Contacts of the helix formed by residues 37 - 55 (chain D) in PDB entry 4TVQ
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 37 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C GLU* 3.3 12.3 + - - +
55C ASN* 3.9 26.9 + - - +
33D LEU* 2.9 18.4 + - + +
36D VAL* 1.3 80.7 + - + +
38D LEU* 1.3 67.7 + - - +
39D SER* 2.5 26.9 + - - +
40D ALA* 3.0 20.9 + - + +
41D ALA* 3.1 18.0 + - - +
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Residues in contact with LEU 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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34D GLU* 3.6 45.1 + - + +
36D VAL 4.1 0.4 - - - -
37D ASN* 1.3 73.2 - - - +
39D SER* 1.3 57.7 + - - +
41D ALA* 3.5 3.0 + - + +
42D GLN* 2.9 38.3 + - + +
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Residues in contact with SER 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C GLU* 3.8 8.6 + - - -
37D ASN* 2.5 30.9 + - - -
38D LEU* 1.3 80.3 - - - +
40D ALA* 1.3 53.2 + - - +
42D GLN* 3.4 4.7 + - - +
43D THR* 2.7 39.7 + - - -
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Residues in contact with ALA 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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51C ALA* 4.1 28.7 - - + +
54C GLU* 4.6 3.8 - - - +
55C ASN* 4.7 1.6 - - - +
58C LEU* 4.5 4.5 - - + -
33D LEU* 4.3 12.3 - - + -
37D ASN* 3.0 24.3 + - + +
39D SER* 1.3 78.3 + - - +
41D ALA* 1.3 61.3 + - - +
43D THR* 3.8 4.5 - - - -
44D LEU* 2.9 36.0 + - - +
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Residues in contact with ALA 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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30D PHE* 3.5 31.4 - - - +
33D LEU* 4.0 12.0 - - + +
34D GLU* 3.7 20.2 - - + +
37D ASN 3.1 16.2 + - - +
38D LEU* 3.7 3.6 - - - +
40D ALA* 1.3 76.9 - - - +
42D GLN* 1.3 57.2 + - - +
44D LEU* 4.0 2.4 - - - +
45D ARG* 2.9 38.0 + - - +
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Residues in contact with GLN 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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34D GLU* 5.1 4.1 + - - +
38D LEU* 2.9 27.6 + - + +
39D SER* 3.9 4.9 - - - +
41D ALA* 1.3 74.6 - - - +
43D THR* 1.3 60.2 + - - +
45D ARG* 4.1 19.4 + - - +
46D ALA* 2.9 44.3 + - + +
49D ILE* 5.9 2.2 - - - +
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Residues in contact with THR 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C THR* 6.5 0.9 - - + -
47C ALA* 3.7 26.7 - - + +
50C LYS* 5.4 14.3 + - + +
39D SER* 2.7 25.0 + - - -
40D ALA* 3.8 5.6 - - - -
42D GLN* 1.3 74.7 - - - +
44D LEU* 1.3 60.1 + - - +
46D ALA* 3.3 5.4 + - - +
47D ALA* 2.9 28.3 + - + +
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Residues in contact with LEU 44 (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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47C ALA* 3.7 34.3 - - + +
48C PHE* 4.0 29.8 - - + +
51C ALA* 4.2 6.3 - - + -
58C LEU* 4.1 9.4 - - + -
62C ILE* 3.9 22.4 - - + -
30D PHE* 3.7 19.5 - - + -
33D LEU* 3.9 23.3 - - + -
40D ALA 2.9 20.2 + - - +
41D ALA 4.0 1.3 - - - +
43D THR* 1.3 76.0 - - - +
45D ARG* 1.3 56.8 + - - +
47D ALA* 3.2 3.0 + - + +
48D PHE* 2.9 36.2 + - + -
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Residues in contact with ARG 45 (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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27D TYR* 3.8 38.5 - - + -
30D PHE* 3.5 51.8 + - + +
31D ASN* 2.8 27.8 + - - -
34D GLU* 2.8 28.2 + - - +
41D ALA* 2.9 21.8 + - - +
42D GLN* 3.8 22.0 + - - +
44D LEU* 1.3 77.4 - - - +
46D ALA* 1.3 56.5 + - - +
48D PHE* 3.4 2.3 + - - +
49D ILE* 2.9 48.0 + - + +
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Residues in contact with ALA 46 (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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42D GLN* 2.9 31.0 + - + +
43D THR* 3.7 6.1 - - - +
44D LEU 3.3 0.2 - - - -
45D ARG* 1.3 75.0 - - - +
47D ALA* 1.3 58.9 + - - +
49D ILE* 3.6 10.9 - - - +
50D LYS* 2.9 30.1 + - - +
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Residues in contact with ALA 47 (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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40C ALA* 5.7 0.5 - - - +
43C THR* 3.9 29.0 - - + +
44C LEU* 3.6 22.7 - - + +
47C ALA* 4.2 13.2 - - + -
43D THR* 2.9 17.8 + - + +
44D LEU 3.5 4.7 - - - +
46D ALA* 1.3 76.6 - - - +
48D PHE* 1.3 57.4 + - - +
50D LYS* 3.3 4.8 + - - +
51D ALA* 2.9 29.8 + - - +
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Residues in contact with PHE 48 (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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26C MET* 5.5 0.2 - - + -
44C LEU* 3.7 22.2 - - + -
48C PHE* 3.9 24.9 - + - -
22D LEU* 3.8 17.5 - - + -
26D MET* 3.6 30.3 - - + -
30D PHE* 3.5 18.4 - + + -
44D LEU* 2.9 28.3 + - + +
45D ARG 3.8 3.1 - - - +
47D ALA* 1.3 72.1 - - - +
49D ILE* 1.3 60.7 + - - +
51D ALA* 3.9 4.4 - - + +
52D GLU* 2.9 34.1 + - - +
59D THR* 3.7 31.9 + - + -
62D ILE* 3.7 34.5 - - + -
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Residues in contact with ILE 49 (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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22D LEU* 4.8 6.3 - - + -
23D TYR* 6.1 0.2 - - - +
27D TYR* 3.5 29.2 - - + +
42D GLN* 5.9 2.7 - - - +
45D ARG* 2.9 36.9 + - + +
46D ALA* 3.6 9.2 - - - +
47D ALA 3.3 0.2 - - - -
48D PHE* 1.3 74.7 - - + +
50D LYS* 1.3 60.8 + - - +
52D GLU* 4.1 3.2 - - - +
53D LYS* 2.9 44.3 + - + +
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Residues in contact with LYS 50 (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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39C SER* 3.3 24.9 + - - -
40C ALA* 4.2 7.9 - - + +
43C THR* 4.3 27.6 - - + +
46D ALA 2.9 13.8 + - - +
47D ALA* 3.5 8.7 - - - +
49D ILE* 1.3 77.7 - - - +
51D ALA* 1.3 57.3 + - - +
53D LYS* 3.8 5.6 - - - +
54D GLU* 2.7 75.8 + - - +
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Residues in contact with ALA 51 (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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40C ALA* 3.9 22.9 - - + -
44C LEU* 4.2 16.2 - - + -
47D ALA 2.9 17.2 + - - +
48D PHE* 3.9 6.7 - - + +
50D LYS* 1.3 76.5 - - - +
52D GLU* 1.3 51.8 + - - +
54D GLU* 3.4 2.6 + - - +
55D ASN* 2.8 39.0 + - - +
58D LEU* 3.8 22.9 - - + +
59D THR* 5.8 0.9 - - - +
62D ILE* 6.1 0.4 - - + -
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Residues in contact with GLU 52 (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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18D VAL 3.7 0.2 - - - +
19D SER* 2.9 41.4 + - - +
22D LEU* 4.1 18.2 - - + -
48D PHE 2.9 20.7 + - - +
49D ILE 4.1 1.1 - - - +
51D ALA* 1.3 74.3 - - - +
53D LYS* 1.3 63.7 + - - +
55D ASN 3.9 2.0 - - - -
56D PRO* 3.1 28.6 - - - +
57D GLY* 2.7 28.0 + - - -
58D LEU* 3.3 2.2 + - - +
59D THR* 2.8 48.4 + - - +
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Residues in contact with LYS 53 (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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49D ILE* 2.9 28.2 + - + +
50D LYS* 3.8 6.1 - - - +
52D GLU* 1.3 80.4 - - - +
54D GLU* 1.3 70.6 + - + +
56D PRO* 4.1 7.7 - - - +
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Residues in contact with GLU 54 (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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37C ASN* 2.7 30.4 + - - +
39C SER* 4.0 1.8 + - - -
40C ALA* 4.5 1.2 - - - +
50D LYS* 2.7 61.9 + - + +
51D ALA 3.9 0.7 - - - +
53D LYS* 1.3 90.0 + - - +
55D ASN* 1.3 74.7 + - - +
56D PRO* 3.8 5.1 - - - +
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Residues in contact with ASN 55 (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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36C VAL* 3.4 34.8 + - + +
37C ASN* 2.6 35.2 + - - +
51D ALA 2.8 16.0 + - - +
52D GLU* 3.2 4.9 - - - +
54D GLU* 1.3 79.7 + - - +
56D PRO* 1.3 68.4 - - - +
57D GLY 3.3 0.2 + - - -
58D LEU* 3.1 33.2 + - + +
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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
------------------------------------------------------------
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