Contacts of the helix formed by residues 30 - 44 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C ASN* 3.7 43.1 - - + +
26D ILE* 2.9 23.5 + - + +
29D THR* 1.3 95.3 + - - +
31D HIS* 1.3 62.5 + - - +
32D HIS 3.6 0.2 - - - -
33D GLN* 3.8 1.3 - - - +
34D THR* 2.8 34.3 + - - -
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Residues in contact with HIS 31 (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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176C GLU* 3.8 10.5 + - - -
180C TYR* 2.6 30.1 + + - -
185C ASN* 3.6 27.5 - - + +
26D ILE* 3.2 17.6 + - + -
27D HIS* 3.4 24.9 - - + +
30D LYS* 1.3 73.5 - - - +
32D HIS* 1.3 64.9 + - - +
34D THR* 3.2 15.5 + - - -
35D TYR* 3.2 29.5 + - + -
177D HIS* 3.5 37.6 + + + +
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Residues in contact with HIS 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D LEU* 3.4 12.0 - - + +
6D PRO* 3.5 18.4 - - + -
27D HIS* 2.9 16.0 + - - +
28D HIS* 3.4 15.0 + - - +
31D HIS* 1.3 72.4 - - - +
33D GLN* 1.3 63.0 + - - +
35D TYR* 3.1 10.2 + - + +
36D VAL* 3.1 17.6 + - + +
77D GLY 4.4 1.6 - - - -
78D HIS* 2.9 39.7 + - - -
81D HIS* 3.5 17.0 - - + +
82D SER* 3.4 25.1 - - - -
85D TRP* 2.9 30.6 + - + -
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Residues in contact with GLN 33 (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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5D LEU* 3.4 35.8 - - + +
28D HIS 3.3 5.7 + - - +
29D THR 3.2 29.3 - - - +
30D LYS 3.8 1.3 - - - +
31D HIS 3.3 0.4 - - - -
32D HIS* 1.3 78.1 - - - +
34D THR* 1.3 57.1 + - - +
36D VAL* 3.2 14.9 + - - +
37D ASP* 2.8 65.7 + - - +
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Residues in contact with THR 34 (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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30D LYS* 2.8 23.6 + - - -
31D HIS* 3.2 7.1 + - - -
33D GLN* 1.3 76.1 - - - +
35D TYR* 1.3 64.4 + - + +
37D ASP* 3.3 8.1 + - - +
38D ASN* 2.8 50.3 + - - +
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Residues in contact with TYR 35 (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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130C PHE* 3.6 27.1 - + - -
31D HIS* 3.2 30.6 + - + +
32D HIS* 3.1 8.5 + - - +
34D THR* 1.3 81.4 - - + +
36D VAL* 1.3 56.0 + - - +
39D ALA* 2.9 32.2 + - - +
73D ASN 4.1 8.3 - - - -
74D ASN* 3.4 36.2 - - - +
77D GLY* 3.9 11.7 - - - -
78D HIS* 3.8 8.3 - - - +
81D HIS* 3.4 30.5 - + - -
152D GLN* 2.9 22.6 + - + -
175D TRP* 3.7 18.5 - - - -
177D HIS* 4.2 6.8 - + - -
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Residues in contact with VAL 36 (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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3D TYR* 3.4 34.4 - - + +
4D THR* 3.9 14.8 - - - +
5D LEU* 4.1 7.4 - - + +
32D HIS* 3.1 21.6 + - + +
33D GLN* 3.2 18.1 + - - +
35D TYR* 1.3 73.1 - - - +
37D ASP* 1.3 65.9 + - - +
39D ALA* 3.8 4.6 - - - +
40D ASN* 3.1 28.1 + - - +
78D HIS* 3.5 37.2 - - + +
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Residues in contact with ASP 37 (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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33D GLN* 2.8 52.5 + - - +
34D THR* 3.6 7.5 - - + +
36D VAL* 1.3 76.3 - - - +
38D ASN* 1.3 65.3 + - - +
40D ASN* 3.5 8.7 + - - +
41D LYS* 3.2 41.5 + - - +
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Residues in contact with ASN 38 (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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34D THR* 2.8 37.7 + - - +
37D ASP* 1.3 74.7 - - - +
39D ALA* 1.3 62.2 + - - +
41D LYS* 3.5 25.9 + - - +
42D ALA* 3.2 22.0 + - - +
70D ALA* 5.5 0.7 - - - +
74D ASN* 3.3 35.5 + - - +
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Residues in contact with ALA 39 (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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3D TYR* 3.7 31.0 - - + -
35D TYR 2.9 18.1 + - - +
36D VAL* 3.4 1.3 + - - +
38D ASN* 1.3 73.6 - - - +
40D ASN* 1.3 65.9 + - - +
42D ALA* 3.1 8.2 + - - +
43D LEU* 3.0 29.3 + - - +
71D LEU* 4.1 4.4 - - + +
74D ASN* 3.7 6.6 - - - +
75D ALA* 3.9 20.4 - - + +
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Residues in contact with ASN 40 (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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2D ALA* 3.7 16.0 - - + +
3D TYR* 2.8 55.5 + - - +
36D VAL* 3.1 26.8 + - - +
37D ASP* 3.8 8.5 + - - +
39D ALA* 1.3 76.3 - - - +
41D LYS* 1.3 61.5 + - - +
43D LEU* 3.3 9.0 + - - +
44D GLU* 3.1 28.3 + - - +
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Residues in contact with LYS 41 (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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37D ASP* 3.2 28.6 + - - +
38D ASN* 3.7 26.0 + - - +
39D ALA 3.3 0.2 - - - -
40D ASN* 1.3 77.7 - - + +
42D ALA* 1.3 61.7 - - - +
43D LEU 3.4 0.5 + - - -
44D GLU* 3.8 21.2 + - - +
67D LYS* 4.7 3.1 + - - -
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Residues in contact with ALA 42 (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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38D ASN 3.2 10.5 + - - +
39D ALA* 3.1 9.7 + - - +
41D LYS* 1.3 78.5 - - - +
43D LEU* 1.4 58.8 + - - +
46D THR* 3.3 9.4 - - - +
67D LYS* 3.0 40.2 + - + +
70D ALA* 4.1 20.0 - - + -
71D LEU* 3.7 24.5 - - + +
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Residues in contact with LEU 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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3D TYR* 3.7 37.9 - - + +
39D ALA 3.0 21.9 + - - +
40D ASN* 3.9 8.1 - - - +
41D LYS 3.2 0.4 - - - -
42D ALA* 1.4 77.5 - - - +
44D GLU* 1.3 57.9 + - - +
45D GLY 3.0 0.7 + - - -
46D THR* 2.8 52.0 + - - +
48D PHE* 3.9 25.1 - - + +
49D ALA* 4.0 24.4 - - + +
56D LEU* 4.1 5.4 - - + -
71D LEU* 3.8 27.1 - - + -
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Residues in contact with GLU 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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40D ASN* 3.1 17.3 + - - +
41D LYS* 3.9 18.6 - - - +
42D ALA 3.7 0.4 - - - -
43D LEU* 1.3 74.1 - - - +
45D GLY* 1.4 57.1 + - - +
46D THR 4.0 0.7 + - - -
49D ALA* 5.4 3.4 - - - -
67D LYS* 4.2 10.4 + - - -
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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