Contacts of the helix formed by residues 51 - 63 (chain D) in PDB entry 4UNA
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 HIS 51 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D TYR* 2.6 38.5 + + - -
47D LEU* 2.9 35.2 + - + +
50D GLN* 1.3 82.2 - - + +
52D ILE* 1.3 80.1 + - + +
54D PRO* 3.7 5.9 - - - +
55D LEU* 3.4 29.4 + - + +
115D VAL* 6.0 1.3 - - + -
184D PRO* 4.8 2.7 - - + -
185D LEU 3.0 31.2 + - - -
186D PRO* 3.9 4.8 - - + +
187D PRO* 4.4 5.8 - - + +
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Residues in contact with ILE 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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14D LEU* 4.3 9.8 - - + +
17D LEU* 3.9 20.6 - - + -
40D ILE* 3.8 38.6 - - + -
42D GLN* 5.0 4.3 - - + +
47D LEU* 2.9 40.7 + - + +
48D ILE* 3.8 20.9 - - + +
51D HIS* 1.3 88.5 - - + +
53D ALA* 1.3 66.3 + - - +
55D LEU* 2.9 20.3 + - - +
56D MET* 3.0 11.3 + - + +
80D LEU* 4.0 14.6 - - + -
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Residues in contact with ALA 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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48D ILE 2.9 22.6 + - - +
49D LYS* 3.8 10.1 - - - +
52D ILE* 1.3 73.1 - - - +
54D PRO* 1.4 63.4 - - + +
56D MET* 4.4 0.7 - - - +
57D GLN* 2.8 28.5 + - - +
69D ILE* 3.3 21.1 - - + +
71D ILE* 4.8 4.5 - - + -
80D LEU* 3.7 19.0 - - + +
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Residues in contact with PRO 54 (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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49D LYS 3.3 21.1 - - - +
50D GLN* 3.2 27.4 - - - +
51D HIS 3.7 3.1 - - - +
52D ILE 3.5 3.1 - - - -
53D ALA* 1.4 88.3 - - + +
55D LEU* 1.3 63.3 + - + +
57D GLN* 3.4 6.4 + - + +
58D PHE* 3.1 23.7 + - - +
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Residues in contact with LEU 55 (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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10D ILE* 3.9 21.2 - - + +
13D TYR* 3.7 24.7 - - + -
14D LEU* 4.1 12.1 - - + -
51D HIS* 3.4 25.4 - - + +
52D ILE* 2.9 9.6 + - - +
54D PRO* 1.3 74.5 - - + +
56D MET* 1.3 65.5 + - - +
58D PHE* 3.4 6.9 + - + +
59D LEU* 3.2 21.5 + - - +
184D PRO* 3.5 43.3 - - + -
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Residues in contact with MET 56 (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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14D LEU* 3.7 28.3 - - + +
18D ILE* 4.5 4.7 - - + -
38D VAL* 4.1 21.1 - - + -
40D ILE* 4.2 23.3 - - + -
52D ILE* 3.0 12.0 + - + +
53D ALA* 3.3 4.7 + - - +
55D LEU* 1.3 76.0 - - - +
57D GLN* 1.3 51.7 + - - +
59D LEU* 3.2 5.5 + - - +
60D ILE* 2.8 41.2 + - + +
69D ILE* 3.7 14.6 - - + -
80D LEU* 4.3 14.8 - - + -
82D VAL* 3.8 20.2 - - + -
87D LEU* 3.9 23.3 - - - -
91D PHE* 4.3 5.8 - - + -
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Residues in contact with GLN 57 (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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53D ALA 2.8 18.1 + - - +
54D PRO* 3.6 7.6 - - + +
56D MET* 1.3 77.4 - - - +
58D PHE* 1.3 62.8 + - - +
60D ILE* 3.2 13.1 + - - +
61D ASP* 2.9 59.0 + - - +
67D SER 5.4 0.7 + - - +
68D LYS* 5.8 0.8 - - - +
69D ILE* 3.3 31.1 - - + +
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Residues in contact with PHE 58 (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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6D ASN* 4.0 18.8 - - - -
7D VAL* 4.7 11.4 - - + -
10D ILE* 3.5 35.9 - - + -
54D PRO 3.1 10.6 + - - +
55D LEU* 3.6 10.8 - - + +
56D MET 3.3 0.2 - - - -
57D GLN* 1.3 77.4 - - - +
59D LEU* 1.3 61.6 + - - +
61D ASP* 3.1 9.5 + - + +
62D GLU* 2.9 67.3 + - + +
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Residues in contact with LEU 59 (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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7D VAL* 4.3 17.7 - - + +
10D ILE* 4.7 5.6 - - + -
11D SER* 3.6 25.8 - - - +
14D LEU* 3.8 14.8 - - + -
55D LEU 3.2 10.8 + - - +
56D MET* 3.5 9.9 - - - +
58D PHE* 1.3 78.1 - - - +
60D ILE* 1.3 66.3 + - - +
62D GLU* 3.8 4.0 - - + +
63D LEU* 3.0 45.6 + - + +
87D LEU* 4.4 5.4 - - + -
90D TYR* 4.0 9.2 - - + +
91D PHE* 3.5 34.8 - - + -
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Residues in contact with ILE 60 (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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56D MET* 2.8 31.3 + - + +
57D GLN* 3.4 24.9 - - - +
59D LEU* 1.3 73.4 - - - +
61D ASP* 1.3 63.8 + - - +
63D LEU 3.6 0.2 + - - -
64D ASN 3.3 1.6 + - - -
65D VAL* 2.9 70.1 + - + +
67D SER 3.9 14.1 - - - +
69D ILE* 4.8 5.8 - - + -
82D VAL* 3.9 12.1 - - + -
87D LEU* 3.4 32.5 - - + -
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Residues in contact with ASP 61 (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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57D GLN* 2.9 41.3 + - - +
58D PHE* 3.6 10.8 - - + +
60D ILE* 1.3 80.5 - - - +
62D GLU* 1.3 64.4 - - + +
64D ASN* 3.0 22.0 + - - +
65D VAL 5.0 1.4 - - - +
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Residues in contact with GLU 62 (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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4D ASN* 4.7 11.7 + - - +
7D VAL* 4.4 22.2 - - + +
58D PHE* 2.9 60.6 + - + +
59D LEU* 3.8 7.2 - - + +
61D ASP* 1.3 77.3 - - - +
63D LEU* 1.3 65.6 + - + +
64D ASN* 3.2 8.1 + - - +
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Residues in contact with LEU 63 (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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7D VAL* 5.5 4.7 - - + -
59D LEU* 3.0 39.9 + - + +
62D GLU* 1.3 79.2 - - + +
64D ASN* 1.3 62.5 + - - +
65D VAL* 3.1 14.3 + - + -
86D LYS* 2.6 40.1 + - - +
87D LEU* 3.8 19.1 - - + -
90D TYR* 3.8 45.1 - - + +
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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