Contacts of the helix formed by residues 28 - 41 (chain A) in PDB entry 1H13
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 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A THR* 1.3 80.2 - - - +
29A ILE* 1.3 64.5 + - - +
30A GLN 3.5 1.6 - - - -
31A GLN* 3.5 14.9 + - + -
32A LYS* 3.1 22.9 + - - +
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Residues in contact with ILE 29 (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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19A ASN* 3.9 8.1 - - - +
21A ALA* 3.7 18.4 - - + -
22A GLN* 3.4 42.2 - - + +
26A LYS* 3.5 31.9 - - + +
27A THR* 3.9 2.5 - - - +
28A ASN* 1.3 77.1 - - - +
30A GLN* 1.3 74.1 + - + +
32A LYS* 3.1 5.0 + - - +
33A VAL* 3.0 21.7 + - - +
369A TRP* 4.2 12.2 - - + -
394A SER* 3.7 28.3 - - - -
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Residues in contact with GLN 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASN* 3.9 8.1 + - - -
28A ASN 3.5 0.2 - - - -
29A ILE* 1.3 87.7 - - + +
31A GLN* 1.3 64.0 + - - +
33A VAL* 3.2 8.1 + - - +
34A ASN* 2.9 40.2 + - - +
90A LEU* 5.9 0.4 - - - +
394A SER* 3.1 22.3 - - - +
396A ASN* 2.8 30.6 + - - +
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Residues in contact with GLN 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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28A ASN* 3.5 20.2 + - + +
29A ILE 3.3 0.8 - - - -
30A GLN* 1.3 76.1 - - - +
32A LYS* 1.3 58.1 + - - +
34A ASN* 3.3 8.3 + - - +
35A SER* 2.9 30.7 + - - -
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Residues in contact with LYS 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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28A ASN 3.1 14.1 + - - +
29A ILE 3.1 8.5 + - - +
31A GLN* 1.3 72.8 - - - +
33A VAL* 1.3 65.7 + - - +
35A SER* 3.0 8.9 + - - +
36A THR* 2.8 32.5 + - - +
369A TRP* 2.7 68.0 + - + +
371A LEU 4.4 5.3 + - - -
386A TYR* 3.6 22.6 + - - +
390A MET* 3.9 14.8 - - + -
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Residues in contact with VAL 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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29A ILE* 3.0 20.5 + - + +
30A GLN* 3.5 9.6 - - - +
32A LYS* 1.3 77.3 - - - +
34A ASN* 1.3 65.1 + - - +
36A THR* 3.2 6.7 + - - -
37A PHE* 3.1 20.4 + - - +
90A LEU* 4.0 27.8 - - + -
387A MET* 4.2 3.9 - - + +
390A MET* 3.7 22.9 - - + +
391A LEU* 4.1 14.1 - - + -
394A SER* 3.3 31.6 - - - +
396A ASN* 4.0 10.3 - - - +
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Residues in contact with ASN 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 GLN* 2.9 32.6 + - - +
31A GLN* 3.6 7.5 - - - +
33A VAL* 1.3 81.5 - - - +
35A SER* 1.3 58.8 + - - +
37A PHE* 3.3 7.1 + - - +
38A ASP* 2.9 39.9 + - - +
90A LEU* 4.7 11.0 - - - +
92A LYS* 5.6 5.6 + - - +
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Residues in contact with SER 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 GLN 2.9 16.4 + - - -
32A LYS* 3.0 18.7 + - - +
34A ASN* 1.3 73.2 - - - +
36A THR* 1.3 60.5 + - - +
38A ASP* 4.2 8.5 - - - -
39A ASN* 2.8 45.4 + - - -
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Residues in contact with THR 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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32A LYS* 2.8 24.7 + - - +
33A VAL* 3.4 7.4 - - - -
35A SER* 1.3 77.9 + - - +
37A PHE* 1.3 62.8 + - - +
40A MET* 3.0 12.3 + - - +
373A GLN* 2.9 40.7 + - - +
386A TYR* 3.7 35.5 + - + -
387A MET* 3.8 23.8 - - + -
390A MET* 3.9 10.8 - - + +
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Residues in contact with PHE 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 VAL 3.1 5.1 + - - +
34A ASN* 3.7 6.5 - - - +
36A THR* 1.3 78.8 - - - +
38A ASP* 1.3 72.5 + - - +
40A MET 3.2 1.0 + - - -
41A PHE* 2.8 79.8 + + + +
86A ALA* 4.2 3.6 - - + -
87A ALA* 3.7 20.6 - - - -
90A LEU* 3.6 31.6 - - + -
92A LYS* 3.6 44.6 - - + -
95A GLU* 4.0 12.6 - - + -
387A MET* 3.7 15.9 - - - -
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Residues in contact with ASP 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 ASN* 2.9 27.5 + - - +
35A SER* 3.7 8.6 - - - +
37A PHE* 1.3 83.8 - - - +
39A ASN* 1.3 61.9 + - - +
41A PHE 3.5 1.9 - - - -
42A GLY* 3.0 27.7 + - - -
44A ASN* 4.5 0.2 + - - -
92A LYS* 3.7 22.5 + - - -
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Residues in contact with ASN 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 SER* 2.8 28.3 + - - +
38A ASP* 1.3 79.5 - - - +
40A MET* 1.4 65.6 + - - +
41A PHE 3.4 0.2 + - - -
42A GLY 3.6 0.9 + - - -
44A ASN* 2.9 26.5 + - - +
47A GLN* 3.6 28.9 + - + +
48A GLN* 3.4 10.9 + - - -
373A GLN* 3.3 23.6 + - - +
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Residues in contact with MET 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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36A THR 3.0 18.2 + - - +
37A PHE* 3.8 3.1 - - - +
39A ASN* 1.4 76.3 - - - +
41A PHE* 1.3 79.2 + - + +
42A GLY 3.4 0.8 + - - -
47A GLN 4.0 9.0 - - - +
48A GLN* 3.4 2.6 - - - +
49A LEU* 2.9 54.5 + - + -
50A TYR 3.3 7.5 + - - +
64A ILE* 4.2 18.6 - - + -
79A GLY 5.8 0.2 - - - +
82A TRP* 5.9 0.9 - - + -
83A GLY* 4.7 8.7 - - - +
373A GLN* 3.8 9.6 - - - +
383A GLY 4.2 7.6 - - - +
384A SER* 4.6 10.8 - - - +
387A MET* 3.6 36.1 - - + -
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Residues in contact with PHE 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 PHE* 2.8 68.3 + + + +
38A ASP* 3.5 4.7 - - - +
40A MET* 1.3 106.5 - - + +
42A GLY* 1.3 56.7 + - - +
43A TYR* 5.1 1.6 - - - -
50A TYR* 3.4 54.6 - + + -
64A ILE* 4.4 2.0 - - + -
83A GLY* 3.7 28.5 - - - -
86A ALA* 4.7 3.8 - - + -
95A GLU* 3.8 18.3 - - + +
99A LEU* 4.1 12.6 - - + -
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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