Contacts of the helix formed by residues 31 - 42 (chain D) in PDB entry 1HYH
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 ASN 31 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30D GLY* 1.3 71.8 - - - +
32D VAL* 1.3 61.4 + - + +
34D ALA* 4.2 3.1 - - - +
35D ALA* 3.3 21.1 + - - +
247D TYR* 3.6 54.3 + - + +
249D SER* 4.0 4.5 - - - -
330D NAD 3.1 35.1 + - - +
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Residues in contact with VAL 32 (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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31D ASN* 1.3 73.6 - - + +
33D GLY* 1.3 64.8 + - - +
35D ALA* 3.1 7.7 + - - +
36D VAL* 3.0 25.6 + - + +
96D THR* 4.2 9.2 - - + -
141D ILE* 3.8 34.5 - - + -
248D THR 3.7 23.1 - - - +
249D SER* 4.6 2.9 - - - +
252D VAL* 4.0 15.5 - - + -
253D ALA* 5.0 1.8 - - + -
330D NAD 2.9 46.7 + - + +
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Residues in contact with GLY 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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26D ILE* 4.1 8.7 - - - +
28D GLY 3.3 24.2 + - - -
29D LEU* 3.9 8.4 - - - +
30D GLY 3.3 5.2 + - - -
32D VAL* 1.3 78.5 - - - +
34D ALA* 1.3 57.2 + - - +
36D VAL* 3.4 4.9 + - - +
37D ALA* 3.1 26.3 + - - +
96D THR* 3.8 14.4 + - - +
330D NAD 4.2 0.2 + - - -
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Residues in contact with ALA 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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250B TYR* 3.1 25.7 + - + +
29D LEU* 3.9 11.7 - - + +
30D GLY 2.9 22.2 + - - +
31D ASN* 4.2 2.9 - - - +
33D GLY* 1.3 68.7 - - - -
35D ALA* 1.3 59.5 + - - +
37D ALA* 3.4 3.6 + - - +
38D HIS* 2.9 29.8 + - - +
58D LYS* 4.3 16.4 - - - +
62D ASP* 4.4 7.2 - - - +
66D PHE* 4.1 1.5 - - + -
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Residues in contact with ALA 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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38B HIS* 3.1 25.2 - - + -
31D ASN 3.3 13.1 + - - +
32D VAL 3.1 9.1 + - - +
34D ALA* 1.3 75.6 - - - +
36D VAL* 1.3 57.6 + - - +
38D HIS* 4.6 1.8 - - - +
39D GLY* 3.0 24.1 + - - -
249D SER* 4.0 18.4 - - - +
250D TYR* 4.5 6.7 - - + -
253D ALA* 3.9 15.7 - - + +
257D ILE* 4.7 0.3 - - - +
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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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26D ILE* 4.1 10.3 - - + -
32D VAL* 3.0 17.3 + - + +
33D GLY* 3.6 10.8 - - - +
35D ALA* 1.3 76.9 - - - +
37D ALA* 1.3 62.5 + - - +
39D GLY 3.5 0.2 + - - -
40D LEU* 3.2 41.2 + - + +
94D ILE* 3.9 25.1 - - + -
141D ILE* 4.3 18.4 - - + -
253D ALA* 3.6 28.7 - - + +
256D ALA* 4.5 2.5 - - + -
257D ILE* 3.7 12.1 - - + +
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Residues in contact with ALA 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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26D ILE* 3.7 14.4 - - + -
29D LEU* 4.5 2.0 - - + -
33D GLY 3.1 16.3 + - - +
34D ALA* 3.7 6.5 - - - +
36D VAL* 1.3 77.9 - - - +
38D HIS* 1.3 57.8 + - - +
40D LEU* 3.4 4.1 + - - +
41D ILE* 2.9 36.1 + - + +
49D TYR* 5.6 1.6 - - + -
51D PHE* 3.7 30.5 - - + -
66D PHE* 3.9 11.7 - - + -
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Residues in contact with HIS 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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35B ALA* 3.2 34.4 + - + -
38B HIS* 3.9 17.9 + + - +
39B GLY* 3.8 18.3 - - - -
250B TYR* 3.7 39.0 - + + +
253B ALA* 5.3 3.7 - - + +
254B THR* 4.8 10.9 + - - -
257B ILE* 5.9 1.0 - - + +
34D ALA 2.9 18.4 + - - +
35D ALA* 4.0 4.0 - - - +
37D ALA* 1.3 76.8 - - - +
39D GLY* 1.3 56.2 + - - +
41D ILE* 3.3 2.2 + - + -
42D ALA* 2.8 39.8 + - + +
66D PHE* 3.6 13.6 - + + -
73D LEU* 6.3 1.7 - - + +
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Residues in contact with GLY 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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38B HIS* 3.8 15.1 - - - -
42B ALA* 4.1 11.4 - - - +
35D ALA 3.0 17.3 + - - -
36D VAL 3.9 1.8 - - - -
38D HIS* 1.3 76.1 - - - +
40D LEU* 1.3 55.2 + - - +
42D ALA 3.9 0.2 + - - -
43D GLN* 2.7 37.8 + - - +
257D ILE* 4.0 12.1 - - - -
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Residues in contact with LEU 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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24D ILE* 4.0 36.3 - - + -
26D ILE* 4.4 5.2 - - + -
36D VAL* 3.2 38.5 + - + +
37D ALA* 3.8 3.1 - - - +
38D HIS 3.3 0.2 - - - -
39D GLY* 1.3 74.6 - - - +
41D ILE* 1.3 60.6 + - - +
43D GLN 3.4 2.1 + - - -
44D GLY 3.0 21.0 + - - -
45D VAL* 3.0 36.8 + - + +
49D TYR* 3.6 22.2 - - + +
94D ILE* 4.9 2.2 - - + -
257D ILE* 4.0 28.5 - - + -
260D ALA* 5.3 4.0 - - + -
261D LYS* 5.6 0.7 - - + -
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Residues in contact with ILE 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 ALA 2.9 22.2 + - - +
38D HIS* 3.9 4.3 - - + +
40D LEU* 1.3 74.8 - - - +
42D ALA* 1.3 63.5 + - - +
44D GLY* 3.1 11.9 + - - +
49D TYR* 3.5 32.1 - - + -
51D PHE* 4.3 9.2 - - + -
66D PHE* 3.8 40.8 - - + -
70D MET* 3.8 13.9 - - + -
73D LEU* 3.6 32.0 - - + +
75D ALA* 5.0 3.8 + - - +
79D ILE* 4.2 15.7 - - + -
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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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39B GLY* 4.1 29.2 - - - +
42B ALA* 4.1 16.6 - - + -
43B GLN* 3.3 26.7 - - + +
38D HIS* 2.8 27.8 + - + +
39D GLY 4.3 0.2 - - - +
41D ILE* 1.3 72.7 - - - +
43D GLN* 1.3 57.7 + - - +
44D GLY 3.9 0.3 + - - -
73D LEU* 4.4 16.4 - - + +
74D GLU* 4.8 1.2 - - - +
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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