Contacts of the helix formed by residues 120 - 131 (chain C) in PDB entry 1KWV
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 PRO 120 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119C MET* 1.3 94.9 - - + +
121C PHE* 1.3 66.2 + - - +
122C SER* 4.2 14.6 - - - +
123C LYS* 3.0 32.7 + - + +
124C VAL* 3.1 10.4 + - - +
156C PHE* 3.8 0.4 - - - -
209C CYS 4.0 4.9 - - - +
210C GLN* 4.0 17.5 - - - +
211C ALA 3.4 10.8 - - - +
212C SER* 3.9 10.1 - - - +
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Residues in contact with PHE 121 (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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120C PRO* 1.3 70.8 - - - +
122C SER* 1.3 65.2 + - - +
124C VAL* 3.0 5.2 + - + +
125C LYS* 2.9 50.8 + - + +
135C VAL* 4.2 13.5 - - + -
156C PHE* 3.4 37.1 - + + -
157C LEU 3.4 21.3 - - - -
158C GLY* 4.5 0.2 - - - -
160C THR* 3.5 21.3 - - + -
162C GLU* 4.4 11.7 - - - -
171C VAL* 3.6 27.4 - - + -
195C CYS* 3.4 22.7 - - + -
209C CYS* 3.1 20.6 + - + +
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Residues in contact with SER 122 (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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120C PRO* 4.2 11.5 - - - +
121C PHE* 1.3 81.4 - - - +
123C LYS* 1.3 64.8 + - - +
125C LYS* 3.4 9.7 + - - +
126C ALA* 3.1 26.3 + - - +
209C CYS* 4.5 1.4 + - - +
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Residues in contact with LYS 123 (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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119C MET* 3.8 21.0 - - + +
120C PRO* 3.0 32.7 + - + +
122C SER* 1.3 85.1 + - - +
124C VAL* 1.3 61.9 + - - +
126C ALA* 3.8 6.0 - - - +
127C LEU* 2.9 30.3 + - - +
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Residues in contact with VAL 124 (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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119C MET* 3.4 28.0 - - + +
120C PRO 3.1 8.7 + - - +
121C PHE* 3.0 10.1 + - + +
123C LYS* 1.3 76.7 - - - +
125C LYS* 1.3 63.0 + - - +
127C LEU* 3.7 1.9 - - - +
128C CYS* 2.9 35.5 + - - -
135C VAL* 3.9 28.5 - - + -
156C PHE* 4.0 22.2 - - + -
213C HIS 4.5 0.4 - - - +
215C ALA* 3.9 26.2 - - + -
216C VAL 4.4 1.6 - - - +
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Residues in contact with LYS 125 (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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121C PHE* 2.9 51.7 + - + +
122C SER* 3.7 9.6 - - - +
123C LYS 3.3 0.2 - - - -
124C VAL* 1.3 78.0 - - - +
126C ALA* 1.3 56.5 + - - +
128C CYS* 4.1 0.7 - - - +
129C SER* 3.0 30.0 + - - -
135C VAL* 3.9 15.0 - - + -
162C GLU* 6.0 0.4 + - - -
171C VAL* 4.3 27.2 + - - +
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Residues in contact with ALA 126 (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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122C SER 3.1 14.8 + - - +
123C LYS* 3.8 7.2 - - - +
124C VAL 3.3 0.2 - - - -
125C LYS* 1.3 79.4 - - - +
127C LEU* 1.3 58.0 + - - +
129C SER* 3.3 6.8 + - - -
130C GLU* 3.0 40.0 + - + +
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Residues in contact with LEU 127 (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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101B PHE* 3.4 39.9 - - + -
107B SER* 4.6 11.4 - - - +
115C ASN* 4.7 2.7 - - - +
119C MET* 4.0 27.1 - - + -
123C LYS 2.9 18.4 + - - +
124C VAL* 3.7 3.8 - - - +
125C LYS 3.3 0.2 - - - -
126C ALA* 1.3 77.0 - - - +
128C CYS* 1.3 62.6 + - - +
130C GLU* 3.2 26.2 + - - +
131C LEU* 3.2 28.9 + - + +
215C ALA* 4.5 4.7 - - + -
217C CYS* 4.8 1.6 - - - -
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Residues in contact with CYS 128 (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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124C VAL* 2.9 35.9 + - - +
125C LYS 4.3 2.0 - - - +
127C LEU* 1.3 78.0 - - - +
129C SER* 1.3 59.8 + - - +
131C LEU* 3.3 3.9 + - - +
132C ARG 3.2 3.6 + - - -
133C GLY 2.8 29.1 + - - -
134C THR* 3.7 26.5 - - - +
135C VAL* 4.0 2.9 - - + +
216C VAL 4.0 1.1 - - - -
217C CYS* 2.0 59.5 - - + -
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Residues in contact with SER 129 (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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125C LYS 3.0 19.9 + - - -
126C ALA* 3.4 9.0 - - - -
127C LEU 3.1 0.2 - - - -
128C CYS* 1.3 74.9 - - - +
130C GLU* 1.3 65.3 + - - +
132C ARG* 2.9 33.7 + - - +
133C GLY 4.0 7.4 + - - -
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Residues in contact with GLU 130 (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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94B LEU* 4.2 8.3 - - - +
97B LYS* 3.7 32.8 + - + +
126C ALA* 3.0 25.1 + - + +
127C LEU* 3.5 21.1 - - + +
129C SER* 1.3 76.1 - - - +
131C LEU* 1.3 63.0 + - + +
132C ARG* 3.2 16.8 + - - +
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Residues in contact with LEU 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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94B LEU* 3.5 17.9 - - + +
97B LYS* 3.7 20.4 - - + +
98B LEU* 3.7 38.4 - - + +
101B PHE* 3.7 42.4 - - + -
127C LEU* 3.2 21.1 + - + +
128C CYS 3.8 7.2 - - - +
129C SER 3.2 0.8 - - - -
130C GLU* 1.3 76.9 - - + +
132C ARG* 1.3 71.0 + - - +
133C GLY 3.2 0.2 - - - -
217C CYS* 4.4 9.4 - - - -
219C PHE* 3.3 21.7 - - + -
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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