Contacts of the helix formed by residues 42 - 53 (chain D) in PDB entry 5TWV
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 ILE 42 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D PHE* 3.2 30.9 + - + +
39D LEU* 4.8 3.4 - - - +
41D PHE* 1.3 78.3 - - - +
43D THR* 1.3 57.8 + - - +
45D PRO* 3.2 21.6 - - - +
46D ILE* 4.2 4.5 + - - +
123D TYR* 4.1 13.4 + - + +
138D ALA* 6.2 3.6 - - + -
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Residues in contact with THR 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LEU 3.5 19.4 + - - -
40D LEU* 3.9 7.2 + - - -
41D PHE 3.4 0.4 - - - -
42D ILE* 1.3 76.3 - - - +
44D PHE* 1.3 60.4 + - - +
45D PRO 3.3 2.7 - - - -
46D ILE* 3.2 2.5 + - - +
47D LEU* 2.7 41.7 + - - +
119D THR* 4.8 11.0 - - - -
123D TYR* 3.6 27.8 + - - -
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Residues in contact with PHE 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C MET* 5.2 25.6 - - + -
81C CYS* 4.4 17.9 - - + -
40D LEU* 3.3 34.3 + - + -
41D PHE* 4.6 11.4 - + - +
42D ILE 3.5 0.2 - - - -
43D THR* 1.3 77.7 - - - +
45D PRO* 1.3 68.9 - - + +
47D LEU* 4.4 6.3 - - + -
48D PHE* 2.8 38.2 + - + +
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Residues in contact with PRO 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C ILE* 5.5 13.3 - - + +
78C SER* 4.6 22.7 - - - -
81C CYS* 5.7 0.2 - - + -
41D PHE 3.7 13.7 - - - +
42D ILE* 3.2 16.4 - - - +
44D PHE* 1.3 98.7 - - + +
46D ILE* 1.3 56.8 + - + +
48D PHE* 4.5 1.3 - - + +
49D ILE* 3.2 27.7 + - - +
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Residues in contact with ILE 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C LEU* 5.1 18.7 - - + +
42D ILE 4.2 6.2 + - - +
43D THR 3.2 6.3 + - - +
45D PRO* 1.3 77.9 - - - +
47D LEU* 1.3 65.3 + - - +
49D ILE* 4.2 4.0 - - - +
50D GLY* 3.6 14.0 + - - -
123D TYR* 4.7 17.3 - - + +
126D ASN* 5.5 5.7 - - - +
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Residues in contact with LEU 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D THR* 2.7 28.5 + - - +
44D PHE* 4.2 5.4 - - + +
46D ILE* 1.3 74.1 - - - +
48D PHE* 1.3 63.3 + - - +
50D GLY* 3.5 2.6 + - - -
51D TRP* 3.1 21.9 + - - +
122D VAL* 4.5 22.0 - - + -
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Residues in contact with PHE 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C LEU* 5.6 9.6 - - + -
74C ILE* 5.1 15.9 - - + -
44D PHE* 2.8 27.2 + - + +
45D PRO* 4.5 2.2 - - + +
47D LEU* 1.3 71.8 - - - +
49D ILE* 1.3 60.1 + - - +
51D TRP* 3.0 18.8 + - + +
52D GLY* 2.9 24.8 + - - -
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Residues in contact with ILE 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C LEU* 6.4 2.7 - - + -
62C THR* 5.8 1.1 - - - +
63C LEU* 4.8 18.8 - - + -
66C LEU* 4.4 9.0 - - + +
74C ILE* 5.1 10.0 - - + +
45D PRO 3.2 20.8 + - - +
46D ILE* 4.5 3.8 - - - +
47D LEU 3.4 0.4 - - - -
48D PHE* 1.3 78.0 - - - +
50D GLY* 1.3 57.7 + - - +
52D GLY* 3.2 1.0 + - - +
53D SER* 2.8 37.9 + - - +
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Residues in contact with GLY 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C LEU* 6.5 1.3 - - - -
46D ILE 3.6 10.3 + - - -
47D LEU 3.5 7.2 + - - -
48D PHE 3.2 0.6 - - - -
49D ILE* 1.3 78.4 - - - +
51D TRP* 1.3 59.9 + - - +
53D SER* 4.3 5.2 - - - -
54D GLN* 3.5 21.7 + - - +
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Residues in contact with TRP 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C HIS* 4.0 31.0 - + - -
73C LEU* 4.6 16.4 - - + -
47D LEU 3.1 13.2 + - - +
48D PHE* 3.0 23.3 + - + +
50D GLY* 1.3 82.4 - - - +
52D GLY* 1.3 62.4 + - - +
54D GLN* 4.2 2.4 + - - +
55D SER* 3.5 21.8 + - - -
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Residues in contact with GLY 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C LEU* 3.6 19.2 - - - +
70C HIS* 4.1 23.3 + - - -
48D PHE 2.9 12.0 + - - -
49D ILE 3.7 1.8 - - - -
51D TRP* 1.3 79.1 - - - +
53D SER* 1.3 60.6 + - - +
54D GLN 3.1 5.2 - - - -
55D SER* 3.1 13.9 + - - -
56D SER* 3.3 11.8 + - - -
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Residues in contact with SER 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C THR* 3.8 28.5 - - - -
66C LEU* 3.8 19.9 - - - +
49D ILE* 2.8 23.4 + - - +
50D GLY* 4.9 3.6 - - - -
52D GLY* 1.3 71.0 - - - +
54D GLN* 1.3 56.9 + - - +
55D SER 3.3 1.3 - - - -
56D SER 4.4 0.9 - - - -
57D LYS 3.0 30.5 - - - +
58D VAL* 3.1 7.8 - - - +
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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