Contacts of the helix formed by residues 46 - 55 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B ALA* 4.9 3.8 - - - +
44B LYS 2.7 5.9 + - - -
45B ASP* 1.3 72.6 - - - +
47B VAL* 1.3 63.4 + - - +
48B ALA* 3.1 4.7 - - - -
49B HIS* 2.8 18.2 + - - +
50B LEU* 3.0 13.5 + - - +
158B PRO 4.4 12.4 + - - -
159B LEU 4.9 0.9 - - - -
160B LEU 4.3 4.9 - - - -
161B TYR* 4.1 25.9 - - - +
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Residues in contact with VAL 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ALA* 5.2 0.2 - - + -
43B THR* 4.0 6.3 - - + +
44B LYS* 2.9 45.6 + - + +
45B ASP 3.7 0.4 - - - -
46B GLY* 1.3 73.2 - - - +
48B ALA* 1.3 52.6 + - - +
50B LEU* 3.3 6.8 + - - +
51B LEU* 2.8 33.5 + - - +
167B VAL* 3.9 19.2 - - + +
171B ASP* 3.7 13.9 - - + +
172B ILE* 3.9 14.6 - - + -
175B PHE* 3.6 34.8 - - + -
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Residues in contact with ALA 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B GLY 3.5 26.0 - - - +
38B GLY 3.9 1.8 - - - +
39B SER* 3.9 21.1 - - - +
42B ALA* 4.3 9.4 - - + +
46B GLY* 3.1 1.3 - - - -
47B VAL* 1.3 75.9 - - - +
49B HIS* 1.3 68.9 + - - +
51B LEU* 3.2 1.6 + - - +
52B ASN* 2.9 22.7 + - - +
82B LEU* 3.7 16.8 - - + +
87B ILE* 3.9 2.4 - - - +
159B LEU 5.1 0.7 - - - +
175B PHE* 4.2 9.5 - - + -
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Residues in contact with HIS 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B GLY 2.8 12.1 + - - +
48B ALA* 1.3 82.4 - - - +
50B LEU* 1.3 56.4 + - - +
52B ASN* 3.0 6.0 + - - +
53B ARG* 2.9 28.3 + - - +
82B LEU* 3.7 13.5 - - - +
127B ALA* 3.4 32.3 + - + -
130B ASP* 3.1 34.9 - - + +
131B TYR 4.5 0.2 + - - -
159B LEU 3.8 10.7 + - - +
160B LEU* 3.5 23.7 - - + +
161B TYR* 2.7 43.1 - - + +
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Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B GLY 3.0 8.5 + - - +
47B VAL* 3.6 7.2 - - - +
49B HIS* 1.3 80.9 - - - +
51B LEU* 1.3 56.7 + - - +
53B ARG* 3.4 4.7 + - - -
54B PHE* 2.9 29.9 + - - +
119B LEU* 4.8 1.8 - - + -
123B VAL* 3.7 25.5 - - + +
124B LEU* 4.2 17.5 - - + -
127B ALA* 4.0 20.9 - - + -
161B TYR* 3.8 31.9 - - + -
167B VAL* 3.9 30.1 - - + +
172B ILE* 4.4 19.1 - - + -
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Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B VAL 2.8 20.1 + - - +
48B ALA 3.9 3.1 - - - +
50B LEU* 1.3 70.7 - - - +
52B ASN* 1.3 55.6 + - - +
54B PHE* 3.1 6.2 + - + +
55B ASN* 2.7 38.6 + - - +
87B ILE* 3.9 8.5 - - + -
114B PHE* 4.1 19.3 - - + -
172B ILE* 4.2 10.5 - - + +
175B PHE* 3.6 33.0 - - + +
176B ALA* 3.9 21.8 - - + -
179B VAL* 4.9 3.4 - - + -
180B TYR* 3.5 43.3 - - + +
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Residues in contact with ASN 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ALA 2.9 12.1 + - - +
49B HIS* 3.2 11.5 + - - +
51B LEU* 1.3 76.6 - - - +
53B ARG* 1.3 70.9 + - - +
54B PHE 3.1 0.9 + - - -
55B ASN* 3.2 14.7 + - - +
80B SER* 2.6 68.9 + - - +
81B THR 3.2 11.7 + - - +
82B LEU* 3.6 28.6 + - + +
87B ILE* 3.8 10.5 - - + +
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Residues in contact with ARG 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A PHE 5.2 0.2 + - - -
291A GLU* 2.6 44.0 + - - -
292A PRO* 4.4 7.4 - - - +
49B HIS* 2.9 20.3 + - + +
50B LEU* 3.6 7.2 - - - +
52B ASN* 1.3 84.0 + - - +
54B PHE* 1.3 59.0 + - - +
55B ASN 4.0 4.7 - - - +
57B GLN* 4.3 8.7 + - - -
79B LYS* 4.7 7.1 - - - +
80B SER 5.7 3.2 + - - -
123B VAL* 3.9 25.6 - - + +
126B ALA* 3.5 37.9 + - + +
127B ALA* 4.1 4.0 - - + +
129B TYR* 4.5 2.8 - - - -
130B ASP* 2.8 49.3 + - - -
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Residues in contact with PHE 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LEU 2.9 15.6 + - - +
51B LEU* 3.4 10.3 - - + +
52B ASN 3.1 0.6 - - - -
53B ARG* 1.3 76.6 - - - +
55B ASN* 1.3 66.0 - - - +
57B GLN* 3.0 28.7 + - + +
112B THR* 4.6 5.9 - - - +
114B PHE* 3.6 48.2 - + + -
115B LYS 4.3 2.9 - - - -
118B GLU* 4.3 14.8 - - + -
119B LEU* 3.8 17.0 - - + -
123B VAL* 3.7 26.0 - - + -
169B LEU* 3.6 32.3 - - + -
172B ILE* 3.8 24.9 - - + -
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Residues in contact with ASN 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B LEU* 2.7 25.0 + - - +
52B ASN* 3.2 11.2 + - - +
53B ARG 4.0 6.2 - - - +
54B PHE* 1.3 81.5 - - - +
56B PHE* 1.3 74.3 - - + +
57B GLN* 3.5 1.7 + - - +
80B SER* 3.2 31.2 + - - +
87B ILE* 3.8 3.5 - - - +
89B LEU* 4.2 8.5 - - + +
108B VAL* 4.0 18.8 + - + +
112B THR* 5.0 4.8 + - - +
114B PHE* 6.3 0.4 - - - -
180B TYR* 2.7 36.2 + - - -
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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