Contacts of the helix formed by residues 130 - 140 (chain C) in PDB entry 1KPS
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 GLN 130 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C LEU 3.4 20.8 + - - -
82C PHE* 4.4 5.9 - - - -
83C HIS 3.0 23.0 + - - +
84C PRO* 3.5 2.1 + - + +
86C VAL 2.6 26.6 + - - +
87C TYR 4.7 1.8 + - - -
88C PRO* 4.2 18.0 - - + +
128C PRO* 3.5 2.0 - - - +
129C ALA* 1.3 83.0 - - - +
131C ALA* 1.3 63.7 + - - +
132C GLU* 4.0 10.3 - - - +
133C ALA* 3.1 30.2 + - + +
134C TYR* 3.2 22.0 - - - +
516D THR* 6.3 0.2 - - - -
525D LEU* 4.6 4.3 - - - -
564D PHE* 4.5 3.8 - - - -
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Residues in contact with ALA 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C PRO* 5.6 0.6 - - - +
130C GLN* 1.3 73.9 - - - +
132C GLU* 1.3 58.9 + - - +
134C TYR* 3.7 1.2 - - - +
135C THR* 3.0 33.3 + - - -
512D ASN* 5.6 2.7 - - - +
515D LEU* 6.1 0.9 - - + -
516D THR* 4.4 19.1 - - + +
519D LEU* 4.6 8.3 - - + -
525D LEU* 4.3 17.1 - - + +
560D LEU* 3.5 16.4 - - + -
564D PHE* 3.7 19.6 - - + -
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Residues in contact with GLU 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C PHE* 4.2 7.0 - - + -
130C GLN* 3.6 9.3 + - - +
131C ALA* 1.3 74.4 - - - +
133C ALA* 1.3 68.1 + - - +
134C TYR 3.2 0.2 + - - -
135C THR* 3.3 2.1 + - - -
136C ILE* 3.1 40.7 + - + +
147C ARG* 3.3 27.0 + - - -
512D ASN* 5.7 6.5 - - - +
560D LEU* 3.7 13.9 - - + +
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Residues in contact with ALA 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C PHE* 3.5 22.9 - - + -
83C HIS* 3.4 15.0 - - - +
84C PRO* 3.2 34.1 - - + -
130C GLN* 3.1 16.1 + - - +
132C GLU* 1.3 77.8 - - - +
134C TYR* 1.3 64.6 + - - +
136C ILE* 3.5 1.4 + - - +
137C TYR* 3.0 25.3 + - - +
144C TYR* 4.1 2.4 - - - -
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Residues in contact with TYR 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575B CYS* 2.9 38.1 + - - +
84C PRO* 4.1 10.6 - - + +
125C ILE* 3.4 32.9 + - + +
126C GLN* 5.9 0.2 - - - -
128C PRO* 3.2 26.0 - - + -
130C GLN 3.2 21.7 + - - +
131C ALA 3.5 1.5 + - - +
132C GLU 3.2 0.6 - - - -
133C ALA* 1.3 81.0 - - - +
135C THR* 1.3 63.9 + - - +
137C TYR* 3.2 5.4 + - - +
138C CYS* 2.9 25.1 + - - -
563D ALA* 3.8 23.1 - - + -
564D PHE* 3.3 30.7 - + + -
567D LYS* 3.3 29.5 - - + +
568D PRO* 4.9 1.0 - - - +
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Residues in contact with THR 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C ALA 3.0 11.8 + - - -
132C GLU 3.3 2.7 + - - -
134C TYR* 1.3 78.7 - - - +
136C ILE* 1.3 66.1 + - + +
138C CYS* 3.1 0.7 + - - +
139C GLN* 3.0 53.0 + - + +
559D PRO* 3.7 20.2 - - + +
560D LEU* 3.0 39.2 + - + +
563D ALA* 3.4 16.7 - - - +
564D PHE* 4.3 1.0 - - - -
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Residues in contact with ILE 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C PHE* 4.2 8.5 - - + -
132C GLU* 3.1 35.9 + - + +
133C ALA 4.1 2.5 - - - +
135C THR* 1.3 79.6 - - + +
137C TYR* 1.3 64.7 + - - +
139C GLN* 4.7 1.3 - - - +
140C ASN* 3.0 28.4 + - + +
143C GLU* 3.8 19.1 - - + -
144C TYR* 3.4 30.2 - - - +
147C ARG* 4.0 23.8 - - - +
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Residues in contact with TYR 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575B CYS* 4.9 2.9 - - + -
577B PHE* 5.2 4.8 - + - -
84C PRO* 5.1 1.6 - - + -
123C PRO* 4.1 16.8 - - + +
125C ILE* 3.4 41.0 - - + +
133C ALA 3.0 18.3 + - - +
134C TYR* 3.2 7.2 + - - +
136C ILE* 1.3 78.6 - - - +
138C CYS* 1.3 65.2 + - - +
141C ARG* 2.7 78.6 + - - -
144C TYR* 3.7 41.2 - + + -
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Residues in contact with CYS 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575B CYS* 2.0 60.8 - - + +
576B SER 3.8 14.4 - - - +
577B PHE* 4.1 8.8 - - - +
580B HIS* 3.9 9.7 - - + +
134C TYR* 2.9 28.3 - - - -
135C THR* 3.1 5.1 + - - +
137C TYR* 1.3 83.8 - - - +
139C GLN* 1.3 65.1 + - + +
140C ASN 3.3 4.4 + - - -
141C ARG* 4.3 1.1 + - - +
563D ALA* 5.8 1.8 - - + -
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Residues in contact with GLN 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580B HIS* 3.6 42.6 + - + +
135C THR* 3.0 25.3 + - + +
136C ILE* 4.1 1.1 - - - -
138C CYS* 1.3 81.8 - - + +
140C ASN* 1.3 66.6 + - - +
559D PRO* 3.2 37.2 + - - +
562D LEU* 3.4 34.2 - - - +
563D ALA* 3.8 11.7 - - + +
566D THR* 4.8 4.0 - - - +
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Residues in contact with ASN 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C ILE* 3.0 22.2 + - + +
138C CYS 3.3 2.4 + - - -
139C GLN* 1.3 83.4 + - + +
141C ARG* 1.3 69.1 + - - +
142C VAL* 3.1 11.0 - - - +
143C GLU* 2.9 42.7 + - + +
144C TYR 3.0 4.9 + - - -
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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