Contacts of the helix formed by residues 47 - 57 (chain A) in PDB entry 1YDY
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 THR 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A PRO* 2.9 29.7 + - + +
45A GLU 2.9 7.1 + - - +
46A HIS* 1.3 78.8 - - - +
48A LEU* 1.3 66.3 + - - +
49A PRO* 3.6 11.7 - - - +
50A ALA* 3.0 15.4 + - - +
51A LYS* 2.8 18.7 + - - +
117A PHE* 3.6 29.6 - - + -
143A PHE* 3.9 22.5 - - + -
144A ARG 4.1 13.0 - - - +
146A HIS* 4.2 7.2 - - - -
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Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A THR* 1.3 72.5 - - - +
49A PRO* 1.3 66.2 - - + +
51A LYS* 3.1 5.0 + - + +
52A ALA* 2.7 30.3 + - - +
144A ARG 5.3 0.6 + - - -
146A HIS* 3.4 47.1 + - + +
150A GLU 5.0 1.1 - - - +
151A GLU* 4.5 7.4 - - + -
154A PHE* 3.6 36.7 - - + -
49B PRO* 3.7 17.5 - - + -
141B SER* 3.8 16.2 - - - +
142B ASP* 3.6 25.8 - - + +
143B PHE* 5.2 0.9 - - + -
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Residues in contact with PRO 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 3.4 10.3 - - + +
47A THR* 3.5 14.1 - - - +
48A LEU* 1.3 92.6 - - + +
50A ALA* 1.3 57.2 + - - +
52A ALA 3.2 0.5 + - - -
53A MET 2.9 24.8 + - - -
143A PHE* 4.1 15.5 - - + -
48B LEU* 3.8 26.0 - - + +
49B PRO* 3.9 12.3 - - + -
52B ALA* 3.3 18.1 - - + +
154B PHE* 3.9 22.2 - - + -
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ARG 4.2 8.7 - - - +
39A ALA* 3.1 33.1 + - - +
43A LEU* 3.7 25.2 - - + +
44A PRO 3.3 26.0 - - - +
47A THR* 3.0 12.7 + - - +
49A PRO* 1.3 78.1 - - - +
51A LYS* 1.3 61.9 + - - +
53A MET* 3.5 1.2 + - - -
54A ALA 3.1 12.3 + - - -
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Residues in contact with LYS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ARG 3.5 6.1 - - - -
38A GLY* 3.3 26.9 - - - +
46A HIS* 3.0 33.4 + - - +
47A THR 2.8 17.2 + - - +
48A LEU* 3.1 9.8 + - + +
50A ALA* 1.3 75.0 - - - +
52A ALA* 1.3 66.2 + - - +
54A ALA* 3.2 3.6 + - - +
55A TYR* 2.9 24.6 + - - +
62A LEU* 3.8 23.1 - - + +
63A GLU 3.1 18.0 + - - +
151A GLU* 2.8 41.9 + - - +
154A PHE* 3.8 18.6 - - + -
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Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU 2.7 20.9 + - - +
49A PRO 3.5 5.2 - - - +
51A LYS* 1.3 71.1 - - - +
53A MET* 1.3 60.1 + - - +
55A TYR* 3.3 6.2 + - - +
56A ALA* 2.9 30.2 + - - +
154A PHE* 3.7 19.6 - - + -
43B LEU* 3.8 8.5 - - + -
49B PRO* 3.3 29.6 - - + +
52B ALA* 4.1 1.8 - - + -
53B MET* 3.8 8.9 - - + +
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Residues in contact with MET 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ALA* 3.7 7.4 - - + -
42A TYR* 3.8 30.7 - - - -
43A LEU* 4.1 11.9 - - + -
49A PRO 2.9 16.5 + - - +
50A ALA 3.8 4.3 - - - +
52A ALA* 1.3 78.4 - - - +
54A ALA* 1.3 57.4 + - - +
56A ALA* 3.2 2.1 + - - +
57A GLN* 2.9 58.1 + - - +
52B ALA* 3.7 22.0 - - + +
55B TYR* 4.0 11.7 - - + -
56B ALA* 3.9 24.2 - - + +
158B LEU* 3.9 22.2 - - + -
162B THR* 5.0 3.1 - - + -
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Residues in contact with ALA 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ALA* 3.4 32.5 - - + -
38A GLY* 3.9 4.0 - - - -
39A ALA* 3.7 13.8 - - - +
50A ALA 3.1 14.2 + - - +
51A LYS 3.2 7.6 + - - +
53A MET* 1.3 76.0 - - - +
55A TYR* 1.3 64.5 + - - +
57A GLN* 3.2 11.5 + - - +
58A GLY 3.4 0.2 + - - -
59A ALA* 3.2 21.8 + - - +
62A LEU* 4.0 6.5 - - + -
348A PRO* 4.0 7.9 - - + -
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Residues in contact with TYR 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LYS 2.9 17.1 + - - +
52A ALA 3.5 4.3 - - - +
54A ALA* 1.3 77.7 - - - +
56A ALA* 1.3 63.9 + - - +
58A GLY* 3.2 13.5 + - - -
59A ALA* 4.3 4.6 + - - +
62A LEU* 4.2 15.5 - - + +
155A VAL* 4.2 8.1 - - + -
158A LEU* 3.5 35.7 - - + -
159A ASN* 2.6 35.9 + - - -
162A THR* 3.0 36.0 + - + -
164A LYS* 3.6 25.2 - - - +
166A ILE* 3.3 31.7 - - + +
53B MET* 4.1 11.9 - - + -
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ALA 2.9 16.9 + - - +
53A MET 3.7 0.2 - - - +
55A TYR* 1.3 78.5 - - - +
57A GLN* 1.3 61.5 + - - +
58A GLY* 3.2 1.4 + - - -
53B MET* 4.0 26.4 - - + +
56B ALA* 3.7 26.9 - - + +
57B GLN* 4.1 17.3 - - + +
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Residues in contact with GLN 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ALA* 3.8 6.2 - - - +
42A TYR* 3.6 12.6 - - - -
53A MET* 2.9 41.0 + - - +
54A ALA 3.2 4.9 + - - +
56A ALA* 1.3 76.0 - - - +
58A GLY* 1.3 58.5 + - - +
59A ALA 3.6 0.7 - - - -
348A PRO* 3.5 19.2 - - + +
349A ASP* 3.5 52.9 + - + +
352A VAL* 3.3 25.2 - - - +
56B ALA* 4.1 18.2 + - + +
162B THR* 6.1 0.6 - - - +
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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