Contacts of the helix formed by residues 46 - 55 (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 GLY 46 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42M ALA* 4.9 4.0 - - - +
44M LYS 2.8 3.2 + - - -
45M ASP* 1.3 73.7 - - - +
47M VAL* 1.3 66.3 + - - +
48M ALA* 3.2 3.8 - - - -
49M HIS* 3.0 10.1 + - - +
50M LEU* 3.0 26.1 + - - +
158M PRO 5.1 6.5 + - - -
159M LEU 5.1 3.4 - - - -
160M LEU 4.5 3.1 + - - -
161M TYR* 4.0 23.3 - - - +
167M VAL* 5.0 0.2 - - - -
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Residues in contact with VAL 47 (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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42M ALA* 4.9 0.9 - - + -
43M THR* 4.3 6.7 - - + +
44M LYS* 2.9 47.0 + - + +
45M ASP 3.7 0.4 - - - -
46M GLY* 1.3 74.1 - - - +
48M ALA* 1.3 62.3 + - - +
50M LEU* 3.8 4.4 - - - +
51M LEU* 2.9 24.8 + - - +
167M VAL* 4.3 14.8 - - + +
171M ASP* 3.7 6.3 - - + +
172M ILE* 3.7 25.4 - - + +
175M PHE* 3.6 35.0 - - + -
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Residues in contact with ALA 48 (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 3.5 22.0 - - - +
38M GLY 3.9 17.5 - - - +
39M SER* 3.9 11.7 - - - +
42M ALA* 4.3 10.3 - - + +
46M GLY* 3.2 1.3 - - - -
47M VAL* 1.3 77.5 - - - +
49M HIS* 1.3 67.3 + - - +
51M LEU* 3.4 1.6 + - - +
52M ASN* 3.1 22.0 + - - +
82M LEU* 4.0 11.5 - - + +
87M ILE* 4.0 2.9 - - - +
159M LEU 5.2 1.3 - - - +
175M PHE* 4.0 13.4 - - + -
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Residues in contact with HIS 49 (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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46M GLY* 3.0 11.5 + - - +
48M ALA* 1.3 77.4 - - - +
50M LEU* 1.3 64.5 + - - +
52M ASN* 2.9 17.0 + - - +
53M ARG* 3.0 14.4 + - - +
82M LEU* 3.9 12.7 - - - +
127M ALA* 3.3 34.1 + - + -
130M ASP* 3.2 31.5 - - + +
159M LEU 4.0 10.7 + - - +
160M LEU* 3.6 25.8 - - + +
161M TYR* 2.8 41.7 - - + +
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Residues in contact with LEU 50 (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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46M GLY 3.0 12.6 + - - +
47M VAL 3.9 3.4 - - - +
49M HIS* 1.3 77.6 - - - +
51M LEU* 1.3 56.9 + - - +
53M ARG* 3.3 2.6 + - - -
54M PHE* 2.8 28.9 + - - +
119M LEU* 5.3 0.7 - - + -
123M VAL* 3.6 19.8 - - + +
124M LEU* 4.5 13.0 - - + -
127M ALA* 3.8 26.5 - - + -
161M TYR* 4.0 31.0 - - + -
167M VAL* 3.8 36.1 - - + +
172M ILE* 3.8 25.6 - - + -
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Residues in contact with LEU 51 (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 2.9 18.7 + - - +
48M ALA 3.7 4.3 - - - +
50M LEU* 1.3 75.9 - - - +
52M ASN* 1.3 64.1 + - - +
54M PHE* 2.9 15.0 + - + +
55M ASN* 3.1 15.6 + - - +
87M ILE* 4.2 8.7 - - + -
114M PHE* 4.0 20.0 - - + -
172M ILE* 4.2 9.7 - - + +
175M PHE* 3.7 30.1 - - + +
176M ALA* 3.9 24.7 - - + -
179M VAL* 5.1 2.0 - - + -
180M TYR* 3.3 42.4 - - + +
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Residues in contact with ASN 52 (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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48M ALA 3.1 11.5 + - - +
49M HIS* 2.9 12.0 + - - +
51M LEU* 1.3 75.5 - - - +
53M ARG* 1.3 63.6 + - - +
55M ASN* 3.2 16.4 + - - +
80M SER* 2.4 70.5 + - - +
81M THR 3.5 14.0 + - - -
82M LEU* 3.4 28.1 + - + +
87M ILE* 3.9 13.8 - - + +
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Residues in contact with ARG 53 (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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291L GLU* 2.8 40.8 + - - -
292L PRO* 4.4 10.5 - - + +
49M HIS* 3.0 13.1 + - - +
50M LEU* 3.6 9.9 - - - +
52M ASN* 1.3 77.5 - - - +
54M PHE* 1.3 59.7 + - - +
55M ASN 3.4 5.5 + - - +
57M GLN* 4.3 9.0 + - - +
79M LYS* 5.9 1.2 - - - +
80M SER 5.8 1.6 + - - -
123M VAL* 3.8 23.8 - - + +
126M ALA* 3.6 32.6 + - + +
127M ALA* 3.8 15.5 - - + +
129M TYR* 4.9 1.2 - - - -
130M ASP* 2.9 42.8 + - - -
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Residues in contact with PHE 54 (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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50M LEU 2.8 14.6 + - - +
51M LEU* 2.9 13.2 + - + +
53M ARG* 1.3 75.6 - - - +
55M ASN* 1.3 64.9 + - - +
56M PHE 3.7 0.2 + - - -
57M GLN* 3.1 19.8 + - + +
112M THR* 4.6 7.6 - - + +
114M PHE* 3.7 53.4 - + + -
115M LYS 4.2 12.3 - - - -
118M GLU* 4.3 15.5 - - + -
119M LEU* 4.1 24.9 - - + -
123M VAL* 3.6 28.5 - - + -
169M LEU* 4.4 6.5 - - + -
172M ILE* 3.6 24.9 - - + -
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Residues in contact with ASN 55 (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* 3.1 17.3 + - - +
52M ASN 3.2 11.1 + - - +
53M ARG 3.9 6.6 - - - +
54M PHE* 1.3 82.8 - - - +
56M PHE* 1.3 80.1 - - + +
57M GLN* 3.3 2.8 + - - +
80M SER* 3.3 21.3 + - - +
87M ILE* 4.1 4.5 - - - +
89M LEU* 3.8 15.5 - - - +
108M VAL* 3.6 22.0 - - + +
112M THR* 4.9 4.6 - - - +
114M PHE* 5.9 0.8 - - - -
180M TYR* 2.9 34.9 + - - -
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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