Contacts of the helix formed by residues 31 - 43 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A GLY* 1.3 72.8 - - - +
32A VAL* 1.3 62.0 + - + +
34A ALA* 4.3 2.0 - - - +
35A ALA* 3.4 20.3 + - - +
100A ILE* 4.2 7.7 - - - +
104A GLN* 5.9 0.2 - - - +
247A TYR* 3.6 53.6 - - + +
249A SER* 3.8 6.8 - - - -
330A NAD 2.9 40.9 + - - +
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Residues in contact with VAL 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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31A ASN* 1.3 70.0 - - - +
33A GLY* 1.3 66.3 + - - +
35A ALA* 3.0 6.7 + - - +
36A VAL* 2.9 29.0 + - + +
96A THR* 3.8 22.0 - - + -
141A ILE* 4.0 13.0 - - + -
248A THR 3.5 23.3 - - - +
249A SER* 4.6 3.4 - - - +
252A VAL* 3.6 23.8 - - + -
253A ALA* 4.7 2.2 - - - +
330A NAD 2.8 49.1 + - + +
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Residues in contact with GLY 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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26A ILE* 4.0 8.0 - - - +
28A GLY 3.5 11.7 + - - -
29A LEU* 3.9 8.7 - - - +
30A GLY 3.6 3.4 + - - +
31A ASN 3.6 0.4 - - - -
32A VAL* 1.3 78.8 - - - +
34A ALA* 1.3 56.2 + - - +
36A VAL* 3.3 5.0 + - - +
37A ALA* 3.0 27.0 + - - +
96A THR* 3.4 29.0 + - - -
330A NAD 4.4 0.8 + - - -
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Residues in contact with ALA 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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29A LEU* 3.8 13.2 - - + +
30A GLY 3.0 20.6 + - - +
31A ASN* 4.4 2.2 - - - +
33A GLY* 1.3 75.7 - - - +
35A ALA* 1.3 56.2 + - - +
37A ALA* 3.5 3.6 + - - +
38A HIS* 2.9 29.1 + - - +
58A LYS* 4.4 4.5 - - - +
62A ASP* 4.2 20.2 - - - +
66A PHE* 4.1 2.3 - - + -
250C TYR* 3.5 22.8 + - + +
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Residues in contact with ALA 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 ASN 3.4 16.4 + - - +
32A VAL 3.0 5.6 + - - +
34A ALA* 1.3 73.8 - - - +
36A VAL* 1.3 60.8 + - - +
38A HIS* 4.4 1.8 - - - +
39A GLY* 2.9 24.6 + - - -
249A SER* 4.0 17.7 - - - +
250A TYR* 4.7 3.8 - - + -
253A ALA* 3.9 16.0 - - + +
257A ILE* 4.8 0.3 - - - +
38C HIS* 3.1 27.4 - - + +
250C TYR* 5.2 1.1 - - - -
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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
----------------------------------------------------------
26A ILE* 4.0 9.4 - - + -
32A VAL* 2.9 25.3 + - + +
33A GLY* 3.4 10.8 - - - +
35A ALA* 1.3 75.9 - - - +
37A ALA* 1.3 63.2 + - - +
39A GLY* 3.3 2.4 + - - -
40A LEU* 3.0 44.6 + - + +
94A ILE* 4.0 23.1 - - + -
96A THR* 4.6 3.1 - - + -
141A ILE* 4.6 4.3 - - + -
253A ALA* 3.7 29.6 - - - +
256A ALA* 4.5 9.4 - - + -
257A ILE* 3.8 12.9 - - + +
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Residues in contact with ALA 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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26A ILE* 3.7 13.9 - - + -
29A LEU* 4.4 1.8 - - + -
33A GLY 3.0 17.2 + - - +
34A ALA* 3.6 7.6 - - - +
36A VAL* 1.3 76.7 - - - +
38A HIS* 1.3 57.5 + - - +
40A LEU* 3.3 4.2 + - - +
41A ILE* 2.7 36.1 + - + +
49A TYR* 5.6 1.3 - - - -
51A PHE* 3.6 31.0 - - + -
66A PHE* 3.9 10.5 - - + -
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Residues in contact with HIS 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 ALA 2.9 17.7 + - - +
35A ALA* 3.9 4.7 - - - +
36A VAL 3.3 0.2 - - - -
37A ALA* 1.3 75.9 - - - +
39A GLY* 1.3 57.9 + - - +
41A ILE* 4.4 2.5 - - + +
42A ALA* 2.9 43.9 + - + +
66A PHE* 3.7 13.2 - + + -
73A LEU* 6.2 2.8 - - + +
35C ALA* 3.1 33.1 + - + -
38C HIS* 4.0 17.8 + + - +
39C GLY* 3.8 18.4 - - - -
250C TYR* 3.6 39.9 - + + +
253C ALA* 5.3 3.7 - - + +
254C THR* 5.0 10.2 + - - -
257C ILE* 5.5 2.0 - - + +
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Residues in contact with GLY 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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35A ALA 2.9 17.3 + - - -
36A VAL 3.3 2.2 + - - -
38A HIS* 1.3 79.9 - - - +
40A LEU* 1.3 58.0 + - - +
42A ALA* 4.1 0.9 - - - +
43A GLN* 3.0 34.6 + - - +
257A ILE* 4.0 11.9 - - - -
38C HIS* 3.9 14.9 - - - -
42C ALA* 4.1 10.2 - - - +
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Residues in contact with LEU 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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24A ILE* 3.8 36.6 - - + -
26A ILE* 4.5 6.5 - - + -
36A VAL* 3.0 37.2 + - + +
37A ALA* 3.7 2.5 - - - +
39A GLY* 1.3 71.7 - - - +
41A ILE* 1.3 62.9 + - - +
43A GLN* 3.2 3.5 + - - -
44A GLY 2.9 23.0 + - - -
45A VAL* 3.2 37.4 + - + +
49A TYR* 3.5 22.9 - - + +
94A ILE* 5.0 2.0 - - + -
257A ILE* 4.0 25.5 - - + +
260A ALA* 5.4 4.3 - - + -
261A LYS* 5.6 0.4 - - + -
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Residues in contact with ILE 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 ALA 2.7 24.9 + - - +
38A HIS* 4.2 3.4 - - + +
40A LEU* 1.3 74.5 - - - +
42A ALA* 1.3 60.7 + - - +
44A GLY* 3.1 12.1 + - - +
49A TYR* 3.5 30.7 - - + -
51A PHE* 4.2 13.9 - - + -
66A PHE* 3.7 38.8 - - + -
70A MET* 4.4 9.4 - - + -
73A LEU* 3.6 34.0 - - + +
75A ALA* 5.1 5.4 - - - +
79A ILE* 4.1 18.2 - - + -
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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 HIS* 2.9 37.9 + - + +
39A GLY 4.1 3.8 - - - +
40A LEU 3.3 0.2 - - - -
41A ILE* 1.3 73.6 - - - +
43A GLN* 1.3 58.9 + - - +
44A GLY 3.8 0.2 + - - -
73A LEU* 4.5 14.6 - - + +
39C GLY* 4.3 14.8 - - - +
42C ALA* 4.2 16.2 - - + -
43C GLN* 3.5 23.0 - - + +
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Residues in contact with GLN 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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39A GLY* 3.0 24.3 + - - +
40A LEU 3.2 1.8 + - - -
42A ALA* 1.3 77.8 - - - +
44A GLY* 1.3 64.6 + - - +
45A VAL* 3.5 15.4 + - + +
75A ALA* 4.9 3.0 - - - +
257A ILE* 4.2 10.3 - - - +
261A LYS* 3.1 32.0 + - - +
42C ALA* 3.6 32.9 + - + +
43C GLN* 4.6 5.6 - - - +
73C LEU* 5.9 2.4 - - - +
74C GLU* 3.6 12.4 + - - +
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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