Contacts of the helix formed by residues 168 - 180 (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 168 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119M LEU* 5.1 1.1 - - - -
166M ARG 4.1 1.2 + - - -
167M VAL* 1.3 76.0 - - - +
169M LEU* 1.3 65.8 + - - +
170M GLN* 3.6 14.1 + - - +
171M ASP* 3.0 34.8 + - - +
172M ILE* 3.3 14.4 + - - +
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Residues in contact with LEU 169 (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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54M PHE* 4.4 17.5 - - + -
114M PHE* 3.8 34.1 - - + +
116M PRO* 3.6 44.6 - - + -
119M LEU* 4.2 26.9 - - + +
168M SER* 1.3 73.8 - - - +
170M GLN* 1.3 61.9 + - - +
172M ILE* 3.5 5.9 + - - +
173M LYS* 3.2 27.7 + - - +
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Residues in contact with GLN 170 (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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168M SER* 3.1 11.1 + - - +
169M LEU* 1.3 77.4 - - - +
171M ASP* 1.3 54.0 + - - +
173M LYS* 2.7 34.3 + - - +
174M ASP* 2.5 67.7 + - - +
177M ASP* 5.6 0.2 - - - +
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Residues in contact with ASP 171 (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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43M THR* 5.2 3.7 - - + +
44M LYS* 3.2 40.1 + - + +
47M VAL* 3.9 7.0 - - + -
167M VAL* 3.6 12.3 - - + -
168M SER* 3.0 34.8 + - - +
170M GLN* 1.3 77.6 - - - +
172M ILE* 1.3 57.0 + - - +
174M ASP* 3.8 12.8 - - - +
175M PHE* 2.8 35.2 + - - +
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Residues in contact with ILE 172 (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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47M VAL* 3.7 10.1 - - + -
50M LEU* 3.8 27.8 - - + -
51M LEU* 4.2 21.5 - - - +
54M PHE* 3.6 28.3 - - + -
114M PHE* 3.8 11.4 - - + -
119M LEU* 3.7 30.5 - - + -
167M VAL* 3.9 14.4 - - + +
168M SER 3.3 13.4 + - - +
169M LEU* 3.6 12.3 - - - +
170M GLN 3.3 0.6 - - - -
171M ASP* 1.3 74.9 - - - +
173M LYS* 1.3 57.1 + - - +
175M PHE* 4.1 2.1 - - - +
176M ALA* 3.2 24.3 + - - +
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Residues in contact with LYS 173 (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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113M ALA 5.5 0.8 + - - -
114M PHE* 4.2 44.9 + - + +
169M LEU* 3.2 21.7 + - - +
170M GLN* 2.7 36.5 + - - +
172M ILE* 1.3 76.8 - - - +
174M ASP* 1.3 62.6 + - - +
175M PHE 3.2 0.9 - - - -
176M ALA* 3.1 6.7 + - + +
177M ASP* 3.0 34.4 + - - +
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Residues in contact with ASP 174 (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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43M THR* 6.2 2.0 - - + -
170M GLN* 2.5 55.0 + - - +
171M ASP* 3.8 12.1 - - - +
173M LYS* 1.3 70.9 - - - +
175M PHE* 1.3 59.7 + - - +
177M ASP* 2.9 34.2 + - - +
178M LYS* 3.2 11.9 + - - +
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Residues in contact with PHE 175 (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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37M GLY* 3.8 17.9 - - - -
41M TYR 2.8 28.7 - - - -
42M ALA* 3.7 11.2 - - + -
43M THR* 3.4 28.4 - - + +
47M VAL* 3.6 21.8 - - + -
48M ALA* 4.0 16.6 - - - -
51M LEU* 3.7 23.8 - - + -
87M ILE* 4.5 0.9 - - + -
171M ASP 2.8 17.9 + - - +
172M ILE 4.1 1.6 - - - +
174M ASP* 1.3 79.0 - - - +
176M ALA* 1.3 60.6 + - - +
178M LYS* 3.3 14.9 + - + +
179M VAL* 3.3 47.5 + - + +
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Residues in contact with ALA 176 (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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51M LEU* 3.9 28.5 - - + -
114M PHE* 4.0 16.8 - - + -
172M ILE 3.2 19.8 + - - +
173M LYS* 3.1 7.9 + - + +
175M PHE* 1.3 78.5 - - - +
177M ASP* 1.3 59.0 + - - +
179M VAL 4.8 0.2 - - - +
180M TYR* 3.1 42.0 + - + +
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Residues in contact with ASP 177 (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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173M LYS* 3.0 25.6 + - - +
174M ASP* 2.9 21.4 + - - +
176M ALA* 1.3 80.4 - - - +
178M LYS* 1.3 60.0 + - + +
180M TYR 4.1 3.2 + - - +
181M THR* 3.3 19.4 - - - +
210M PRO* 6.0 0.3 - - - +
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Residues in contact with LYS 178 (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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41M TYR 5.7 2.4 + - - -
43M THR* 5.3 14.3 - - + -
174M ASP 3.2 10.7 + - - +
175M PHE* 3.7 19.7 - - + +
176M ALA 3.3 0.2 - - - -
177M ASP* 1.3 80.9 - - + +
179M VAL* 1.3 67.0 + - + +
181M THR* 3.4 18.6 + - - +
184M ASN* 4.8 3.6 - - - +
213M LYS 5.2 3.1 - - - +
215M LEU* 4.1 28.4 - - + +
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Residues in contact with VAL 179 (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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35M VAL* 3.1 33.6 - - + +
36M HIS 3.4 18.6 - - - +
37M GLY* 3.5 14.8 - - - -
41M TYR* 5.0 2.2 - - + +
51M LEU* 5.1 1.1 - - + -
87M ILE* 5.0 2.9 - - + -
175M PHE* 3.3 50.0 + - + +
176M ALA 4.7 0.4 - - - +
178M LYS* 1.3 78.9 - - + +
180M TYR* 1.3 69.3 + - + +
181M THR 2.9 9.6 + - - -
184M ASN* 3.2 14.5 + - - +
215M LEU* 5.8 5.8 - - + -
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Residues in contact with TYR 180 (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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35M VAL* 3.9 21.8 - - + -
51M LEU* 3.3 39.5 - - + +
55M ASN* 2.9 37.8 + - - -
87M ILE* 4.2 9.5 - - + +
89M LEU* 4.9 1.1 - - + -
108M VAL 4.9 3.1 - - - -
109M LEU* 3.2 58.8 - - + +
112M THR* 5.1 4.5 - - - -
114M PHE* 6.1 0.2 - + - -
176M ALA* 3.1 26.7 + - + +
177M ASP* 4.1 3.6 - - - +
178M LYS 3.6 0.2 - - - -
179M VAL* 1.3 81.8 - - + +
181M THR* 1.3 62.8 + - - +
185M LEU* 4.6 5.8 - - + -
209M LEU* 4.0 16.1 - - - +
210M PRO* 4.4 3.6 - - - +
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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