Contacts of the helix formed by residues 30 - 44 (chain A) in PDB entry 1Y67
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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26A ILE* 2.9 27.7 + - + +
29A THR* 1.3 102.2 + - - +
31A HIS* 1.3 59.3 + - - +
32A HIS 3.6 0.2 - - - -
33A GLN* 3.7 1.5 + - - +
34A THR* 2.9 35.9 + - - -
185B ASN* 3.7 42.2 - - + +
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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 ILE* 3.2 18.3 + - + -
27A HIS* 3.4 24.2 - - + +
30A LYS* 1.3 72.6 - - - +
32A HIS* 1.3 66.3 + - - +
34A THR* 3.2 7.6 + - - -
35A TYR* 3.2 37.0 + - + -
81A HIS* 5.1 0.2 - - - +
177A HIS* 3.5 40.0 + + + +
176B GLU* 3.8 8.3 + - - -
180B TYR* 2.6 33.6 + + - -
185B ASN* 3.8 22.9 - - + +
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Residues in contact with HIS 32 (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* 3.5 7.9 - - + +
6A PRO* 3.5 24.8 - - + +
27A HIS* 3.0 17.1 + - - +
28A HIS* 3.4 14.3 + - - +
31A HIS* 1.3 72.6 - - - +
33A GLN* 1.3 64.2 + - - +
35A TYR* 3.0 10.6 + - + +
36A VAL* 3.0 29.1 + - + +
77A GLY 4.6 1.1 - - - -
78A HIS* 3.0 35.9 + - - -
81A HIS* 3.4 23.4 - - + +
82A SER* 3.5 13.5 - - - -
85A TRP* 2.9 28.5 + - + -
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Residues in contact with GLN 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* 3.5 34.0 - - + +
28A HIS 3.3 6.6 + - - +
29A THR* 3.2 30.0 - - - +
30A LYS 3.7 1.5 + - - +
31A HIS 3.3 0.4 - - - -
32A HIS* 1.3 78.3 - - - +
34A THR* 1.3 56.0 + - - +
36A VAL* 3.3 15.4 + - - +
37A ASP* 2.9 65.6 + - - +
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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 22.8 + - - -
31A HIS* 3.5 6.5 - - - -
32A HIS 3.2 0.4 - - - -
33A GLN* 1.3 76.1 - - - +
35A TYR* 1.3 64.7 + - + +
37A ASP* 3.4 8.1 + - + +
38A ASN* 3.0 49.4 + - - +
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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* 3.2 31.7 + - + -
32A HIS* 3.0 7.4 + - - +
34A THR* 1.3 80.2 - - + +
36A VAL* 1.3 59.3 + - - +
39A ALA* 2.9 32.7 + - - +
73A ASN 4.2 7.0 - - - -
74A ASN* 3.5 34.1 - - - +
77A GLY* 3.8 6.3 - - - -
78A HIS* 3.9 9.0 - - - +
81A HIS* 3.3 38.4 - + - -
152A GLN* 2.9 22.2 + - + -
175A TRP* 3.6 22.3 - - - -
177A HIS* 4.3 4.0 - + - -
130B PHE* 3.7 25.7 - + - -
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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
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3A TYR* 3.5 33.9 - - + +
4A THR* 4.0 13.0 - - - +
5A LEU* 4.1 9.9 - - + +
32A HIS* 3.0 23.7 + - + +
33A GLN* 3.5 17.9 - - - +
35A TYR* 1.3 76.1 - - - +
37A ASP* 1.3 59.1 + - - +
39A ALA* 3.7 4.5 - - - +
40A ASN* 2.9 39.1 + - - +
78A HIS* 3.6 33.4 - - + +
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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 GLN* 2.9 52.7 + - - +
34A THR* 3.7 7.2 + - - +
36A VAL* 1.3 73.1 - - - +
38A ASN* 1.3 62.5 + - - +
40A ASN* 3.3 10.6 + - - +
41A LYS* 3.1 36.2 + - - +
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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* 3.0 36.4 + - - +
37A ASP* 1.3 76.6 - - - +
39A ALA* 1.3 66.0 + - - +
41A LYS* 3.4 24.2 + - - +
42A ALA* 3.2 22.0 + - - +
70A ALA* 5.5 0.5 - - - +
74A ASN* 3.3 33.5 + - - +
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Residues in contact with ALA 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 TYR* 3.7 27.6 - - + -
35A TYR 2.9 20.0 + - - +
36A VAL* 3.7 3.8 - - - +
38A ASN* 1.3 74.3 - - - +
40A ASN* 1.3 64.4 + - - +
42A ALA* 3.2 3.9 + - - +
43A LEU* 3.0 30.9 + - + +
71A LEU* 4.6 7.2 - - + -
74A ASN* 3.6 15.3 - - + +
75A ALA* 4.0 11.7 - - + +
78A HIS* 5.3 0.4 - - + -
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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 ALA* 3.4 22.6 - - + +
2A ALA* 3.2 10.5 + - - +
3A TYR* 2.8 52.8 + - - +
36A VAL* 2.9 27.9 + - - +
37A ASP* 3.5 9.8 + - - +
38A ASN 3.3 0.2 - - - -
39A ALA* 1.3 76.0 - - - +
41A LYS* 1.3 62.2 + - + +
43A LEU* 3.9 4.6 - - - +
44A GLU* 3.0 24.6 + - - +
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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* 3.1 22.6 + - - +
38A ASN* 3.6 27.9 + - - +
39A ALA 3.2 0.4 - - - -
40A ASN* 1.3 78.6 - - - +
42A ALA* 1.3 60.9 + - - +
43A LEU 3.4 0.3 + - - -
44A GLU* 3.5 16.7 + - - +
67A LYS* 3.9 7.3 + - - -
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Residues in contact with ALA 42 (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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38A ASN 3.2 9.7 + - - +
39A ALA* 3.2 5.0 + - - +
41A LYS* 1.3 78.6 - - - +
43A LEU* 1.3 60.0 + - - +
46A THR* 3.5 6.6 - - - +
67A LYS* 2.9 40.3 + - + +
70A ALA* 4.1 20.0 - - + -
71A LEU* 3.7 29.3 - - + +
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Residues in contact with LEU 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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2A ALA* 3.9 18.2 - - + -
3A TYR* 3.4 40.8 - - + +
39A ALA 3.0 18.3 + - - +
40A ASN 4.0 3.1 - - - +
41A LYS 3.2 0.4 - - - -
42A ALA* 1.3 74.9 - - - +
44A GLU* 1.3 67.4 + - - +
45A GLY 3.2 2.5 - - - -
46A THR* 2.9 27.0 + - - +
48A PHE* 3.8 34.8 - - + +
49A ALA* 4.0 18.7 - - + +
56A LEU* 3.9 8.5 - - + -
71A LEU* 3.7 24.7 - - + -
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Residues in contact with GLU 44 (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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40A ASN 3.0 13.5 + - - +
41A LYS* 3.5 16.4 - - - +
42A ALA 3.5 0.8 - - - -
43A LEU* 1.3 76.7 - - - +
45A GLY* 1.3 59.8 + - - +
46A THR 3.5 4.3 + - - +
49A ALA* 5.6 2.2 - - - +
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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