Contacts of the helix formed by residues 141 - 150 (chain M) in PDB entry 1KYO
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 SER 141 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134M ALA 3.9 11.1 + - - -
135M GLU* 4.1 13.5 + - - -
137M CYS 3.4 7.7 + - - -
138M PRO* 3.8 17.1 - - - +
139M VAL 3.2 0.4 - - - -
140M LYS* 1.3 77.3 - - - +
142M ALA* 1.3 60.7 + - - +
144M ASP* 4.1 5.2 - - - +
145M GLN* 3.2 28.2 + - - +
231M VAL* 5.2 3.7 - - - +
233M PHE* 4.8 5.4 - - - -
356M VAL* 4.4 14.4 - - - +
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Residues in contact with ALA 142 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138M PRO 3.1 17.7 + - - +
139M VAL* 3.5 8.5 - - - +
141M SER* 1.3 77.0 - - - +
143M GLU* 1.3 59.0 + - - +
144M ASP 3.1 1.6 - - - -
145M GLN* 3.1 4.6 + - - +
146M LEU* 2.9 29.6 + - - +
238M VAL* 4.3 7.4 - - + -
240M ALA* 4.4 4.9 - - + -
288M PHE* 4.4 11.9 - - + -
354M VAL* 3.7 17.6 - - + +
356M VAL* 4.1 16.6 - - + -
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Residues in contact with GLU 143 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84M ARG* 3.2 20.9 + - - +
139M VAL 2.8 18.3 + - - +
140M LYS* 4.3 17.7 - - - +
142M ALA* 1.3 76.6 - - - +
144M ASP* 1.3 60.1 + - - +
146M LEU* 3.6 7.1 + - - +
147M TYR* 3.1 36.9 + - + -
275M LYS* 3.2 32.5 + - - +
277M ASP* 5.0 1.4 - - - +
286M THR* 5.1 3.4 - - + -
288M PHE* 4.0 18.8 - - + -
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Residues in contact with ASP 144 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84M ARG* 3.1 27.3 + - - +
140M LYS 3.4 21.1 + - - +
141M SER* 4.4 4.9 - - - +
142M ALA 3.1 0.6 - - - -
143M GLU* 1.3 76.5 - - - +
145M GLN* 1.3 71.4 + - - +
146M LEU 3.1 1.0 + - - -
147M TYR* 3.4 4.9 + - - +
148M ALA* 3.2 20.8 + - - +
156M GLY 5.4 0.2 - - - +
158M PRO* 3.7 23.8 - - - +
159M LEU* 3.8 13.9 + - - +
160M LEU 5.3 0.9 + - - -
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Residues in contact with GLN 145 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B ARG 4.7 5.5 + - - +
232B ARG* 4.9 18.4 - - - +
141M SER 3.2 19.6 + - - +
142M ALA* 3.1 7.1 + - - +
144M ASP* 1.3 80.5 + - - +
146M LEU* 1.3 60.1 - - - +
148M ALA* 3.4 14.4 - - - +
149M ILE* 3.2 28.3 + - - +
229M ASN* 3.4 30.5 + - - +
231M VAL* 3.9 22.7 - - + -
354M VAL* 4.0 15.9 - - + -
356M VAL* 5.5 0.4 - - + -
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Residues in contact with LEU 146 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142M ALA 2.9 15.3 + - - +
143M GLU* 3.6 12.6 - - - +
144M ASP 3.1 0.4 - - - -
145M GLN* 1.3 72.9 - - - +
147M TYR* 1.3 66.7 + - - +
148M ALA 3.0 1.1 - - - -
149M ILE* 2.8 23.9 + - + +
150M THR* 2.8 19.8 + - + +
240M ALA* 4.4 3.4 - - + +
241M ILE 3.9 12.6 - - - +
242M GLY* 4.1 19.7 - - - +
284M LEU* 4.5 7.4 - - + -
286M THR* 3.4 27.8 - - + -
288M PHE* 4.4 8.1 - - + -
352M ASN* 4.3 4.9 - - + +
354M VAL* 3.2 40.8 - - + +
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Residues in contact with TYR 147 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84M ARG* 3.4 44.4 + - + +
143M GLU* 3.1 30.8 + - + -
144M ASP 3.4 6.2 + - - +
146M LEU* 1.3 77.9 - - - +
148M ALA* 1.3 61.5 + - - +
150M THR* 4.5 3.6 - - - -
151M PHE* 3.2 26.7 + + - -
152M ARG 3.5 0.2 + - - -
155M LEU* 3.5 39.7 - - + +
156M GLY* 3.1 15.5 - - - -
277M ASP* 2.8 42.0 + - - +
279M PHE* 3.8 15.3 - + - -
284M LEU* 3.5 25.1 - - + -
286M THR* 5.4 0.4 - - + -
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Residues in contact with ALA 148 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364B TYR* 4.3 6.4 + - - -
144M ASP 3.2 11.6 + - - +
145M GLN* 3.4 24.5 - - - +
146M LEU 3.0 0.2 - - - -
147M TYR* 1.3 80.1 - - - +
149M ILE* 1.3 61.0 + - + +
152M ARG* 3.1 28.5 - - - +
156M GLY* 3.7 19.0 + - - +
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Residues in contact with ILE 149 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B ARG* 6.1 5.2 - - - -
364B TYR* 6.2 1.6 - - + -
145M GLN* 3.3 11.0 - - - +
146M LEU* 2.8 25.7 + - + +
148M ALA* 1.3 76.7 - - + +
150M THR* 1.3 67.8 + - + +
152M ARG* 4.0 9.7 + - - +
224M PHE* 3.9 4.2 - - - +
227M GLU* 3.6 56.7 - - + +
228M GLU* 4.3 5.6 - - - +
229M ASN* 4.2 25.1 - - + +
352M ASN* 4.0 10.1 - - + -
353M TYR 4.3 1.3 - - - +
354M VAL* 3.6 26.9 - - + -
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Residues in contact with THR 150 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146M LEU* 2.8 28.5 + - + +
147M TYR 4.3 0.2 + - - -
149M ILE* 1.3 76.5 - - + +
151M PHE* 1.3 88.2 + - - +
152M ARG 3.1 5.5 + - - -
223M PHE 2.6 27.9 - - - +
224M PHE* 3.4 9.4 - - - +
242M GLY 5.0 1.6 - - - +
244M PRO* 4.1 7.0 - - - -
284M LEU* 3.6 24.0 - - + +
352M ASN* 3.1 37.9 - - + +
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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