Contacts of the helix formed by residues 52 - 61 (chain B) in PDB entry 2ADM
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 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B THR* 6.1 0.4 - - - -
28B VAL* 4.3 13.2 - - + +
45B GLU* 3.4 10.1 - - - +
48B CYS 3.3 11.9 - - - +
50B HIS* 3.2 32.3 - - + +
51B GLY* 1.3 91.2 - - - +
53B PHE* 1.3 62.2 + - + +
55B ARG* 3.9 5.6 + - - +
56B ALA* 3.1 28.4 + - - +
500B SAM 3.7 26.7 - - - +
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Residues in contact with PHE 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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23B THR* 4.0 23.8 - - + -
28B VAL* 4.1 24.2 - - + -
31B MET* 3.6 35.0 - - + -
32B VAL* 4.6 6.2 - - + +
45B GLU* 3.2 30.2 + - + +
52B PRO* 1.3 79.2 - - + +
54B LEU* 1.3 67.7 + - - +
55B ARG 3.2 0.2 - - - -
56B ALA* 4.0 2.6 - - - +
57B PHE* 2.9 28.1 + - - +
103B LEU* 3.8 36.7 - - + +
104B GLY* 3.8 10.3 - - - -
105B ASN* 3.8 16.8 - - + -
500B SAM 3.8 20.0 - - - -
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Residues in contact with LEU 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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43B VAL* 4.1 23.6 - - + +
45B GLU* 3.1 36.2 + - + +
48B CYS* 5.0 0.2 - - + -
51B GLY* 3.3 7.6 + - - +
53B PHE* 1.3 76.8 - - + +
55B ARG* 1.3 63.2 + - + +
57B PHE* 3.7 4.1 - - - +
58B ARG* 3.1 22.5 + - - +
67B PHE* 4.1 19.4 - - + -
68B VAL 3.6 29.8 - - - +
69B GLY* 4.1 6.1 - - - +
79B LEU* 3.9 24.5 - - + -
82B TRP* 3.7 14.6 - - + -
83B ALA* 4.3 10.1 - - + -
103B LEU* 5.6 0.7 - - + -
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Residues in contact with ARG 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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50B HIS* 2.7 45.3 + - - +
51B GLY 3.0 15.8 + - - +
52B PRO* 4.0 5.4 - - - +
54B LEU* 1.3 75.4 - - - +
56B ALA* 1.3 62.7 + - - +
58B ARG* 3.3 4.3 + - - +
59B GLU* 3.0 41.1 + - - +
78B ASP* 3.0 20.2 + - - -
79B LEU* 3.9 0.8 - - - +
80B PRO* 3.1 34.7 - - + +
82B TRP* 3.9 22.2 - - + -
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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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28B VAL* 3.7 23.3 - - + -
29B ASP* 5.3 6.3 - - - +
32B VAL* 3.9 12.1 - - + +
52B PRO 3.1 19.0 + - - +
53B PHE 4.0 0.9 - - - +
55B ARG* 1.3 77.7 - - - +
57B PHE* 1.3 62.5 + - - +
59B GLU* 3.5 11.3 + - - +
60B ALA* 3.1 25.5 + - - +
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Residues in contact with PHE 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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32B VAL* 4.0 11.6 - - + +
35B ALA* 4.0 17.9 - - + -
36B GLU 4.4 3.4 - - - -
37B ALA* 4.1 12.3 - - + -
43B VAL* 3.9 12.6 - - + -
53B PHE 2.9 19.8 + - - +
54B LEU* 3.7 4.0 - - - +
56B ALA* 1.3 75.6 - - - +
58B ARG* 1.3 56.3 + - - +
60B ALA 3.2 0.2 + - - -
61B HIS* 2.6 72.1 + + + +
65B TYR* 3.6 37.0 - + - -
67B PHE* 3.7 15.3 - + - -
101B LEU* 3.3 29.8 - - + -
103B LEU* 3.9 13.2 - - + -
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Residues in contact with ARG 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 LEU 3.1 14.1 + - - +
55B ARG 3.6 4.7 - - - +
57B PHE* 1.3 80.0 - - - +
59B GLU* 1.3 61.1 + - + +
62B GLY* 2.8 50.5 + - - +
63B THR* 3.3 37.7 + - + +
67B PHE* 3.5 25.6 - - + -
82B TRP* 3.6 59.5 - - + +
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Residues in contact with GLU 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 ARG* 3.0 34.7 + - - +
56B ALA* 3.8 9.1 - - - +
58B ARG* 1.3 77.0 - - + +
60B ALA* 1.3 59.0 + - - +
62B GLY 4.8 0.2 - - - -
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Residues in contact with ALA 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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32B VAL* 3.7 21.3 - - + -
56B ALA 3.1 16.9 + - - +
59B GLU* 1.3 79.5 - - - +
61B HIS* 1.3 66.7 + - + +
62B GLY 3.8 0.2 - - - -
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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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32B VAL* 3.0 36.1 - - + +
33B SER* 4.9 4.4 + - - -
35B ALA 3.3 18.7 + - - -
36B GLU* 5.0 4.0 - - + +
37B ALA 5.7 0.4 - - - -
57B PHE* 2.6 46.1 + + + +
60B ALA* 1.3 85.9 - - + +
62B GLY* 1.3 55.1 + - - -
65B TYR* 3.7 24.8 + - - +
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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