Contacts of the helix formed by residues 51 - 61 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B TRP* 3.7 24.5 - - + +
49B VAL 3.4 3.3 - - - +
50B LEU* 1.3 82.8 - - - +
52B SER* 1.3 60.7 + - - +
54B LYS* 3.1 16.9 + - + +
55B ALA* 3.1 24.1 + - - +
318B GLN* 4.1 15.0 - - - +
322B ASP* 3.3 26.2 - - - +
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Residues in contact with SER 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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50B LEU* 3.8 7.3 - - - +
51B PRO* 1.3 78.2 - - - +
53B VAL* 1.3 61.6 + - - +
55B ALA* 3.8 6.0 + - - +
56B ALA* 3.2 24.6 + - - +
309B LEU* 3.4 26.9 - - - +
315B LEU* 3.7 8.2 - - - +
318B GLN* 3.8 10.9 - - - +
319B TRP* 3.7 26.2 - - - +
322B ASP* 2.7 23.9 + - - -
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Residues in contact with VAL 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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68A HIS* 4.5 0.9 - - + +
49B VAL* 3.3 23.1 - - + -
50B LEU* 3.1 27.4 + - + +
52B SER* 1.3 84.6 - - - +
54B LYS* 1.3 60.9 + - - +
55B ALA 3.2 1.3 - - - -
56B ALA* 3.7 6.8 - - - +
57B GLU* 2.9 39.7 + - - +
260B ALA 3.7 22.0 - - - +
262B MET* 4.0 15.3 - - + -
305B ILE* 4.1 13.9 - - + -
309B LEU* 4.2 16.8 - - + -
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Residues in contact with LYS 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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48B TRP* 6.5 0.2 - - - -
49B VAL* 3.5 41.5 - - + +
50B LEU 3.1 12.1 + - - +
51B PRO* 3.1 18.8 + - + +
53B VAL* 1.3 77.9 - - - +
55B ALA* 1.3 61.9 + - - +
57B GLU* 3.5 9.1 + - - +
58B LYS* 3.2 22.2 + - - +
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Residues in contact with ALA 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 PRO 3.1 12.4 + - - +
52B SER* 3.8 1.1 - - - +
54B LYS* 1.3 80.0 - - - +
56B ALA* 1.3 61.4 + - - +
58B LYS* 3.3 13.4 + - - +
59B LEU* 3.2 28.9 + - + +
315B LEU* 3.7 24.7 - - + -
318B GLN* 6.4 0.2 - - + -
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Residues in contact with ALA 56 (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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52B SER 3.2 16.2 + - - +
53B VAL* 3.8 7.9 - - - +
54B LYS 3.4 0.2 - - - -
55B ALA* 1.3 78.0 - - - +
57B GLU* 1.3 63.1 + - - +
59B LEU* 3.5 6.1 + - - +
60B ILE* 3.2 30.0 + - - +
305B ILE* 4.0 24.5 - - + +
308B LYS* 4.0 8.0 - - + +
309B LEU* 4.7 3.4 - - + +
315B LEU* 3.6 21.9 - - + +
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Residues in contact with GLU 57 (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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61A HIS* 3.2 11.4 + - + +
66A TYR* 2.8 25.4 + - - -
68A HIS* 2.9 29.7 + - - -
49B VAL* 4.2 4.5 - - - +
53B VAL* 2.9 30.1 + - - +
54B LYS* 3.8 6.6 - - - +
55B ALA 3.3 0.2 - - - -
56B ALA* 1.3 75.4 - - - +
58B LYS* 1.3 62.3 + - - +
60B ILE* 3.6 6.8 + - - +
61B HIS* 3.0 32.7 + - - -
301B TYR* 2.7 26.9 + - - +
305B ILE* 3.6 19.7 - - + -
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Residues in contact with LYS 58 (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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54B LYS 3.2 13.6 + - - +
55B ALA* 3.5 13.2 - - - +
56B ALA 3.2 0.6 - - - -
57B GLU* 1.3 77.9 - - - +
59B LEU* 1.3 91.1 + - - +
61B HIS* 3.6 3.2 + - - -
62B ASN* 2.8 50.3 + - - +
376C THR* 5.5 12.4 + - + +
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Residues in contact with LEU 59 (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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55B ALA* 3.2 16.1 + - + +
56B ALA* 3.7 1.1 - - - +
58B LYS* 1.3 97.6 - - - +
60B ILE* 1.3 64.5 + - - +
62B ASN* 3.2 15.5 + - + +
63B ASP* 3.3 13.2 + - - +
308B LYS* 3.6 34.4 - - + -
312B THR* 5.0 7.2 - - + +
315B LEU* 3.9 20.6 - - + -
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Residues in contact with ILE 60 (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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56B ALA 3.2 17.9 + - - +
57B GLU* 3.7 6.3 - - - +
58B LYS 3.4 0.2 - - - -
59B LEU* 1.3 77.4 - - - +
61B HIS* 1.3 59.0 + - + +
63B ASP* 3.4 17.5 - - - +
66B TYR* 3.4 39.1 - - + -
301B TYR* 4.2 14.4 - - + +
304B LYS* 3.4 44.2 - - + +
305B ILE* 3.5 22.4 - - + +
308B LYS* 4.1 21.1 - - + +
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Residues in contact with HIS 61 (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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57A GLU* 3.2 33.3 - - + +
61A HIS* 3.4 15.7 - + - -
301A TYR* 3.3 7.2 - - - -
57B GLU 3.0 26.0 + - - +
58B LYS* 4.2 4.9 - - - +
59B LEU 3.2 0.4 - - - -
60B ILE* 1.3 77.2 - - + +
62B ASN* 1.3 63.5 + - - +
63B ASP 3.2 9.8 + - - +
66B TYR* 3.7 21.6 - + - +
301B TYR* 2.8 35.6 + + - -
29C ARG* 4.2 15.2 - - - +
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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