Contacts of the helix formed by residues 3 - 19 (chain A) in PDB entry 1UA4
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 THR 3 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A PRO* 1.3 77.3 - - + +
4A TRP* 1.3 65.9 + - - +
5A GLU* 3.5 8.9 + - - +
6A GLU* 3.0 37.7 + - - +
7A LEU* 3.0 21.4 + - - +
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Residues in contact with TRP 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A THR* 1.3 75.1 - - - +
5A GLU* 1.3 57.4 + - - +
7A LEU* 3.1 24.1 + - + +
8A TYR* 2.9 37.8 + + + -
359A ARG* 4.2 4.9 - - - -
363A LEU* 4.0 14.1 - - + -
392A VAL* 4.7 12.8 - - + -
400A GLU* 3.1 36.4 + - - -
411A GLU* 3.8 9.4 - - - -
412A GLY* 3.8 21.3 - - - -
423A PHE* 3.3 24.5 - + - -
424A ILE* 4.0 13.5 - - + -
425A PRO* 3.4 42.3 - - + +
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Residues in contact with GLU 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A THR* 3.3 8.2 - - - +
4A TRP* 1.3 78.8 - - + +
6A GLU* 1.3 62.0 + - + +
8A TYR* 3.3 6.5 + - - +
9A LYS* 3.1 22.7 + - - +
388A THR* 3.7 12.0 - - - +
390A VAL 4.6 0.3 - - - +
391A PRO* 4.9 2.1 - - - +
392A VAL* 3.5 19.1 + - + +
427A LYS* 2.8 33.1 + - - -
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Residues in contact with GLU 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PRO* 3.1 19.5 - - + +
3A THR* 3.0 42.2 + - - +
5A GLU* 1.3 75.6 - - + +
7A LEU* 1.3 65.3 + - - +
9A LYS* 3.3 7.0 + - - +
10A ASN* 2.9 33.9 + - - +
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Residues in contact with LEU 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PRO* 3.5 33.4 - - + +
3A THR 3.0 16.6 + - - +
4A TRP* 3.1 40.1 + - + +
6A GLU* 1.3 76.4 - - - +
8A TYR* 1.3 63.4 + - - +
10A ASN* 3.4 9.9 + - + +
11A ALA* 3.0 24.8 + - - +
359A ARG* 3.8 38.1 - - - +
360A ASP* 4.9 2.2 - - - +
363A LEU* 3.6 15.4 - - + +
411A GLU* 4.4 10.3 - - + +
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Residues in contact with TYR 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TRP* 2.9 27.5 + - + -
5A GLU* 3.5 10.5 - - - +
7A LEU* 1.3 77.2 - - - +
9A LYS* 1.3 63.6 + - - +
11A ALA* 3.2 4.7 + - - +
12A ILE* 3.0 24.0 + - - +
363A LEU* 3.5 46.6 - - + +
366A ALA* 3.5 15.6 - - + +
367A LEU* 3.7 24.0 - - + +
388A THR* 5.2 4.5 - - + -
392A VAL* 4.1 11.7 - - + -
424A ILE* 4.3 0.7 - - - +
425A PRO* 2.6 33.1 + - + -
426A THR* 3.4 13.0 - - - -
427A LYS* 3.6 41.9 + - + -
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Residues in contact with LYS 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLU 3.1 11.3 + - - +
6A GLU* 3.6 10.8 - - - +
7A LEU 3.3 0.2 - - - -
8A TYR* 1.3 79.9 - - - +
10A ASN* 1.3 67.8 - - - +
12A ILE* 3.1 25.1 - - + +
13A GLU* 2.8 47.7 + - + +
385A ARG* 4.5 14.8 - - - +
388A THR* 5.2 10.5 - - + +
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Residues in contact with ASN 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A PRO* 5.3 4.6 - - - +
6A GLU* 2.9 28.2 + - - +
7A LEU* 3.9 14.6 - - + +
9A LYS* 1.3 80.0 - - - +
11A ALA* 1.3 57.3 + - - +
13A GLU* 3.5 5.8 + - - +
14A LYS* 3.0 30.8 + - - +
360A ASP* 6.2 1.1 - - - -
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Residues in contact with ALA 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU 3.0 17.7 + - - +
8A TYR 3.4 5.6 - - - +
10A ASN* 1.3 77.6 - - - +
12A ILE* 1.3 58.8 + - - +
14A LYS* 3.4 5.6 + - - +
15A ALA* 2.9 30.0 + - - +
360A ASP* 3.6 36.7 - - + +
363A LEU* 3.7 18.6 - - + -
364A PHE* 4.4 4.6 - - - +
367A LEU* 5.8 0.2 - - + -
453A PHE* 4.2 2.9 - - - -
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Residues in contact with ILE 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A TYR 3.0 9.6 + - - +
9A LYS* 3.1 25.8 - - + +
11A ALA* 1.3 73.8 - - - +
13A GLU* 1.3 72.0 + - - +
15A ALA* 4.4 1.6 - - - -
16A ILE* 2.9 60.4 + - + +
364A PHE* 3.7 20.6 - - + -
367A LEU* 3.5 19.7 - - + +
381A LEU* 5.6 0.4 - - + -
384A ILE* 3.7 31.0 - - + -
385A ARG* 4.0 17.7 - - + -
388A THR* 4.5 7.9 - - + -
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Residues in contact with GLU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LYS* 2.8 53.1 + - + +
10A ASN* 3.9 6.1 - - - +
12A ILE* 1.3 83.1 - - - +
14A LYS* 1.3 63.6 + - - +
16A ILE* 3.6 4.6 + - - +
17A LYS* 3.6 16.8 + - - +
385A ARG* 3.1 37.3 + - - -
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Residues in contact with LYS 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ASN 3.0 19.3 + - - +
11A ALA* 3.7 5.2 - - - +
13A GLU* 1.3 78.5 - - - +
15A ALA* 1.3 57.0 + - - +
17A LYS* 3.3 13.7 + - + +
18A SER* 3.0 28.8 + - - +
357A HIS* 5.2 5.5 - - - +
360A ASP* 4.7 16.0 + - + +
453A PHE* 3.4 49.1 + - + +
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Residues in contact with ALA 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ALA 2.9 18.1 + - - +
12A ILE 3.8 2.2 - - - +
14A LYS* 1.3 73.6 - - - +
16A ILE* 1.3 65.8 + - - +
17A LYS 3.0 1.8 - - - -
18A SER* 3.5 9.0 - - - -
19A VAL* 2.9 33.2 + - + +
364A PHE* 3.6 40.8 - - + -
381A LEU* 6.0 0.2 - - - -
453A PHE* 3.7 12.0 - - + -
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Residues in contact with ILE 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ILE* 2.9 45.4 + - + +
13A GLU 4.0 4.9 - - - +
14A LYS 3.4 0.2 - - - -
15A ALA* 1.3 72.5 - - - +
17A LYS* 1.3 57.6 + - + +
20A PRO* 3.2 22.9 - - - +
381A LEU* 4.3 36.1 - - + +
382A GLU* 5.1 1.1 - - - +
385A ARG* 3.0 50.5 - - + +
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Residues in contact with LYS 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLU 3.6 8.6 + - - +
14A LYS* 3.3 13.7 + - + +
15A ALA 3.0 0.2 - - - -
16A ILE* 1.3 81.8 - - - +
18A SER* 1.3 77.0 + - - +
20A PRO* 3.6 8.8 - - - +
21A LYS* 2.8 49.7 - - - +
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Residues in contact with SER 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LYS* 3.0 19.2 + - - -
15A ALA* 3.5 1.7 - - - -
17A LYS* 1.3 92.1 - - - +
19A VAL* 1.3 66.5 + - - +
20A PRO 3.3 0.7 - - - -
21A LYS* 2.9 25.6 + - - +
22A VAL 4.0 0.2 + - - -
452A SER* 2.8 45.9 + - - -
453A PHE* 3.2 18.0 - - - -
455A LEU* 4.6 0.5 - - - +
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Residues in contact with VAL 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ALA* 2.9 27.7 + - + +
16A ILE* 5.5 0.2 - - - -
18A SER* 1.3 71.5 + - - +
20A PRO* 1.3 64.1 - - + +
21A LYS 2.9 6.1 + - - -
22A VAL* 3.1 17.8 + - - +
125A TYR* 3.9 28.7 - - + -
127A VAL* 3.5 22.5 - - + +
364A PHE* 3.9 27.8 - - + -
381A LEU* 5.7 3.8 - - + -
448A ILE* 4.0 8.5 - - + -
449A GLY* 4.2 9.0 - - - -
452A SER* 3.8 17.7 - - - +
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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