Contacts of the helix formed by residues 47 - 60 (chain B) in PDB entry 3A9L
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 47 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B GLY 4.3 2.8 + - - -
45B GLU 3.4 0.2 + - - -
46B VAL* 1.3 79.2 - - - +
48B THR* 1.3 59.7 + - - +
49B THR 3.5 1.6 - - - -
50B GLU* 3.1 22.3 + - - +
51B LEU* 3.2 27.4 + - - +
171B ARG* 4.9 5.6 - - - -
174B PHE* 4.4 10.6 - - - -
175B PHE* 4.1 16.6 - - - -
185B ARG* 5.1 0.2 - - - +
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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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38B SER* 3.7 6.0 + - - +
40B HIS 3.4 1.9 + - - -
41B ALA* 3.2 19.6 - - - -
45B GLU* 2.9 26.7 + - + +
47B GLY* 1.3 75.4 - - - +
49B THR* 1.3 68.6 + - - +
51B LEU* 3.9 5.0 - - + +
52B ILE* 3.0 31.9 + - - +
65B LEU* 4.7 0.4 - - - -
102B PHE* 3.6 38.1 - - + +
103B HIS* 3.9 17.7 - - - +
104B GLY 4.2 0.2 - - - +
166B ILE* 5.7 2.7 - - + -
171B ARG* 4.8 6.7 - - - -
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Residues in contact with THR 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ALA* 3.2 6.3 - - - +
42B GLY* 2.7 34.4 + - - +
48B THR* 1.3 82.7 + - - +
50B GLU* 1.3 79.7 + - - +
52B ILE* 3.8 1.9 - - - +
53B TYR* 3.1 50.9 + - + +
65B LEU* 3.9 10.8 - - + +
67B GLN* 2.7 23.3 + - - +
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Residues in contact with GLU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLY* 5.6 0.5 - - - +
47B GLY* 3.1 29.4 + - - +
48B THR 3.4 0.4 - - - -
49B THR* 1.3 88.2 - - + +
51B LEU* 1.3 62.3 + - - +
53B TYR* 3.4 12.2 + - + +
54B ARG* 3.2 17.8 + - - +
175B PHE* 3.8 10.9 - - + -
185B ARG* 3.2 58.0 + - + +
188B VAL* 5.0 1.8 - - + -
192B PHE* 3.3 24.3 - - + -
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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
----------------------------------------------------------
47B GLY 3.2 18.1 + - - +
48B THR* 4.0 5.8 - - - +
49B THR 3.3 0.4 - - - -
50B GLU* 1.3 76.4 - - - +
52B ILE* 1.3 59.0 + - - +
54B ARG* 3.4 1.2 + - - +
55B VAL* 2.8 30.7 + - + +
102B PHE* 3.5 33.4 - - + -
166B ILE* 3.9 12.6 - - + -
174B PHE* 4.3 8.5 - - + -
192B PHE* 3.6 19.4 - - + +
195B TYR* 3.7 28.7 - - + -
196B ALA* 3.7 33.4 - - + +
199B ILE* 5.6 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
----------------------------------------------------------
36B TYR* 4.0 19.1 - - + +
37B PHE* 3.2 37.7 - - - +
38B SER* 3.5 11.4 - - - +
48B THR 3.0 14.1 + - - +
49B THR 3.9 2.0 - - - +
51B LEU* 1.3 73.2 - - - +
53B TYR* 1.3 58.2 + - - +
55B VAL* 4.3 4.7 - - - +
56B VAL* 2.8 44.0 + - + +
63B LEU* 4.1 10.5 - - + -
65B LEU* 3.6 23.1 - - + -
102B PHE* 3.5 30.1 - - + -
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Residues in contact with TYR 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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26B GLU* 2.5 40.2 + - - -
49B THR* 3.1 39.0 + - + +
50B GLU* 3.4 13.7 - - + +
52B ILE* 1.3 75.9 - - - +
54B ARG* 1.3 56.7 + - - +
56B VAL* 3.8 2.0 - - - +
57B GLU* 2.9 45.6 + - - +
63B LEU* 3.7 21.8 - - + -
65B LEU* 3.5 10.8 - - + -
67B GLN* 4.2 1.9 + - - -
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Residues in contact with ARG 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 GLU 3.2 2.0 + - - +
51B LEU 3.7 3.6 - - - +
53B TYR* 1.3 77.2 - - - +
55B VAL* 1.3 65.1 + - - +
57B GLU* 3.3 23.8 + - - +
58B LEU* 3.0 58.8 + - + +
192B PHE* 3.6 33.7 - - + -
193B LEU* 3.7 29.2 + - + +
196B ALA* 3.5 20.4 - - + -
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Residues in contact with VAL 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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36B TYR* 3.7 42.2 - - + -
51B LEU* 2.8 33.6 + - + +
52B ILE* 4.1 5.6 - - - +
54B ARG* 1.3 70.5 - - - +
56B VAL* 1.3 58.3 + - - +
58B LEU* 3.1 7.1 + - - -
59B THR* 2.6 38.2 + - + +
102B PHE* 4.6 4.9 - - + -
196B ALA* 3.6 33.9 - - + +
199B ILE* 3.9 19.3 - - + -
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Residues in contact with VAL 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LYS* 5.2 6.1 - - + +
30B GLN* 3.5 13.8 + - - +
36B TYR* 4.1 9.0 - - + -
52B ILE* 2.8 32.8 + - + +
53B TYR* 3.8 2.9 - - - +
55B VAL* 1.3 72.7 - - - +
57B GLU* 1.3 58.5 + - + +
59B THR* 3.5 5.4 - - - -
60B GLY* 2.9 29.5 + - - -
61B GLY 3.4 16.8 - - - +
62B SER 3.7 14.4 - - - +
63B LEU* 3.7 35.9 - - + -
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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
----------------------------------------------------------
53B TYR* 2.9 34.7 + - - +
54B ARG* 3.5 35.5 + - - +
56B VAL* 1.3 74.9 - - + +
58B LEU* 1.3 63.4 + - + +
59B THR 3.5 0.2 + - - -
60B GLY 4.4 2.4 + - - -
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Residues in contact with LEU 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 ARG* 3.0 54.1 + - - +
55B VAL* 3.1 6.5 + - - +
57B GLU* 1.3 79.6 - - - +
59B THR* 1.3 59.8 + - - +
193B LEU 5.2 0.9 - - - +
196B ALA* 3.6 38.1 - - + +
197B GLU* 3.8 22.9 - - + +
200B LYS* 3.7 28.6 - - + +
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Residues in contact with THR 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ASN* 4.9 3.8 + - - -
36B TYR* 3.4 13.4 - - - +
55B VAL* 2.6 30.7 + - + +
56B VAL* 3.4 2.4 + - - -
58B LEU* 1.3 77.7 - - - +
60B GLY* 1.3 62.6 + - - +
61B GLY 3.1 10.9 + - - -
200B LYS* 3.6 36.8 - - + -
203B GLU* 3.2 32.1 - - - +
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Residues in contact with GLY 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLN* 3.6 23.5 - - - +
31B ASN* 3.5 19.6 + - - +
56B VAL 2.9 12.1 + - - -
57B GLU 4.4 2.4 + - - -
58B LEU 3.8 1.0 - - - -
59B THR* 1.3 75.3 - - - +
61B GLY* 1.3 63.8 + - - +
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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