Contacts of the helix formed by residues 31 - 43 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C GLY* 1.3 72.4 - - - +
32C VAL* 1.3 63.4 + - + +
34C ALA* 4.4 1.9 - - - +
35C ALA* 3.5 19.2 + - - +
247C TYR* 3.3 57.9 + - + +
249C SER* 3.9 5.5 - - - -
330C NAD 3.1 32.0 + - - +
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Residues in contact with VAL 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ASN* 1.3 72.2 - - - +
33C GLY* 1.3 58.6 + - - +
35C ALA* 3.2 4.0 + - - +
36C VAL* 2.9 31.9 + - + +
96C THR* 4.1 11.0 - - + -
141C ILE* 3.6 33.2 - - + -
248C THR 3.8 15.9 - - - +
249C SER* 4.5 5.8 - - - -
252C VAL* 3.8 17.3 - - + -
253C ALA 4.7 1.6 - - - +
330C NAD 2.8 54.6 + - + +
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Residues in contact with GLY 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ILE* 4.0 8.3 - - - +
28C GLY 3.3 23.6 + - - -
29C LEU* 3.7 9.5 - - - +
30C GLY 3.3 5.5 + - - +
32C VAL* 1.3 79.7 - - - +
34C ALA* 1.3 59.4 + - - +
36C VAL* 3.5 4.9 + - - +
37C ALA* 3.1 21.8 + - - +
96C THR* 3.9 13.1 + - - +
330C NAD 4.2 0.2 + - - -
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Residues in contact with ALA 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A TYR* 5.9 2.0 - - - +
250A TYR* 3.2 25.1 + - + +
29C LEU* 3.9 11.0 - - + +
30C GLY 2.8 21.0 + - - +
31C ASN* 4.4 2.0 - - - +
33C GLY* 1.3 71.9 - - - -
35C ALA* 1.3 57.0 + - - +
37C ALA* 3.3 3.6 + - - +
38C HIS* 2.8 30.7 + - - +
58C LYS* 4.2 5.8 - - - +
62C ASP* 4.0 19.5 - - - +
66C PHE* 4.1 1.4 - - + -
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Residues in contact with ALA 35 (chain C).
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* 3.1 26.1 - - + +
250A TYR* 5.2 0.7 - - - -
31C ASN 3.5 13.2 + - - +
32C VAL 3.2 9.3 + - - +
34C ALA* 1.3 73.8 - - - +
36C VAL* 1.3 59.9 + - - +
38C HIS* 3.4 2.4 + - - +
39C GLY* 2.9 24.9 + - - -
249C SER* 4.0 16.6 - - - +
250C TYR* 4.6 6.5 - - + -
253C ALA* 4.0 15.2 - - + +
257C ILE* 4.7 0.2 - - - +
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Residues in contact with VAL 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ILE* 4.1 9.6 - - + -
32C VAL* 2.9 27.0 + - + +
33C GLY* 3.7 9.4 - - - +
35C ALA* 1.3 75.8 - - - +
37C ALA* 1.3 63.7 + - - +
39C GLY* 3.4 1.2 + - - -
40C LEU* 3.1 33.1 + - + +
94C ILE* 3.8 32.5 - - + -
96C THR* 5.1 0.2 - - + -
141C ILE* 4.3 10.8 - - + -
253C ALA* 3.6 28.7 - - + +
256C ALA* 4.5 1.8 - - + -
257C ILE* 3.9 12.9 - - + +
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Residues in contact with ALA 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ILE* 3.8 14.1 - - + +
29C LEU* 4.3 2.0 - - + -
33C GLY 3.1 12.3 + - - +
34C ALA* 3.4 10.3 - - - +
36C VAL* 1.3 79.3 - - - +
38C HIS* 1.3 57.4 + - - +
40C LEU* 3.2 5.0 + - - +
41C ILE* 2.9 33.5 + - + +
49C TYR* 5.6 0.9 - - - -
51C PHE* 3.8 24.7 - - + -
66C PHE* 3.8 17.0 - - + -
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Residues in contact with HIS 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ALA* 3.1 35.7 + - + +
38A HIS* 4.0 16.0 + - - +
39A GLY* 3.9 16.1 - - - -
250A TYR* 3.5 40.1 - + + +
253A ALA* 5.1 4.0 - - + +
254A THR* 4.9 10.9 + - - -
257A ILE* 5.7 2.0 - - + +
34C ALA 2.8 19.6 + - - +
35C ALA* 3.9 5.4 - - - +
37C ALA* 1.3 69.5 - - - +
39C GLY* 1.3 59.5 + - - +
41C ILE* 4.5 2.9 - - + +
42C ALA* 2.9 43.0 + - + +
66C PHE* 3.7 11.4 - + - -
73C LEU* 6.3 0.8 - - + +
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Residues in contact with GLY 39 (chain C).
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* 3.8 15.3 - - - -
42A ALA* 4.3 8.8 - - - +
35C ALA 2.9 17.4 + - - -
36C VAL 3.8 2.7 - - - -
37C ALA 3.3 0.2 - - - -
38C HIS* 1.3 76.9 - - - +
40C LEU* 1.3 59.4 + - - +
42C ALA* 4.2 1.4 - - - +
43C GLN* 3.0 34.0 + - - +
257C ILE* 3.9 13.7 - - - -
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Residues in contact with LEU 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ILE* 3.7 42.6 - - + -
26C ILE* 4.3 6.7 - - + -
36C VAL* 3.1 30.7 + - + +
37C ALA* 3.7 4.5 - - - +
39C GLY* 1.3 76.1 - - - +
41C ILE* 1.3 60.1 + - - +
43C GLN 3.3 2.3 + - - -
44C GLY 2.9 22.7 + - - -
45C VAL* 3.0 34.7 + - + +
49C TYR* 3.4 22.6 + - + +
94C ILE* 4.9 2.7 - - + -
257C ILE* 4.2 24.9 - - + +
260C ALA* 5.2 5.2 - - + -
261C LYS* 5.8 0.2 - - + -
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Residues in contact with ILE 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ALA 2.9 18.6 + - - +
38C HIS* 4.1 4.3 - - + +
40C LEU* 1.3 73.5 - - - +
42C ALA* 1.3 65.1 + - - +
44C GLY* 3.0 13.6 + - - +
49C TYR* 3.6 31.4 - - + -
51C PHE* 4.4 9.2 - - + -
66C PHE* 3.5 44.4 - - + -
70C MET* 3.8 13.2 - - + -
73C LEU* 3.6 33.1 - - + +
75C ALA* 5.0 3.8 - - - +
79C ILE* 4.0 17.0 - - + -
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Residues in contact with ALA 42 (chain C).
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* 4.1 31.6 - - - +
42A ALA* 4.2 13.0 - - + -
43A GLN* 3.6 23.2 - - + +
38C HIS* 2.9 29.3 + - + +
39C GLY 4.2 0.2 - - - +
41C ILE* 1.3 73.3 - - - +
43C GLN* 1.3 60.3 + - - +
73C LEU* 4.2 17.2 - - + +
74C GLU* 4.8 2.6 - - - +
75C ALA* 6.0 0.2 - - - +
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Residues in contact with GLN 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ALA* 3.5 32.3 + - + +
43A GLN* 4.6 6.3 - - - +
73A LEU* 6.1 2.2 - - - +
74A GLU* 4.0 9.7 + - - +
39C GLY* 3.0 22.5 + - - +
40C LEU 3.3 1.6 + - - -
41C ILE 3.2 0.4 - - - -
42C ALA* 1.3 79.3 - - - +
44C GLY* 1.3 61.9 + - - +
45C VAL* 3.7 16.5 - - + +
75C ALA* 4.8 3.8 - - - +
257C ILE* 4.2 12.1 - - - +
261C LYS* 2.7 32.2 + - - +
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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