Contacts of the helix formed by residues 45 - 54 (chain B) in PDB entry 2YZ2
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 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B ALA* 3.7 18.2 - - - -
23B LEU* 3.7 6.4 - - - +
43B GLY* 3.2 6.1 + - - -
44B SER* 1.3 78.5 + - - +
46B LYS* 1.3 63.7 + - - +
47B SER* 3.3 3.6 - - - -
48B THR* 3.1 16.8 + - - -
49B LEU 3.0 16.5 + - - -
211B LEU* 3.9 3.8 - - - -
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Residues in contact with LYS 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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38B VAL* 3.6 41.0 + - + +
39B ALA* 3.9 10.1 - - - +
40B GLY 3.1 28.3 + - - +
41B ASN 4.7 2.2 - - - -
44B SER* 3.1 18.1 - - - +
45B GLY* 1.3 77.0 - - - +
47B SER* 1.3 57.5 + - - +
49B LEU* 3.1 4.7 + - - +
50B LEU* 2.9 31.5 + - - +
164B GLU* 4.4 13.6 + - - -
194B ILE* 4.0 23.7 - - + +
195B SER 4.8 10.3 + - - +
196B HIS* 4.9 8.5 - - - +
198B ILE* 5.8 0.6 - - - +
211B LEU* 3.6 13.2 - - + +
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Residues in contact with SER 47 (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 GLY* 3.3 0.9 - - - -
46B LYS* 1.3 78.1 - - - +
48B THR* 1.3 67.2 + - - +
49B LEU 3.1 0.2 - - - -
50B LEU* 3.4 3.0 + - - +
51B GLN* 3.1 37.4 + - - +
84B PHE* 5.7 0.2 - - - -
163B ASP* 2.6 26.0 + - - +
194B ILE* 3.8 12.8 - - - +
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Residues in contact with THR 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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10B HIS* 3.9 12.6 - - + -
12B PHE* 3.7 35.9 - - + -
22B ALA* 3.9 11.5 - - + +
23B LEU* 3.9 8.5 - - + -
45B GLY* 3.1 13.9 + - - -
47B SER* 1.3 78.6 - - - +
49B LEU* 1.3 64.0 + - - +
51B GLN* 3.2 6.4 + - - +
52B ILE* 2.9 40.1 + - + +
57B ILE* 4.1 7.4 - - + -
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Residues in contact with LEU 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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5B VAL* 4.1 26.5 - - + -
8B VAL* 5.1 1.6 - - + -
23B LEU* 3.7 21.3 - - + +
26B VAL* 4.1 21.5 - - + -
28B LEU* 4.2 21.1 - - + -
38B VAL* 4.3 20.9 - - + -
45B GLY 3.0 9.2 + - - +
46B LYS* 3.4 9.0 - - - +
47B SER 3.1 0.4 - - - -
48B THR* 1.3 77.3 - - - +
50B LEU* 1.4 65.2 + - + +
52B ILE* 3.0 13.1 + - + +
53B VAL* 3.0 25.9 + - + +
209B VAL* 5.4 0.4 - - + -
211B LEU* 4.0 20.9 - - + -
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Residues in contact with LEU 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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38B VAL* 4.0 17.3 - - + -
46B LYS 2.9 20.6 + - - +
47B SER* 3.4 5.4 + - - +
48B THR 3.3 0.2 - - - -
49B LEU* 1.4 79.3 - - + +
51B GLN* 1.3 59.0 - - + +
53B VAL* 3.3 9.6 + - + +
54B ALA* 2.8 30.1 + - - +
82B ILE* 4.9 4.5 - - + -
161B ILE* 3.5 31.3 - - + +
162B LEU 4.3 6.3 - - - +
163B ASP* 4.5 7.2 - - + +
192B ILE* 3.6 27.6 - - + +
193B LEU 4.5 2.0 - - - -
194B ILE* 3.4 38.4 - - + +
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Residues in contact with GLN 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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47B SER* 3.1 31.2 + - - +
48B THR* 3.6 4.6 + - - +
49B LEU 3.1 0.2 - - - -
50B LEU* 1.3 76.8 - - + +
52B ILE* 1.3 61.9 + - - +
54B ALA* 3.4 5.2 + - - -
55B GLY 3.3 2.8 + - - -
56B LEU* 2.8 53.9 + - + +
57B ILE* 3.4 32.8 + - + +
82B ILE* 4.8 2.2 - - + -
84B PHE* 4.4 22.6 - - + -
163B ASP* 5.2 0.2 - - - +
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Residues in contact with ILE 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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5B VAL* 5.7 0.2 - - + -
8B VAL* 4.1 10.5 - - + -
10B HIS* 3.9 16.4 - - + -
23B LEU* 3.6 29.8 - - + -
48B THR* 2.9 21.0 + - + +
49B LEU* 3.3 13.2 - - + +
51B GLN* 1.3 74.7 - - - +
53B VAL* 1.3 64.5 + - + +
55B GLY* 3.1 13.7 + - - -
57B ILE* 3.7 30.1 - - + +
59B PRO* 3.9 27.0 - - + +
64B VAL* 3.8 23.0 - - + +
66B TYR* 3.7 5.4 + - - -
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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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3B ILE* 4.1 28.7 - - + -
5B VAL* 3.9 28.7 - - + -
28B LEU* 6.1 0.2 - - + -
30B ILE* 5.1 4.9 - - + -
49B LEU* 3.0 23.8 + - + +
50B LEU* 3.7 11.2 - - + +
52B ILE* 1.3 75.0 - - + +
54B ALA* 1.3 57.4 + - - +
55B GLY 3.0 1.1 + - - -
64B VAL* 4.4 6.3 - - + -
66B TYR* 2.8 28.5 + - - -
76B ILE* 4.3 0.9 - - - +
80B ILE* 4.4 2.8 - - - +
159B ILE* 5.1 2.9 - - + -
161B ILE* 4.1 8.3 - - + -
192B ILE* 4.1 24.2 - - + -
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Residues in contact with ALA 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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50B LEU 2.8 17.4 + - - +
51B GLN* 3.8 7.2 - - - +
52B ILE 3.2 0.6 - - - -
53B VAL* 1.3 76.7 - - - +
55B GLY* 1.3 60.0 + - - +
56B LEU* 3.5 11.9 + - + +
73B GLY 5.0 0.2 - - - +
76B ILE* 3.9 11.8 - - - +
77B ARG* 4.8 8.8 + - - +
80B ILE* 4.0 18.0 - - + +
82B ILE* 3.8 25.4 - - + -
161B ILE* 3.9 13.4 - - + +
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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