Contacts of the helix formed by residues 27 - 47 (chain U) in PDB entry 3H1J
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 THR 27 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23U HIS* 4.0 6.1 + - - -
24U CYS* 2.8 25.5 + - - -
26U GLN* 1.3 78.2 - - - +
28U GLU* 1.3 72.4 + - + +
29U LYS* 3.7 15.7 - - + +
30U CYS* 3.3 11.8 + - - +
31U VAL* 2.8 26.9 + - - +
68U CYS* 4.3 12.8 - - + -
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Residues in contact with GLU 28 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26U GLN 3.7 1.2 + - - -
27U THR* 1.3 79.2 - - + +
29U LYS* 1.3 74.4 + - + +
31U VAL* 3.3 6.2 + - - +
32U LYS* 3.3 40.2 + - + +
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Residues in contact with LYS 29 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27U THR* 3.5 9.4 - - + +
28U GLU* 1.3 83.7 - - + +
30U CYS* 1.3 68.6 + - - +
32U LYS* 3.0 8.9 + - - +
33U ALA* 2.7 25.1 + - + +
64U ALA* 4.3 18.4 - - + -
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Residues in contact with CYS 30 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24U CYS* 3.1 24.7 - - - -
25U GLU* 3.7 17.9 - - - +
27U THR* 3.3 14.4 + - - +
29U LYS* 1.3 75.9 - - - +
31U VAL* 1.3 54.2 + - - +
33U ALA* 2.7 12.2 + - - +
34U ARG* 2.4 39.8 + - - +
61U PHE* 3.8 9.8 - - + -
64U ALA* 4.2 8.0 - - - +
65U ARG* 3.7 35.4 - - - -
68U CYS* 5.4 1.1 - - - -
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Residues in contact with VAL 31 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25U GLU 3.3 12.8 + - - +
26U GLN* 2.8 21.1 - - - +
27U THR 2.8 21.3 - - - +
28U GLU* 3.3 8.1 - - - +
30U CYS* 1.3 75.3 - - - +
32U LYS* 1.3 77.7 + - - +
34U ARG* 3.5 7.3 - - - +
35U GLU* 2.8 33.0 + - + +
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Residues in contact with LYS 32 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28U GLU* 3.3 30.3 + - - +
29U LYS* 3.0 9.2 + - - +
31U VAL* 1.3 91.8 - - - +
33U ALA* 1.3 57.5 + - - +
35U GLU* 3.6 23.9 + - - +
36U ARG* 2.8 39.3 + - + +
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Residues in contact with ALA 33 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29U LYS 2.7 14.4 + - - +
30U CYS* 2.7 15.4 + - - +
32U LYS* 1.3 70.1 - - - +
34U ARG* 1.3 63.9 + - - +
36U ARG* 3.1 16.2 + - - +
37U LEU* 2.8 24.4 + - - +
57U GLU 4.8 0.5 - - - +
60U ASP* 4.3 9.6 - - + +
61U PHE* 3.7 32.6 - - - +
64U ALA* 5.1 1.8 - - + -
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Residues in contact with ARG 34 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25U GLU* 3.0 28.4 + - + +
30U CYS* 2.4 31.1 + - + +
31U VAL* 3.5 8.5 - - - +
33U ALA* 1.3 67.3 - - - +
35U GLU* 1.3 59.2 + - - +
37U LEU* 3.1 19.2 + - - +
38U GLU* 2.9 64.0 + - + +
61U PHE* 3.5 35.9 - - + -
65U ARG* 5.7 0.4 - - - +
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Residues in contact with GLU 35 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31U VAL* 2.8 18.1 + - + +
32U LYS* 3.6 32.2 + - - +
34U ARG* 1.3 74.9 - - - +
36U ARG* 1.3 67.0 + - + +
37U LEU 3.1 0.3 + - - -
38U GLU* 3.2 11.1 + - + +
39U LEU* 3.0 40.1 + - + +
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Residues in contact with ARG 36 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71T ARG* 4.6 3.3 - - - +
72T LYS* 5.7 0.4 - - - +
32U LYS* 2.8 30.8 + - + +
33U ALA* 3.4 12.2 + - - +
35U GLU* 1.3 76.9 - - + +
37U LEU* 1.3 60.7 + - - +
39U LEU* 3.4 13.5 - - + +
40U CYS* 3.2 19.6 + - - +
43U ARG* 5.3 0.2 + - - -
56U GLU* 4.6 8.5 + - - -
57U GLU* 3.5 39.7 + - - +
60U ASP* 3.6 29.7 + - - +
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Residues in contact with LEU 37 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138Q PRO* 5.0 2.5 - - + -
33U ALA 2.8 12.0 + - - +
34U ARG* 3.2 25.1 - - - +
36U ARG* 1.3 74.6 - - - +
38U GLU* 1.3 70.0 + - - +
39U LEU 3.0 1.3 - - - -
40U CYS* 2.8 14.4 + - - +
41U ASP* 2.8 18.3 + - + +
54U CYS* 3.8 18.4 - - + +
57U GLU* 3.4 27.8 - - + +
58U LEU* 3.5 37.2 - - + +
61U PHE* 4.4 16.4 - - + -
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Residues in contact with GLU 38 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34U ARG* 2.9 58.1 + - + +
35U GLU* 3.2 9.6 + - + +
37U LEU* 1.3 78.3 - - - +
39U LEU* 1.3 57.9 + - + +
41U ASP* 3.4 9.7 + - - +
42U ALA* 2.8 33.1 + - - +
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Residues in contact with LEU 39 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35U GLU* 3.0 35.5 + - + +
36U ARG* 3.4 17.3 - - + +
38U GLU* 1.3 76.1 - - + +
40U CYS* 1.3 68.4 + - - +
42U ALA* 3.4 7.2 + - + +
43U ARG* 3.2 28.6 + - - +
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Residues in contact with CYS 40 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72T LYS* 3.6 1.6 - - - -
36U ARG 3.2 8.7 + - - +
37U LEU 2.8 13.3 + - - +
39U LEU* 1.3 79.0 - - - +
41U ASP* 1.3 64.3 + - - +
43U ARG* 3.0 16.4 + - - +
44U VAL* 3.0 26.3 + - - +
52U GLU* 3.5 24.0 - - - -
53U GLN 3.5 2.7 - - - -
54U CYS* 2.0 51.4 - - + -
57U GLU* 3.6 15.5 - - + -
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Residues in contact with ASP 41 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138Q PRO* 5.2 0.7 - - - +
139Q ALA* 3.3 32.6 + - + +
37U LEU* 2.8 19.6 + - + +
38U GLU* 3.5 16.8 - - - +
40U CYS* 1.3 71.3 - - - +
42U ALA* 1.3 53.8 + - - +
44U VAL* 3.2 0.3 + - - +
45U SER* 2.4 52.7 + - - -
54U CYS* 3.3 2.5 - - - -
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Residues in contact with ALA 42 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38U GLU 2.8 21.5 + - - +
39U LEU* 3.4 10.1 - - + +
40U CYS 3.0 0.4 + - - -
41U ASP* 1.3 77.0 + - - +
43U ARG* 1.3 61.2 + - - +
45U SER* 3.3 4.6 + - - -
46U SER* 2.8 25.6 + - - -
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Residues in contact with ARG 43 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72T LYS* 4.1 7.5 - - - +
74T PRO* 6.0 4.6 - - - +
77T TYR* 5.3 8.8 - - - +
36U ARG 5.3 0.4 + - - -
39U LEU* 3.2 12.9 + - - +
40U CYS* 3.0 43.2 + - - +
42U ALA* 1.3 77.5 - - - +
44U VAL* 1.3 63.4 + - + +
46U SER* 2.7 17.9 + - - -
47U ARG* 2.9 23.6 + - + +
52U GLU* 2.6 40.4 + - - -
57U GLU* 4.6 1.0 + - - -
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Residues in contact with VAL 44 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139Q ALA* 3.6 8.7 - - + -
140Q GLY* 3.8 26.2 - - - +
40U CYS* 3.0 22.1 + - - +
43U ARG* 1.3 79.4 - - + +
45U SER* 1.3 63.0 + - - +
46U SER 3.0 6.0 + - - -
47U ARG* 3.2 19.9 - - - +
50U THR* 4.1 16.1 - - + +
52U GLU* 3.9 33.4 - - + +
54U CYS* 3.4 19.3 - - - -
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Residues in contact with SER 45 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139Q ALA* 4.2 4.2 - - - +
41U ASP* 2.4 49.3 + - - -
42U ALA* 3.7 5.8 - - - -
44U VAL* 1.3 72.2 - - - +
46U SER* 1.3 59.1 + - - +
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Residues in contact with SER 46 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42U ALA 2.8 15.1 + - - -
43U ARG* 2.7 17.7 + - - -
44U VAL 3.0 0.2 - - - -
45U SER* 1.3 81.3 - - - +
47U ARG* 1.3 73.8 + - - +
48U SER* 2.8 15.2 + - - -
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Residues in contact with ARG 47 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77T TYR 4.5 5.7 + - - -
79T ASN* 2.5 40.4 + - - +
43U ARG* 2.9 19.4 + - + +
44U VAL* 3.2 14.5 - - - +
46U SER* 1.3 75.1 + - - +
48U SER* 1.3 73.3 + - - +
49U HIS 5.1 3.6 + - - -
50U THR* 3.6 34.4 + - - +
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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