Contacts of the helix formed by residues 129 - 145 (chain N) in PDB entry 1K2V
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 129 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125N SER* 3.7 3.1 - - - -
126N ASP* 2.9 20.7 + - - +
128N LYS* 1.3 102.9 + - + +
130N PRO* 1.3 66.3 - - - +
131N LEU 3.3 1.6 - - - +
132N ALA* 3.2 29.2 + - + +
133N MET* 3.3 10.6 + - - +
199N GLU* 4.1 19.9 + - + +
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Residues in contact with PRO 130 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124N PHE* 3.3 52.0 - - + +
125N SER* 3.4 11.2 - - - +
128N LYS 3.4 6.1 - - - +
129N GLN* 1.3 83.5 - - - +
131N LEU* 1.3 52.1 + - - +
133N MET* 3.1 5.7 + - - +
134N ALA* 2.8 32.4 + - - +
194N ASN 3.1 29.2 - - - +
195N SER 3.8 13.7 - - - +
196N LEU* 3.9 12.6 - - + -
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Residues in contact with LEU 131 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129N GLN 3.3 0.8 - - - -
130N PRO* 1.3 77.1 - - - +
132N ALA* 1.3 66.3 + - - +
134N ALA* 3.2 10.3 + - + +
135N ARG* 3.1 31.0 + - - +
158N TYR* 3.1 27.1 - - + +
196N LEU* 3.6 37.4 + - + +
199N GLU* 3.4 45.1 - - + +
200N ILE* 3.8 14.1 - - + -
277N ALA 4.2 6.5 - - - +
278N THR* 4.6 2.7 - - + -
281N ALA* 3.7 18.2 - - + -
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Residues in contact with ALA 132 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126N ASP* 6.3 0.7 - - - -
129N GLN* 3.2 32.5 + - + +
131N LEU* 1.3 78.8 - - - +
133N MET* 1.3 63.7 + - - +
135N ARG* 3.3 29.2 + - - +
136N LYS* 3.3 11.3 + - - +
199N GLU* 4.1 2.9 + - - +
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Residues in contact with MET 133 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123N ASN* 3.2 48.0 - - + +
124N PHE 3.6 12.1 - - - +
125N SER* 3.7 27.8 - - - +
126N ASP* 4.1 13.7 - - + +
129N GLN 3.3 4.1 + - - +
130N PRO 3.1 8.8 + - - +
132N ALA* 1.3 78.1 - - - +
134N ALA* 1.3 55.1 + - - +
136N LYS* 2.9 15.3 + - - +
137N SER* 2.7 41.0 + - - +
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Residues in contact with ALA 134 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44N LEU* 5.8 2.2 - - + -
48N LEU* 4.3 2.6 - - - +
123N ASN 5.6 0.7 - - - -
124N PHE 4.6 1.5 + - - +
130N PRO 2.8 17.7 + - - +
131N LEU* 3.2 14.1 + - + +
133N MET* 1.3 73.8 - - - +
135N ARG* 1.3 57.0 - - - +
137N SER* 3.2 7.8 + - - -
138N LEU* 2.9 30.7 + - - +
196N LEU* 5.4 0.2 - - + -
276N GLY 4.9 1.1 - - - +
277N ALA* 3.6 36.1 - - + +
278N THR* 4.0 12.5 - - + +
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Residues in contact with ARG 135 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131N LEU* 3.1 10.2 + - - +
132N ALA* 3.3 38.2 - - - +
134N ALA* 1.3 77.0 - - - +
136N LYS* 1.3 60.6 + - - +
138N LEU* 3.5 3.3 + - - +
139N THR* 2.9 28.3 + - - -
155N LEU* 3.8 30.7 - - + +
158N TYR* 4.0 23.8 - - - -
159N GLU* 6.2 1.2 - - - +
199N GLU* 2.5 33.9 + - - -
278N THR* 4.7 8.5 - - + +
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Residues in contact with LYS 136 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132N ALA 3.3 8.3 + - - +
133N MET* 2.9 22.2 + - - +
135N ARG* 1.3 77.3 - - - +
137N SER* 1.3 59.1 + - - +
139N THR* 3.2 8.2 + - - -
140N GLU* 2.8 31.9 + - - +
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Residues in contact with SER 137 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44N LEU* 5.7 2.0 - - - -
48N LEU* 3.7 24.7 - - - -
122N PHE* 3.6 12.1 - - - +
123N ASN 3.2 24.4 + - - -
133N MET* 2.7 26.4 + - - +
134N ALA* 3.5 8.0 - - - -
136N LYS* 1.3 73.2 - - - +
138N LEU* 1.3 56.2 + - - +
140N GLU* 3.2 14.1 + - - +
141N MET* 2.8 30.5 + - - +
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Residues in contact with LEU 138 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48N LEU* 3.7 37.6 - - + +
51N ALA* 3.8 13.9 - - + -
52N LEU* 3.7 20.4 - - + +
134N ALA 2.9 17.3 + - - +
135N ARG* 3.8 5.6 - - - +
137N SER* 1.3 75.4 - - - +
139N THR* 1.3 52.3 + - - +
141N MET* 3.2 3.8 + - - +
142N ALA* 2.8 35.7 + - - +
151N ALA* 3.8 13.0 - - + +
154N HIS* 3.3 30.7 - - + +
155N LEU* 3.7 24.7 - - + -
278N THR* 4.9 4.7 - - + +
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Residues in contact with THR 139 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135N ARG 2.9 13.7 + - - -
136N LYS* 3.2 11.7 + - - -
138N LEU* 1.3 78.5 - - - +
140N GLU* 1.3 58.0 + - - +
142N ALA* 3.2 8.2 + - + +
143N ASP* 2.9 30.3 + - + +
148N GLN* 5.9 0.3 - - - +
151N ALA* 4.7 6.0 - - + +
155N LEU* 4.0 15.1 - - - +
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Residues in contact with GLU 140 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120N ARG* 2.8 45.6 + - - +
121N GLY 4.2 3.3 - - - +
122N PHE* 3.5 25.1 - - + -
123N ASN* 5.5 5.0 + - - -
136N LYS 2.8 12.3 + - - +
137N SER* 3.4 13.1 + - - +
139N THR* 1.3 74.8 - - - +
141N MET* 1.3 66.2 + - - +
143N ASP* 3.1 8.4 + - - +
144N LEU* 3.1 22.5 + - - +
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Residues in contact with MET 141 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38N ILE* 6.0 0.2 - - - -
45N PRO* 4.1 4.5 - - + +
48N LEU* 3.9 24.5 - - + -
49N LEU* 3.6 34.8 - - + -
52N LEU* 3.5 19.5 - - + -
99N PHE* 5.7 1.1 - - - -
101N VAL* 3.8 17.0 - - + -
122N PHE* 3.4 41.2 - - + -
137N SER 2.8 19.9 + - - +
138N LEU* 3.5 7.0 - - - +
140N GLU* 1.3 72.1 - - - +
142N ALA* 1.3 63.9 + - - +
144N LEU* 3.2 9.5 + - - +
145N LEU* 3.1 32.2 + - + +
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Residues in contact with ALA 142 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52N LEU* 3.6 11.8 - - + +
138N LEU 2.8 21.4 + - - +
139N THR* 3.4 5.6 - - - +
141N MET* 1.3 74.0 - - - +
143N ASP* 1.3 55.8 + - - +
145N LEU 3.2 0.9 + - - +
146N ASN* 2.7 25.3 + - - -
147N LEU* 2.7 28.5 + - - +
148N GLN* 4.0 5.6 - - + +
151N ALA* 3.4 28.5 - - + -
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Residues in contact with ASP 143 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139N THR* 2.9 15.1 + - + +
140N GLU* 3.1 10.3 + - - +
142N ALA* 1.3 76.5 - - - +
144N LEU* 1.3 64.1 + - - +
146N ASN* 3.1 19.1 + - - +
148N GLN* 3.1 26.3 - - + +
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Residues in contact with LEU 144 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32N ALA 4.3 18.9 + - - +
33N ILE* 5.4 0.7 + - - -
99N PHE* 3.9 32.5 - - + -
120N ARG* 3.4 51.6 - - + +
122N PHE* 4.1 13.5 - - + -
140N GLU 3.1 12.1 + - - +
141N MET* 3.5 10.8 - - - +
143N ASP* 1.3 78.9 - - - +
145N LEU* 1.3 70.2 + - + +
146N ASN* 3.7 5.9 + - - -
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Residues in contact with LEU 145 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32N ALA* 3.7 27.1 - - - +
33N ILE 5.1 2.9 - - - +
35N PRO* 5.3 7.9 - - + +
38N ILE* 4.4 13.7 - - + -
49N LEU* 4.0 19.7 - - + -
52N LEU* 4.9 0.9 - - + -
54N ILE* 3.9 31.0 - - + -
99N PHE* 5.6 3.1 - - + -
141N MET* 3.1 26.3 + - + +
144N LEU* 1.3 87.7 - - + +
146N ASN* 1.3 72.7 + - - +
147N LEU* 3.2 24.1 + - + +
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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