Contacts of the helix formed by residues 37 - 51 (chain D) in PDB entry 1FIU
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
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Residue Dist Surf HB Arom Phob DC
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34D ASP* 2.9 26.1 + - - +
35D GLY 4.6 0.9 - - - -
36D SER* 1.3 77.4 - - - +
38D THR* 1.3 65.8 + - - +
39D ARG* 3.2 11.1 + - - +
40D SER* 3.0 28.2 + - - -
41D PHE* 2.9 22.5 + - - +
224D THR* 4.7 5.3 - - - +
227D ARG* 3.8 18.2 - - - +
2G G 3.3 42.6 + - + +
3G C 4.9 3.0 + - - +
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Residues in contact with THR 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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35D GLY 5.8 0.2 - - - -
36D SER 3.8 4.9 + - - -
37D ASN* 1.3 71.7 + - - +
39D ARG* 1.3 73.2 + - + +
41D PHE* 3.3 5.8 + - - +
42D ASN* 3.0 45.1 + - - +
258D TYR* 4.4 5.4 - - - +
1G T 5.5 8.6 + - - -
2G G 5.1 6.1 + - - -
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Residues in contact with ARG 39 (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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37D ASN* 3.2 8.0 + - - +
38D THR* 1.3 79.7 - - - +
40D SER* 1.3 60.1 + - - +
43D ILE* 2.9 43.8 + - + +
224D THR* 5.1 2.7 - - + -
258D TYR* 3.6 61.8 - - + +
261D ALA* 5.6 5.8 - - - -
1G T 4.0 13.5 + - - -
2G G 2.7 48.1 + - - +
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Residues in contact with SER 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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33D ALA* 3.4 6.7 - - - -
34D ASP* 2.9 29.6 + - - +
37D ASN* 3.0 33.1 + - - -
39D ARG* 1.3 75.8 - - - +
41D PHE* 1.3 64.3 + - - +
43D ILE* 4.1 1.0 - - - +
44D ALA* 2.9 28.1 + - - +
222D GLU* 4.6 1.7 + - - -
223D PRO* 3.5 12.8 - - - +
224D THR* 3.6 20.0 - - - +
227D ARG* 4.7 0.7 - - - -
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Residues in contact with PHE 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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27D ARG 4.0 6.7 - - - -
28D GLY* 3.2 39.3 - - - -
29D VAL* 3.8 26.5 - - + -
30D VAL* 5.2 2.2 + - - +
33D ALA* 4.0 10.4 - - - +
34D ASP 4.7 3.4 - - - +
35D GLY 4.5 10.1 - - - +
37D ASN 2.9 16.8 + - - +
38D THR* 3.5 7.6 - - - +
40D SER* 1.3 78.6 - - - +
42D ASN* 1.3 75.3 + - - +
44D ALA* 3.9 1.7 - - - +
45D LYS* 3.0 40.9 + - + +
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Residues in contact with ASN 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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38D THR* 3.0 34.7 + - - +
39D ARG 4.1 1.1 - - - +
41D PHE* 1.3 93.2 - - - +
43D ILE* 1.3 64.3 + - - +
45D LYS* 3.5 11.1 + - - +
46D GLY* 3.1 19.6 + - - -
252D ILE* 4.0 0.9 - - - +
256D LEU* 3.9 25.2 - - + +
258D TYR* 3.2 24.7 + - - +
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Residues in contact with ILE 43 (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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39D ARG* 2.9 29.9 + - + +
40D SER 4.1 2.0 - - - +
42D ASN* 1.3 74.8 - - - +
44D ALA* 1.3 63.4 + - - +
46D GLY* 3.2 2.3 + - - -
47D ILE* 3.0 26.3 + - + +
223D PRO* 3.4 35.0 - - + +
224D THR* 4.4 7.2 - - + -
225D PRO* 4.1 10.1 - - + -
249D LEU* 3.5 17.0 - - + -
252D ILE* 3.8 11.0 - - + +
253D LEU* 3.7 27.8 - - + -
256D LEU* 4.1 16.4 - - + -
258D TYR* 4.2 7.6 - - + -
261D ALA* 5.2 1.6 - - + -
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Residues in contact with ALA 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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30D VAL* 3.8 10.8 - - + +
32D ASN* 3.6 19.6 - - - +
33D ALA* 3.5 22.9 - - + -
40D SER 2.9 19.1 + - - +
41D PHE 3.9 0.9 - - - +
43D ILE* 1.3 78.9 - - - +
45D LYS* 1.3 58.0 + - - +
47D ILE* 3.4 7.6 + - - +
48D ALA* 3.0 28.6 + - - +
223D PRO* 4.1 12.3 - - + +
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Residues in contact with LYS 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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28D GLY* 5.2 4.9 + - - +
30D VAL* 3.6 18.3 - - + +
41D PHE* 3.0 37.8 + - + +
42D ASN* 3.7 11.4 - - - +
43D ILE 3.3 0.2 - - - -
44D ALA* 1.3 74.9 - - - +
46D GLY* 1.3 58.4 + - - +
48D ALA* 3.3 2.3 + - + +
49D ASP* 2.9 47.9 + - - +
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Residues in contact with GLY 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 ASN 3.1 10.7 + - - -
43D ILE 3.2 0.2 + - - -
45D LYS* 1.3 77.3 - - - +
47D ILE* 1.3 60.9 + - - +
49D ASP* 3.3 9.4 + - - +
50D LEU* 3.0 28.4 + - - +
252D ILE* 3.6 35.7 - - - -
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Residues in contact with ILE 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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22D LEU* 5.6 1.1 - - + -
32D ASN* 5.3 2.2 - - - +
43D ILE* 3.0 32.6 + - + +
44D ALA* 3.8 5.8 - - - +
46D GLY* 1.3 76.9 - - - +
48D ALA* 1.3 62.9 + - - +
50D LEU* 3.1 2.3 + - - -
51D LEU* 2.9 31.4 + - + +
223D PRO* 4.7 8.5 - - + -
243D HIS* 4.3 15.0 - - + -
244D PHE* 3.9 18.4 - - + -
245D ALA* 3.8 23.3 - - + +
248D GLU* 4.1 10.1 - - + -
249D LEU* 4.0 39.0 - - + +
252D ILE* 4.2 2.7 - - + -
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Residues in contact with ALA 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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22D LEU* 4.9 8.1 - - + -
24D THR* 4.8 4.0 - - - +
30D VAL* 3.9 25.1 - - + -
44D ALA 3.0 17.7 + - - +
45D LYS 3.3 4.5 + - - +
47D ILE* 1.3 77.3 - - - +
49D ASP* 1.3 64.5 + - - +
51D LEU* 3.1 6.1 + - - -
52D HIS 3.1 3.8 + - - -
53D SER* 2.9 46.4 + - - +
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Residues in contact with ASP 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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45D LYS* 2.9 41.1 + - - +
46D GLY* 3.5 11.5 - - - +
48D ALA* 1.3 78.0 - - - +
50D LEU* 1.3 60.6 + - + +
52D HIS* 2.9 26.2 + - - -
53D SER 4.8 8.6 - - - +
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Residues in contact with LEU 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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10D ARG* 5.4 0.2 + - - -
46D GLY* 3.0 22.5 + - - +
47D ILE 3.7 1.3 - - - +
49D ASP* 1.3 76.0 - - + +
51D LEU* 1.3 61.8 + - - +
52D HIS* 3.2 14.7 + - + -
248D GLU* 3.7 48.9 - - + +
251D GLN* 3.6 42.0 - - + +
252D ILE* 4.7 4.9 - - + +
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Residues in contact with LEU 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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10D ARG* 3.0 27.5 + - - +
13D HIS* 3.6 51.1 - - + +
17D LEU* 3.7 12.6 - - + +
22D LEU* 3.6 28.7 - - + -
47D ILE* 2.9 25.3 + - + +
48D ALA* 3.6 6.3 - - - +
49D ASP 3.1 0.4 - - - -
50D LEU* 1.3 78.4 - - - +
52D HIS* 1.3 69.2 + - - +
53D SER 3.4 1.5 + - - +
244D PHE* 4.2 9.0 - - + -
245D ALA* 4.5 0.7 - - + -
248D GLU* 3.7 26.5 - - + +
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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