Contacts of the helix formed by residues 44 - 54 (chain B) in PDB entry 2YYU
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 44 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A GLY* 4.2 14.1 - - - -
45A PRO* 4.1 1.6 - - - +
40B TYR* 2.7 33.8 + - - -
42B GLN 3.8 0.2 - - - -
43B GLU* 1.3 69.6 - - - +
45B PRO* 1.3 69.6 - - - +
46B ALA 2.9 11.9 + - - -
47B ILE* 3.1 23.2 + - - +
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Residues in contact with PRO 45 (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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40A TYR 4.8 0.2 - - - +
41A TYR 3.7 16.4 - - - +
42A GLN* 3.6 20.6 - - - +
43A GLU 4.3 3.8 - - - +
44A GLY* 4.1 16.2 - - - +
40B TYR* 3.6 24.4 - - + +
43B GLU 4.7 0.4 - - - +
44B GLY* 1.3 81.6 - - - +
46B ALA* 1.3 63.8 + - - +
47B ILE 3.2 0.4 - - - -
48B VAL* 3.2 14.4 + - - +
49B ALA* 3.3 11.8 + - - +
81B VAL* 4.0 17.6 - - + +
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Residues in contact with ALA 46 (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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16B LYS* 6.5 0.2 - - - -
43B GLU* 3.7 16.4 - - - +
44B GLY 2.9 0.6 + - - -
45B PRO* 1.3 83.6 - - + +
47B ILE* 1.3 63.0 + - - +
49B ALA* 3.2 8.5 + - - +
50B PHE* 3.1 22.7 + - - +
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Residues in contact with ILE 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LYS* 3.9 40.4 - - + -
19B VAL* 4.6 8.5 - - + -
35B VAL* 4.2 12.1 - - + -
39B LEU* 4.0 26.9 - - + -
40B TYR* 4.0 11.2 - - + -
43B GLU* 3.8 16.8 + - + +
44B GLY 3.1 18.4 + - - +
46B ALA* 1.3 77.1 - - - +
48B VAL* 1.3 71.1 + - + +
50B PHE* 3.3 14.2 + - + +
51B LEU* 3.0 41.2 + - + +
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Residues in contact with VAL 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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35B VAL* 5.0 0.9 - - + -
40B TYR* 3.6 21.1 - - + -
45B PRO 3.2 7.3 + - - +
47B ILE* 1.3 81.3 - - + +
49B ALA* 1.3 66.1 + - - +
51B LEU* 3.4 6.9 + - - +
52B LYS* 3.0 35.8 + - + +
58B VAL* 4.5 14.6 - - + -
60B LEU* 3.6 32.5 - - + -
81B VAL* 3.8 32.5 - - + +
82B GLY 4.6 3.1 - - - -
83B ALA* 4.7 0.9 - - - +
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Residues in contact with ALA 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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45B PRO 3.3 7.5 + - - +
46B ALA* 3.2 12.4 + - - +
48B VAL* 1.3 79.0 - - - +
50B PHE* 1.3 57.7 + - - +
52B LYS* 3.4 7.7 + - - +
53B GLU* 2.9 44.1 + - + +
81B VAL* 5.0 6.0 + - + +
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Residues in contact with PHE 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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16B LYS* 3.5 36.6 - - + +
19B VAL* 4.7 6.5 - - + -
20B GLU* 3.4 39.9 - - + -
23B LEU* 5.2 3.6 - - + -
46B ALA 3.1 13.4 + - - +
47B ILE* 3.4 18.8 - - + +
48B VAL 3.1 0.2 - - - -
49B ALA* 1.3 77.6 - - - +
51B LEU* 1.3 80.6 + - + +
53B GLU* 3.1 26.8 + - - +
54B GLN* 3.2 50.1 + - + +
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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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11B LEU* 3.7 21.8 - - + -
19B VAL* 4.0 10.1 - - + -
23B LEU* 3.7 29.6 - - + -
33B VAL* 3.7 12.6 - - + -
35B VAL* 3.6 31.2 - - + -
47B ILE* 3.0 30.3 + - + +
48B VAL* 3.4 1.1 + - - +
50B PHE* 1.3 82.7 - - + +
52B LYS* 1.3 60.5 + - - +
54B GLN* 3.4 8.6 + - - -
55B GLY 3.4 0.2 + - - -
56B HIS* 3.0 34.5 + - + +
58B VAL* 3.8 17.3 - - + -
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Residues in contact with LYS 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 VAL* 3.0 24.9 + - + +
49B ALA* 3.7 6.1 - - - +
51B LEU* 1.3 74.3 - - - +
53B GLU* 1.3 66.9 + - + +
55B GLY* 2.9 14.6 + - - -
56B HIS 3.8 12.6 + - - +
58B VAL* 4.2 14.4 - - + -
81B VAL 3.8 8.3 - - - +
82B GLY* 2.9 46.7 + - - +
84B ASP* 3.9 14.3 + - - -
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Residues in contact with GLU 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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49B ALA* 2.9 40.0 + - + +
50B PHE* 3.1 18.0 + - + +
52B LYS* 1.3 77.3 - - - +
54B GLN* 1.3 62.4 - - + +
55B GLY* 3.1 5.5 + - - -
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Residues in contact with GLN 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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23B LEU* 5.6 2.2 - - + -
28B GLY 6.0 0.3 + - - -
30B PRO* 5.3 2.8 - - - +
50B PHE* 3.2 51.5 - - + +
51B LEU* 3.5 3.1 - - + +
52B LYS 3.2 0.4 - - - -
53B GLU* 1.3 77.6 - - - +
55B GLY* 1.3 59.8 + - - +
56B HIS* 3.5 33.1 + - + +
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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