Contacts of the helix formed by residues 37 - 51 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B ASP* 2.9 22.0 + - - +
35B GLY 3.2 1.5 - - - -
36B SER* 1.3 79.1 + - - +
38B THR* 1.3 54.4 + - - +
39B ARG* 3.0 22.0 + - - +
40B SER* 3.0 19.4 + - - +
41B PHE* 2.8 35.6 + - - +
224B THR* 4.7 6.5 - - - +
227B ARG* 4.0 14.1 - - - +
2F G 4.0 22.6 + - - +
3F C 4.0 22.9 + - + -
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Residues in contact with THR 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B SER 3.9 3.0 + - - -
37B ASN* 1.3 72.4 + - - +
39B ARG* 1.3 59.2 + - + +
41B PHE* 3.4 7.6 + - + +
42B ASN* 3.0 53.2 + - - +
258B TYR* 4.8 1.8 - - - +
1F T 5.7 0.2 - - - -
2F G 3.6 21.1 + - - -
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Residues in contact with ARG 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ASN* 3.0 9.4 + - - +
38B THR* 1.3 77.3 - - + +
40B SER* 1.3 59.1 + - - +
42B ASN* 3.9 0.5 - - - +
43B ILE* 2.9 41.4 + - + +
224B THR* 5.5 2.5 - - + -
258B TYR* 3.6 53.7 - - + +
261B ALA* 5.5 5.8 - - - -
2F G 3.4 36.6 + - - +
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Residues in contact with SER 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ALA* 3.6 5.7 - - - -
34B ASP* 3.0 28.8 + - - +
37B ASN* 3.0 32.9 + - - -
39B ARG* 1.3 77.7 - - - +
41B PHE* 1.3 63.7 + - - +
43B ILE* 4.0 1.3 - - - +
44B ALA* 2.9 26.3 + - - +
222B GLU* 4.8 1.4 + - - -
223B PRO* 3.7 11.0 - - - +
224B THR* 3.7 20.7 - - - +
227B ARG* 4.8 0.4 + - - -
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Residues in contact with PHE 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ARG 4.2 6.7 - - - -
28B GLY* 3.2 40.4 - - - -
29B VAL* 3.7 27.4 - - + -
30B VAL* 5.0 1.9 + - - +
33B ALA* 4.1 10.5 - - - +
34B ASP 4.2 4.2 + - - +
35B GLY 4.6 10.5 - - - +
37B ASN 2.8 21.1 + - - +
38B THR* 3.6 9.6 - - + +
40B SER* 1.3 72.9 - - - +
42B ASN* 1.3 74.4 + - - +
44B ALA* 3.9 1.9 - - - +
45B LYS* 3.0 42.5 + - + +
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Residues in contact with ASN 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B THR* 3.0 34.2 + - - +
39B ARG 4.0 0.9 - - - +
41B PHE* 1.3 91.5 - - - +
43B ILE* 1.3 59.8 + - - +
45B LYS* 3.3 7.5 + - - +
46B GLY* 2.9 24.9 + - - -
252B ILE* 2.9 7.3 - - - +
256B LEU* 3.9 16.6 - - + +
258B TYR* 3.0 26.6 + - - +
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Residues in contact with ILE 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ARG* 2.9 27.7 + - + +
40B SER 4.0 2.0 - - - +
42B ASN* 1.3 75.0 - - - +
44B ALA* 1.3 64.5 + - - +
47B ILE* 2.9 30.4 + - + +
223B PRO* 3.5 30.5 - - + +
224B THR* 4.5 7.9 - - + -
225B PRO* 4.3 9.6 - - + -
249B LEU* 3.6 16.6 - - + -
252B ILE* 2.9 17.0 - - + +
253B LEU* 3.7 26.2 - - + -
256B LEU* 4.3 4.3 - - + -
258B TYR* 4.1 20.4 - - + -
261B ALA* 5.3 1.8 - - + -
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Residues in contact with ALA 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B VAL* 3.7 10.8 - - + +
32B ASN* 3.6 19.9 - - - +
33B ALA* 3.5 25.4 - - + -
40B SER 2.9 18.3 + - - +
41B PHE 3.9 1.1 - - - +
43B ILE* 1.3 78.1 - - - +
45B LYS* 1.3 56.0 + - - +
47B ILE* 3.5 5.7 + - - +
48B ALA* 3.0 28.9 + - - +
223B PRO* 4.2 11.6 - - + +
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Residues in contact with LYS 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B THR* 6.4 0.9 - - + -
28B GLY* 5.2 9.0 - - - +
30B VAL* 3.5 18.5 - - + +
41B PHE* 3.0 32.6 + - + +
42B ASN* 3.7 7.9 - - - +
44B ALA* 1.3 72.7 - - - +
46B GLY* 1.3 68.2 + - - +
48B ALA* 3.2 2.1 + - + +
49B ASP* 3.0 43.8 + - - +
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Residues in contact with GLY 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ASN 2.9 11.7 + - - -
45B LYS* 1.3 78.3 - - - +
47B ILE* 1.3 60.9 + - - +
49B ASP* 3.4 8.2 + - - +
50B LEU* 3.2 25.3 + - - +
252B ILE* 3.0 28.5 - - - -
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Residues in contact with ILE 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LEU* 5.6 1.6 - - + -
32B ASN* 5.4 2.2 - - - +
43B ILE* 2.9 37.0 + - + +
44B ALA* 3.8 4.7 - - - +
46B GLY* 1.3 76.7 - - - +
48B ALA* 1.3 63.6 + - - +
50B LEU* 3.0 13.0 + - - +
51B LEU* 3.1 18.1 + - + +
223B PRO* 4.6 9.9 - - + -
243B HIS* 4.4 12.6 - - + -
244B PHE* 3.9 26.9 - - + -
245B ALA* 4.0 14.8 - - + +
248B GLU* 4.1 9.4 - - + +
249B LEU* 4.0 29.4 - - + +
252B ILE* 3.9 13.0 - - + +
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Residues in contact with ALA 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LEU* 4.9 7.9 - - + -
24B THR* 4.8 3.6 - - - +
30B VAL* 4.0 24.9 - - + -
44B ALA 3.0 17.2 + - - +
45B LYS* 3.2 5.6 + - + +
47B ILE* 1.3 78.4 - - - +
49B ASP* 1.3 64.0 + - - +
51B LEU* 3.2 6.2 + - - +
52B HIS 3.1 4.2 + - - -
53B SER* 2.9 45.0 + - - +
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Residues in contact with ASP 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LYS* 3.0 40.7 + - - +
46B GLY* 3.6 10.4 - - - +
47B ILE 3.2 0.2 - - - -
48B ALA* 1.3 79.1 - - - +
50B LEU* 1.3 60.1 + - + +
52B HIS* 2.8 30.2 + - - +
53B SER 4.7 8.4 - - - +
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Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B GLY 3.2 13.4 + - - +
47B ILE 3.0 8.8 + - - +
49B ASP* 1.3 79.5 - - + +
51B LEU* 1.3 62.9 + - - +
52B HIS* 3.1 16.3 + - + -
248B GLU* 3.6 43.5 - - + +
251B GLN* 3.2 44.2 - - + +
252B ILE* 4.8 4.0 - - + +
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Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B HIS* 3.4 52.9 - - + +
17B LEU* 3.6 21.8 - - + +
22B LEU* 3.7 27.8 - - + -
47B ILE* 3.1 21.2 + - + +
48B ALA* 3.8 5.8 - - - +
49B ASP 3.1 0.4 - - - -
50B LEU* 1.3 78.0 - - - +
52B HIS* 1.3 73.3 + - - +
53B SER 3.3 0.8 + - - +
244B PHE* 4.0 11.0 - - + -
245B ALA* 4.5 0.2 - - + -
248B GLU* 3.7 25.1 - - + +
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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