Contacts of the helix formed by residues 51 - 62 (chain D) in PDB entry 1YAA
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 PRO 51 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48D TRP* 3.4 29.8 - - + +
49D VAL 3.7 3.6 - - - +
50D LEU* 1.3 82.2 - - - +
52D SER* 1.3 60.2 + - - +
54D LYS* 3.3 28.2 - - + +
55D ALA* 3.3 13.5 + - - +
318D GLN* 4.2 13.2 - - + +
322D ASP* 3.5 20.6 - - - +
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Residues in contact with SER 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D LEU* 4.5 3.4 - - - -
51D PRO* 1.3 78.4 - - - +
53D VAL* 1.3 56.9 + - - +
55D ALA* 3.3 8.7 - - - +
56D ALA* 3.1 23.6 + - - +
309D LEU* 3.2 20.0 - - - +
315D LEU* 3.0 25.4 + - - +
318D GLN* 3.9 11.8 - - - +
319D TRP* 3.5 19.7 - - - +
322D ASP* 3.0 20.1 + - - -
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Residues in contact with VAL 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C HIS* 4.3 1.8 - - + +
49D VAL* 4.1 10.3 - - + -
50D LEU* 2.8 21.4 + - + +
52D SER* 1.3 73.4 - - - +
54D LYS* 1.3 56.8 + - - +
55D ALA 2.9 4.9 - - - -
56D ALA* 3.0 7.3 + - - +
57D GLU* 2.9 42.4 + - - +
260D ALA* 3.6 24.7 - - + +
262D MET* 3.3 28.7 - - + -
305D ILE* 3.8 8.3 - - + -
309D LEU* 3.8 21.5 - - + -
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Residues in contact with LYS 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D VAL* 3.3 35.1 - - + +
50D LEU 3.0 19.6 + - - +
51D PRO* 3.3 25.8 - - + +
53D VAL* 1.3 74.1 - - - +
55D ALA* 1.3 58.4 + - - +
57D GLU* 4.0 13.7 - - - +
58D LYS* 3.4 24.1 + - - +
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Residues in contact with ALA 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D PRO 3.3 12.6 + - - +
52D SER* 3.3 12.8 - - - +
53D VAL 2.9 0.4 - - - -
54D LYS* 1.3 77.5 - - - +
56D ALA* 1.3 64.7 + - - +
57D GLU 3.2 0.2 - - - -
58D LYS* 3.3 10.5 + - - +
59D LEU* 3.2 28.4 + - - +
315D LEU* 4.3 18.2 - - + -
318D GLN* 6.3 0.4 - - + -
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Residues in contact with ALA 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D SER 3.1 7.2 + - - +
53D VAL* 3.0 9.1 + - - +
55D ALA* 1.3 81.0 - - - +
57D GLU* 1.3 60.3 + - - +
59D LEU* 3.5 5.2 + - - +
60D ILE* 3.1 30.6 + - - +
305D ILE* 3.6 33.4 - - + +
308D LYS* 4.2 4.5 - - + -
309D LEU* 4.4 4.7 - - + +
315D LEU* 3.7 23.5 - - + +
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Residues in contact with GLU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C HIS* 3.3 11.5 + - + +
66C TYR* 2.9 25.5 + - - -
68C HIS* 2.8 29.2 + - - -
49D VAL* 4.3 3.5 - - - +
53D VAL* 2.9 22.9 + - + +
54D LYS* 4.0 12.0 - - - +
56D ALA* 1.3 75.0 - - - +
58D LYS* 1.3 65.0 + - - +
60D ILE* 3.1 16.0 + - - +
61D HIS* 3.1 21.0 + - - -
301D TYR* 2.7 24.7 + - - +
305D ILE* 3.5 22.9 - - + -
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Residues in contact with LYS 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D LYS 3.4 14.8 + - - +
55D ALA* 3.3 14.8 + - - +
57D GLU* 1.3 79.7 - - - +
59D LEU* 1.3 64.6 + - + +
61D HIS* 3.2 5.7 + - - +
62D ASN* 3.0 22.0 + - - +
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Residues in contact with LEU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D ALA* 3.2 12.6 - - + +
56D ALA 3.6 4.7 - - - +
57D GLU 3.2 0.2 - - - -
58D LYS* 1.3 79.1 - - + +
60D ILE* 1.3 62.4 + - - +
62D ASN* 3.1 22.8 + - + +
63D ASP* 3.3 12.1 + - - +
308D LYS* 3.7 32.0 - - + -
312D THR* 4.8 6.5 - - + +
315D LEU* 3.6 35.4 - - + -
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Residues in contact with ILE 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ALA 3.1 24.8 + - - +
57D GLU* 3.1 8.7 + - - +
59D LEU* 1.3 75.5 - - - +
61D HIS* 1.3 63.7 + - - +
63D ASP* 3.3 21.4 - - - +
66D TYR* 3.5 37.5 - - + +
301D TYR* 3.7 20.2 - - + +
304D LYS* 3.7 31.2 - - + +
305D ILE* 4.4 4.9 - - + +
308D LYS* 3.5 35.0 - - + -
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Residues in contact with HIS 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C GLU* 3.5 7.3 + - + -
61C HIS* 3.2 23.9 + + - -
301C TYR* 3.4 9.9 + - - -
57D GLU 3.1 22.4 + - - +
58D LYS* 3.8 7.2 - - - +
60D ILE* 1.3 74.3 - - + +
62D ASN* 1.3 59.2 + - - +
63D ASP 3.1 12.7 + - - +
66D TYR* 3.3 36.8 + + - +
301D TYR* 2.9 38.5 + + - -
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Residues in contact with ASN 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D LYS* 3.0 13.4 + - + +
59D LEU* 3.1 19.7 + - + +
61D HIS* 1.3 75.3 - - - +
63D ASP* 1.3 62.6 + - - +
64D SER* 3.4 4.3 + - - -
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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