Contacts of the helix formed by residues 30 - 43 (chain A) in PDB entry 1UES
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 LYS 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A GLU* 4.0 15.4 + - + +
26A PHE* 2.9 26.9 + - + +
29A GLY* 1.3 88.6 + - - +
31A HIS* 1.3 66.7 + - - +
32A LEU 3.5 0.7 - - - -
33A LYS* 3.0 18.0 + - + +
34A THR* 2.9 29.3 + - - -
369B ASN* 3.6 35.4 - - - +
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Residues in contact with HIS 31 (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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26A PHE 2.8 31.2 + - - -
27A HIS* 3.2 19.7 - - + +
30A LYS* 1.3 72.2 - - - +
32A LEU* 1.3 64.0 + - - +
34A THR* 3.2 8.2 + - - -
35A TYR* 3.0 42.2 + - + -
161A HIS* 3.4 35.1 + + + +
360B GLU* 3.5 11.4 - - - -
363B TYR* 6.4 0.2 - + - -
364B TYR* 2.8 31.8 + + - -
369B ASN* 3.4 28.2 - - + +
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Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 3.6 20.0 - - + -
6A ILE* 4.0 7.4 - - + +
27A HIS 3.0 9.4 + - - +
28A HIS* 3.4 27.1 + - + +
30A LYS 3.5 0.2 - - - -
31A HIS* 1.3 76.1 - - - +
33A LYS* 1.3 67.5 + - - +
35A TYR* 3.1 9.0 + - + -
36A VAL* 3.0 36.2 + - + +
71A THR* 4.0 23.8 - - - +
74A HIS* 3.6 38.8 - - + +
75A ASN* 3.9 14.6 - - - +
78A PHE* 4.0 6.7 - - + -
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Residues in contact with LYS 33 (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 LEU* 3.9 24.1 - - + +
28A HIS 3.6 4.0 + - - -
29A GLY 3.3 23.1 - - - +
30A LYS* 3.0 43.2 + - + +
31A HIS 3.3 0.2 - - - -
32A LEU* 1.3 77.3 - - - +
34A THR* 1.3 77.4 + - - +
36A VAL* 3.7 4.1 - - - +
37A ASP* 2.9 57.0 + - - +
369B ASN* 5.0 2.0 + - - -
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Residues in contact with THR 34 (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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30A LYS 2.9 19.2 + - - -
31A HIS* 3.2 7.4 + - - -
33A LYS* 1.3 93.1 + - - +
35A TYR* 1.3 63.3 + - + +
37A ASP* 3.4 4.3 + - - +
38A ASN* 2.9 51.4 + - - +
369B ASN* 4.8 5.0 + - - -
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Residues in contact with TYR 35 (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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31A HIS* 3.0 39.3 + - + -
32A LEU* 3.5 12.3 - - + +
34A THR* 1.3 79.6 - - + +
36A VAL* 1.3 57.9 + - - +
38A ASN* 5.5 0.4 - - - -
39A LEU* 2.9 31.0 + - - +
67A ASN* 3.4 25.6 - - - +
70A GLN* 3.0 44.1 + - + -
71A THR* 3.8 14.4 - - - +
74A HIS* 3.5 27.8 - + - -
159A TRP* 3.6 21.8 - - - -
161A HIS* 4.2 5.0 - + - -
319B PHE* 4.1 13.9 - + - -
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Residues in contact with VAL 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A HIS* 3.0 38.5 - - + +
4A GLU 3.6 22.4 - - - +
5A LEU* 4.1 8.3 - - + +
32A LEU* 3.0 29.5 + - + +
33A LYS* 3.7 6.3 - - - +
35A TYR* 1.3 74.1 - - - +
37A ASP* 1.3 63.3 + - - +
39A LEU* 3.3 5.2 + - - +
40A ASN* 2.9 33.5 + - - +
71A THR* 4.0 22.9 - - + -
75A ASN* 5.8 0.4 - - - +
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Residues in contact with ASP 37 (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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33A LYS* 2.9 45.8 + - - +
34A THR* 3.8 5.2 - - - +
36A VAL* 1.3 83.4 - - - +
38A ASN* 1.3 66.0 + - - +
40A ASN* 3.3 10.7 + - - +
41A LYS* 3.0 30.0 + - - +
444C ILE* 3.9 41.3 - - + +
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Residues in contact with ASN 38 (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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34A THR* 2.9 39.2 + - - +
35A TYR* 5.5 0.6 - - - -
37A ASP* 1.3 74.9 - - - +
39A LEU* 1.3 66.8 + - - +
41A LYS* 3.2 16.2 + - - +
42A LEU* 2.9 33.7 + - + +
67A ASN* 3.4 28.7 + - - +
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Residues in contact with LEU 39 (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 HIS* 3.9 30.3 - - + +
35A TYR 2.9 19.5 + - - +
36A VAL* 3.6 4.0 - - - +
38A ASN* 1.3 77.0 - - - +
40A ASN* 1.3 62.9 + - - +
42A LEU* 3.3 2.6 + - - -
43A ILE* 3.2 43.1 + - + +
53A LEU* 3.8 28.9 - - + -
56A ILE* 4.6 3.8 - - + -
64A ILE* 4.1 14.4 - - + +
67A ASN* 3.9 10.0 - - + +
68A ALA* 4.1 24.9 - - + +
71A THR* 4.1 9.6 - - - +
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Residues in contact with ASN 40 (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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1A MET 4.0 2.1 - - - +
2A THR* 3.7 16.1 - - - +
3A HIS* 2.7 61.3 + - - +
36A VAL* 2.9 23.2 + - - +
37A ASP* 3.6 10.2 + - - +
38A ASN 3.2 0.2 - - - -
39A LEU* 1.3 77.9 - - - +
41A LYS* 1.3 61.3 + - - +
43A ILE* 3.7 10.5 - - - +
44A ILE* 3.5 19.4 - - - +
441C LYS* 3.8 25.5 + - + +
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Residues in contact with LYS 41 (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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37A ASP* 3.0 22.1 + - - +
38A ASN* 3.8 15.6 + - - +
39A LEU 3.2 0.2 - - - -
40A ASN* 1.3 75.8 - - - +
42A LEU* 1.3 68.8 + - + +
43A ILE 3.4 0.5 + - - -
44A ILE* 3.4 26.8 + - - +
441C LYS* 3.1 32.5 - - + +
442C LEU* 4.1 20.1 + - + +
444C ILE* 2.8 43.4 + - - +
445C GLY* 5.0 0.8 - - - -
446C THR* 5.4 0.4 - - - +
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Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASN* 2.9 21.4 + - + +
39A LEU* 4.1 2.7 - - - +
41A LYS* 1.3 81.0 - - + +
43A ILE* 1.3 60.7 + - - +
44A ILE 3.5 2.3 + - - +
46A THR* 3.5 15.4 - - - +
63A GLY* 3.7 22.4 - - - +
64A ILE* 3.5 20.7 - - + +
67A ASN* 3.3 30.1 - - + +
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Residues in contact with ILE 43 (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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1A MET 4.4 11.0 - - - +
3A HIS* 3.7 34.1 - - + +
39A LEU* 3.2 34.1 + - + +
40A ASN* 3.7 11.2 - - - +
42A LEU* 1.3 78.1 - - - +
44A ILE* 1.3 67.8 + - + +
45A GLY 3.2 0.3 + - - -
46A THR* 2.8 28.8 + - - +
48A PHE* 3.9 33.4 - - + +
49A GLU* 3.3 16.9 - - - +
56A ILE* 4.4 2.7 - - + -
64A ILE* 4.1 12.8 - - + -
441C LYS* 6.0 0.9 - - - +
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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