Contacts of the helix formed by residues 27 - 34 (chain P) in PDB entry 1YIT
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 ARG 27 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24P ASN* 2.9 28.7 + - + +
26P GLU* 1.3 86.4 - - + +
28P GLN* 1.3 64.7 + - - +
29P GLY 3.3 2.2 - - - +
30P ASP* 3.0 42.9 + - + +
31P ILE* 2.9 24.5 + - + +
43P LEU* 3.9 10.2 - - - +
46P GLU* 2.7 37.6 + - - +
48P ALA* 3.8 27.6 - - + +
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Residues in contact with GLN 28 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13860 G 3.4 28.7 + - - +
13870 G 3.4 34.6 + - - +
13960 C 4.4 2.1 + - - +
13970 C 3.6 29.8 + - - +
1P THR* 3.8 14.8 + - - +
3P LEU* 3.9 23.5 - - + +
23P PHE* 6.3 0.2 - - + -
24P ASN 3.7 2.2 + - - +
25P PRO* 3.4 24.9 + - + +
26P GLU 3.7 1.8 - - - -
27P ARG* 1.3 74.8 - - - +
29P GLY* 1.3 54.9 + - - +
31P ILE* 3.0 4.2 + - + +
32P ALA* 2.6 38.1 + - - +
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Residues in contact with GLY 29 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13870 G 5.8 0.2 + - - -
1P THR* 5.1 5.6 - - - +
26P GLU 5.4 0.2 + - - -
27P ARG 3.3 0.8 - - - -
28P GLN* 1.3 78.5 - - - +
30P ASP* 1.3 62.3 + - - +
32P ALA* 3.1 21.0 - - - +
33P ASP* 3.1 17.8 + - - +
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Residues in contact with ASP 30 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26P GLU 5.4 0.3 - - - +
27P ARG* 3.0 54.0 + - + +
28P GLN 3.2 0.6 - - - -
29P GLY* 1.3 73.8 - - - +
31P ILE* 1.3 64.6 + - - +
33P ASP* 3.0 22.6 + - - +
34P ALA 3.2 8.1 + - - -
43P LEU* 4.0 11.8 - - + +
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Residues in contact with ILE 31 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3P LEU* 3.8 10.8 - - + -
6P GLN* 3.3 14.4 - - + +
23P PHE* 3.7 61.9 - - + -
24P ASN 4.2 7.9 - - - +
27P ARG* 2.9 31.8 + - + +
28P GLN* 3.5 5.8 - - - +
30P ASP* 1.3 76.1 - - - +
32P ALA* 1.3 64.6 + - - +
34P ALA* 2.9 18.4 + - - +
43P LEU* 3.8 19.1 - - + -
48P ALA* 4.3 6.7 - - + +
49P ILE* 4.3 18.2 - - + -
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Residues in contact with ALA 32 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1P THR* 4.0 23.6 - - + -
2P ASP 5.8 0.4 - - - +
3P LEU* 3.2 19.3 - - + +
6P GLN* 3.6 13.0 + - - -
28P GLN 2.6 16.7 + - - +
29P GLY* 3.1 13.2 - - - +
30P ASP 3.1 0.2 - - - -
31P ILE* 1.3 74.3 - - - +
33P ASP* 1.3 65.0 + - - +
34P ALA 3.2 1.2 + - - +
35P ILE* 5.1 3.8 - - - +
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Residues in contact with ASP 33 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29P GLY 3.1 16.6 - - - +
30P ASP* 3.0 14.6 + - - +
32P ALA* 1.3 75.5 - - - +
34P ALA* 1.3 64.9 + - - +
35P ILE* 3.0 16.5 + - - +
39P ASP* 4.7 1.7 - - - +
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Residues in contact with ALA 34 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6P GLN* 2.5 42.5 + - + +
9P LEU* 5.7 0.3 - - - +
30P ASP 3.2 4.6 + - - -
31P ILE* 2.9 15.7 + - + +
32P ALA 3.7 0.3 - - - +
33P ASP* 1.3 72.8 - - - +
35P ILE* 1.3 58.9 + - - +
36P THR 3.9 0.4 - - - -
39P ASP* 3.8 20.2 - - + -
40P VAL* 4.7 8.5 - - + +
43P LEU* 3.6 26.5 - - + -
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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