Contacts of the helix formed by residues 55 - 64 (chain M) in PDB entry 1U3E
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 VAL 55 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19M GLY* 3.4 35.0 - - - +
21M VAL* 4.5 7.0 - - + -
32M HIS* 3.6 31.9 - - + +
40M HIS* 2.8 31.4 + - + +
42M ILE* 4.0 20.2 - - + -
53M PHE 3.8 1.8 + - - -
54M GLN* 1.3 68.9 - - - +
56M HIS* 1.3 64.0 + - - +
58M LEU* 3.3 11.5 + - - +
59M VAL* 3.0 24.5 + - + +
83M ASN* 4.5 8.1 - - + +
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Residues in contact with HIS 56 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C T 2.6 25.6 + - - -
39M TYR* 3.5 26.8 - + + +
40M HIS* 4.4 4.8 + - - +
54M GLN* 2.8 37.6 - - + +
55M VAL* 1.3 80.2 + - - +
57M ARG* 1.3 64.0 + - + +
59M VAL* 3.9 1.8 - - - -
60M ALA* 3.1 23.7 + - - +
73M VAL* 3.6 22.2 + - + +
75M HIS* 3.2 33.3 - + + +
83M ASN* 3.6 13.8 + - - +
88M LEU* 3.5 17.6 - - + +
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Residues in contact with ARG 57 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C T 3.0 34.8 + - - +
25C T 3.4 38.0 + - - -
54M GLN* 2.7 35.1 + - + +
56M HIS* 1.3 72.7 - - - +
58M LEU* 1.3 56.2 + - + +
60M ALA* 3.3 0.7 + - - +
61M ILE* 2.6 57.3 + - + +
67M TYR* 4.8 7.9 - - - -
71M LEU 3.3 17.2 + - - -
72M VAL* 4.5 0.2 - - - +
73M VAL* 4.2 10.8 - - + +
90M TRP* 3.1 35.4 - - - -
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Residues in contact with LEU 58 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6M ILE* 4.4 23.8 - - + -
15M VAL* 4.4 12.4 - - + +
21M VAL* 4.2 16.8 - - + -
42M ILE* 4.0 29.4 - - + -
44M LEU* 4.3 7.6 - - + -
53M PHE* 4.0 29.4 - - + -
54M GLN 3.1 14.2 + - - +
55M VAL* 3.6 8.1 - - - +
57M ARG* 1.3 80.6 - - + +
59M VAL* 1.3 63.0 + - - +
61M ILE* 4.5 8.1 - - + -
62M HIS* 2.7 37.8 + - + +
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Residues in contact with VAL 59 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M VAL* 4.3 6.3 - - + -
16M SER 3.9 6.5 - - - +
17M ASN* 3.9 6.5 - - - +
19M GLY* 3.7 28.5 - - - -
55M VAL* 3.0 21.1 + - + +
56M HIS* 4.5 0.9 - - - -
57M ARG 3.2 0.2 - - - -
58M LEU* 1.3 76.1 - - - +
60M ALA* 1.3 57.5 + - - +
62M HIS 2.9 2.8 + - - -
63M PHE* 2.7 49.0 + - + -
83M ASN 3.9 7.0 - - - +
85M SER* 3.5 41.1 - - - +
88M LEU* 3.9 8.3 - - + -
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Residues in contact with ALA 60 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56M HIS 3.1 17.6 + - - +
57M ARG 3.6 0.4 - - - +
59M VAL* 1.3 78.7 - - - +
61M ILE* 1.3 63.3 + - - +
64M CYS* 3.0 43.7 + - + +
73M VAL* 3.5 32.5 - - + -
88M LEU* 4.3 5.5 - - + +
89M ARG 5.5 0.9 - - - +
90M TRP* 3.3 16.2 + - + +
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Residues in contact with ILE 61 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7M LYS* 3.9 24.5 + - + +
57M ARG* 2.6 46.1 + - + +
58M LEU* 4.9 7.6 - - + +
60M ALA* 1.3 73.8 - - - +
62M HIS* 1.3 82.7 + - + +
64M CYS 5.1 0.7 - - - +
67M TYR* 5.0 9.2 - - + +
90M TRP* 3.6 22.2 - - + +
400M EDO 4.0 8.7 + - - -
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Residues in contact with HIS 62 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4M LYS* 3.0 43.2 + - + +
5M ASP 3.6 15.3 - - - -
6M ILE* 3.5 17.6 - - + -
7M LYS* 3.0 49.1 + - + +
15M VAL* 3.9 11.7 - - + +
58M LEU* 2.7 33.8 + - + +
59M VAL 2.9 3.3 + - - +
61M ILE* 1.3 95.2 - - + +
63M PHE* 1.3 72.9 + - + +
400M EDO 3.0 12.2 + - - -
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Residues in contact with PHE 63 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2M GLU* 3.6 25.4 - - + -
4M LYS* 3.9 32.8 - - + +
15M VAL* 3.4 35.4 - - + -
16M SER 3.4 6.7 - - - -
17M ASN* 3.4 37.5 - - + -
59M VAL* 2.7 25.7 + - + +
62M HIS* 1.3 82.0 - - + +
64M CYS* 1.3 64.7 + - - +
65M GLU* 4.3 0.8 - - - +
85M SER* 3.7 20.1 + - - +
400M EDO 3.9 3.4 - - - -
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Residues in contact with CYS 64 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60M ALA* 3.0 34.2 + - + +
61M ILE* 5.1 0.9 - - - +
63M PHE* 1.3 86.0 - - - +
65M GLU* 1.3 66.3 + - - +
66M GLY 3.7 0.5 + - - -
67M TYR* 4.3 3.1 + - - +
85M SER* 3.6 31.6 - - - -
88M LEU* 3.9 14.8 - - - +
89M ARG* 5.1 2.9 - - - -
90M TRP* 3.3 24.5 + - + +
400M EDO 3.4 11.7 + - - -
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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