Contacts of the helix formed by residues 51 - 66 (chain P) in PDB entry 2I2X
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 GLU 51 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46P ALA* 3.2 10.4 + - - +
49P GLU* 4.3 19.0 - - + +
50P GLY* 1.3 75.5 - - - +
52P GLU* 1.3 70.7 + - - +
53P ASP* 3.3 7.0 - - + +
54P ASP* 3.0 44.0 + - + +
55P VAL* 3.2 12.3 + - - +
104P ALA* 4.3 0.9 - - - -
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Residues in contact with GLU 52 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50P GLY 3.4 11.8 + - - +
51P GLU* 1.3 77.9 - - - +
53P ASP* 1.3 82.4 + - - +
55P VAL* 3.0 20.6 + - - +
56P VAL* 3.1 19.5 + - - +
103P ASP 5.5 0.2 - - - -
104P ALA* 3.9 25.9 - - - +
107P GLU* 3.6 35.4 - - + +
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Residues in contact with ASP 53 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51P GLU* 3.3 4.2 - - + +
52P GLU* 1.3 100.3 - - - +
54P ASP* 1.3 63.6 - - - +
56P VAL* 3.8 4.6 + - - +
57P GLU* 3.1 31.7 + - - +
107P GLU* 4.8 2.3 - - - +
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Residues in contact with ASP 54 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42P PRO* 4.6 3.0 - - - +
43P ILE* 5.2 0.2 - - - -
46P ALA* 3.6 19.5 - - + +
49P GLU* 5.3 3.5 - - - +
51P GLU* 3.0 32.1 + - + +
53P ASP* 1.3 80.2 - - - +
55P VAL* 1.3 60.1 + - - +
57P GLU* 4.2 14.2 - - - +
58P GLY* 3.0 25.2 + - - -
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Residues in contact with VAL 55 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43P ILE* 4.2 7.9 - - + +
46P ALA* 3.5 25.4 - - + +
47P ILE* 3.7 24.2 - - + +
51P GLU 3.2 7.2 + - - +
52P GLU 3.0 9.0 + - - +
54P ASP* 1.3 74.5 - - - +
56P VAL* 1.3 61.2 + - + +
58P GLY* 3.4 1.4 + - - -
59P LEU* 2.9 30.1 + - + +
77P LEU* 3.9 26.2 - - + -
104P ALA* 3.7 27.6 - - + +
108P GLY* 4.0 12.8 - - - +
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Residues in contact with VAL 56 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52P GLU 3.1 13.6 + - - +
53P ASP* 4.3 4.9 - - - +
55P VAL* 1.3 77.0 - - + +
57P GLU* 1.3 57.8 + - - +
59P LEU* 3.0 11.9 + - - +
60P GLN* 2.9 40.6 + - - +
107P GLU* 4.3 34.1 - - + +
108P GLY* 4.9 2.2 - - - -
111P TYR* 3.6 40.5 - - + -
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Residues in contact with GLU 57 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53P ASP 3.1 19.4 + - - +
54P ASP* 4.2 15.6 - - - +
56P VAL* 1.3 79.2 - - - +
58P GLY* 1.3 60.7 + - - +
60P GLN* 3.5 24.8 + - + +
61P ALA* 3.7 12.0 + - - +
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Residues in contact with GLY 58 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P LEU 4.7 2.9 - - - +
42P PRO* 5.0 13.5 - - - +
43P ILE* 3.8 21.1 - - - +
54P ASP 3.0 21.2 + - - -
55P VAL 3.7 0.9 - - - -
56P VAL 3.2 0.2 - - - -
57P GLU* 1.3 76.2 - - - +
59P LEU* 1.3 62.0 + - - +
61P ALA* 3.8 7.6 + - - +
62P ALA* 3.7 11.3 + - - +
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Residues in contact with LEU 59 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43P ILE* 3.8 23.6 - - + -
55P VAL* 2.9 17.9 + - + +
56P VAL* 3.0 9.8 + - - +
58P GLY* 1.3 77.2 - - - +
60P GLN* 1.3 59.1 + - - +
62P ALA* 2.8 20.2 + - - +
63P ILE* 3.2 20.9 + - + +
72P LEU* 3.6 37.0 - - + -
76P ALA* 4.7 0.4 - - + -
77P LEU* 4.2 12.3 - - + -
108P GLY* 3.9 33.7 - - - +
111P TYR* 4.3 15.0 - - + -
112P CYS* 4.2 11.9 - - - -
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Residues in contact with GLN 60 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56P VAL* 2.9 32.8 + - - +
57P GLU* 3.7 21.0 - - - +
58P GLY 3.4 0.2 - - - -
59P LEU* 1.3 76.2 - - - +
61P ALA* 1.3 61.9 + - - +
62P ALA 3.2 1.2 + - - -
63P ILE* 3.6 11.2 + - - +
64P GLU* 3.3 27.3 + - - +
111P TYR* 3.0 27.3 + - + +
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Residues in contact with ALA 61 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39P LEU* 5.9 1.3 - - - +
57P GLU 3.7 8.4 + - - +
58P GLY* 4.2 9.0 - - - +
59P LEU 3.3 0.4 - - - -
60P GLN* 1.3 77.7 - - - +
62P ALA* 1.3 57.1 + - - +
64P GLU* 3.8 11.6 - - - +
65P ALA* 3.1 29.8 + - - +
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Residues in contact with ALA 62 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39P LEU* 4.7 20.4 - - + +
43P ILE* 4.1 12.6 - - + -
58P GLY 3.7 10.4 + - - +
59P LEU 2.8 13.6 + - - +
61P ALA* 1.3 77.1 - - - +
63P ILE* 1.3 56.8 + - - +
64P GLU 3.1 4.0 - - - -
65P ALA* 5.5 0.2 - - - -
66P GLY* 3.0 28.0 + - - +
67P LYS 3.4 5.7 + - - +
72P LEU* 3.8 21.8 - - + -
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Residues in contact with ILE 63 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59P LEU* 3.2 30.6 + - + +
60P GLN* 3.7 10.8 - - - +
62P ALA* 1.3 73.5 - - - +
64P GLU* 1.3 58.1 + - + +
66P GLY 2.9 14.7 - - - +
67P LYS* 3.2 29.2 + - - +
68P ASP 4.0 1.1 - - - +
69P PRO* 4.0 25.1 - - + +
72P LEU* 4.1 12.6 - - + -
111P TYR* 5.0 11.4 - - + -
112P CYS* 5.8 4.3 - - - -
115P ASN* 5.1 15.9 - - + +
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Residues in contact with GLU 64 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60P GLN* 3.3 19.5 + - - +
61P ALA* 3.9 9.4 - - - +
62P ALA 3.1 0.4 - - - -
63P ILE* 1.3 77.1 - - + +
65P ALA* 1.3 60.6 + - + +
66P GLY 3.1 9.7 + - - +
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Residues in contact with ALA 65 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P LEU* 5.3 17.3 - - + +
61P ALA 3.1 14.5 + - - +
62P ALA* 5.5 0.2 - - - -
64P GLU* 1.3 77.4 - - + +
66P GLY* 1.3 55.3 + - - +
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Residues in contact with GLY 66 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39P LEU* 5.2 8.3 - - - +
62P ALA* 3.0 15.6 + - - +
63P ILE 2.9 13.3 - - - +
64P GLU 3.5 5.5 - - - +
65P ALA* 1.3 80.4 - - - +
67P LYS* 1.3 71.1 - - - +
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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