* 5.7 2.8 - - + +
205A ILE* 3.8 25.4 - - + -
230A VAL* 3.9 18.8 - - + -
231A VAL* 5.3 10.3 - - + +
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Residues in contact with THR 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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98A ALA* 3.6 36.1 - - + +
99A GLY* 3.8 8.3 - - - +
118A SER* 3.0 20.5 + - - +
119A HIS* 3.4 13.3 - - - -
121A ILE* 1.3 81.3 - - + +
123A SER* 1.3 68.5 + - - +
124A PRO* 3.3 7.6 - - - +
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Residues in contact with SER 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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119A HIS* 2.7 42.9 + - - -
120A ARG 4.6 0.6 - - - -
121A ILE 3.7 2.2 - - - +
122A THR* 1.3 73.9 + - - +
124A PRO* 1.3 69.2 - - - +
125A ARG* 3.0 24.5 + - - +
126A HIS* 2.9 49.3 + - - +
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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