Contacts of the helix formed by residues 24 - 38 (chain B) in PDB entry 3IFS
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 LEU 24 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLU 3.5 17.5 - - - +
21B ILE 3.1 9.9 + - - +
22B THR 3.1 1.4 - - - -
23B TYR* 1.3 82.6 - - + +
25B ARG* 1.3 63.1 + - - +
26B ASP 3.3 2.7 - - - -
27B ALA* 3.1 15.8 + - + +
28B VAL* 2.9 24.6 + - + +
246B LEU* 4.4 0.2 - - - -
256B VAL* 3.8 35.9 - - + +
259B ASN* 5.2 7.6 - - + -
260B ALA* 5.8 3.6 - - + +
411B LEU* 4.6 17.3 - - + -
298C LYS* 6.3 0.7 - - - +
410C TYR 5.8 0.7 - - - +
411C LEU 6.1 0.2 - - - +
412C LEU 5.4 0.4 - - - +
413C GLY* 3.9 25.1 - - - -
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Residues in contact with ARG 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B THR* 3.2 32.5 + - - +
23B TYR 3.4 0.6 - - - -
24B LEU* 1.3 76.9 - - - +
26B ASP* 1.3 60.9 + - - +
28B VAL* 3.3 4.1 + - - +
29B LYS* 3.0 43.9 + - - +
244B SER 5.3 0.9 - - - +
245B GLU* 2.7 26.8 + - - -
246B LEU* 3.8 32.1 - - + +
247B GLU* 2.4 36.1 + - - +
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Residues in contact with ASP 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TYR 4.7 4.3 + - - +
24B LEU 3.3 0.6 - - - -
25B ARG* 1.3 82.3 - - - +
27B ALA* 1.3 61.9 + - - +
29B LYS* 3.5 9.7 + - - +
30B VAL* 3.2 28.6 + - - +
30C VAL* 4.0 31.8 - - + +
31C THR* 5.7 2.1 - - - +
34C ALA* 4.4 17.3 - - - +
39C THR* 5.3 1.0 + - - -
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Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 3.1 18.8 + - + +
26B ASP* 1.3 75.8 - - - +
28B VAL* 1.3 64.4 + - - +
30B VAL* 3.2 10.1 - - - +
31B THR* 2.9 30.5 + - - -
411B LEU* 4.0 19.5 - - + -
27C ALA* 5.3 10.5 - - + -
30C VAL* 5.1 3.1 - - - +
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Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 2.9 19.6 + - + +
25B ARG* 3.6 9.4 - - - +
27B ALA* 1.3 74.5 - - - +
29B LYS* 1.3 60.2 + - - +
31B THR 3.2 0.7 + - - -
32B HIS* 2.8 28.4 + - - +
244B SER 4.0 12.3 - - - +
246B LEU* 4.2 14.4 - - + -
252B TYR* 3.6 33.7 - - + -
256B VAL* 3.5 30.5 - - + -
407B MSE 3.6 21.4 - - + +
411B LEU* 4.5 4.0 - - + -
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Residues in contact with LYS 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ARG* 3.0 28.0 + - - +
26B ASP* 3.7 11.4 + - - +
27B ALA 3.3 0.2 - - - -
28B VAL* 1.3 78.3 - - - +
30B VAL* 1.3 64.2 + - + +
32B HIS* 3.2 9.5 + - - +
33B HIS* 3.1 50.7 + - + +
244B SER* 4.0 19.0 + - - +
245B GLU* 2.9 36.1 + - - -
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Residues in contact with VAL 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ASP 3.2 13.6 + - - +
27B ALA* 3.2 21.3 - - - +
29B LYS* 1.3 78.5 - - + +
31B THR* 1.3 63.0 + - - +
33B HIS* 3.4 15.9 + - + +
34B ALA* 3.1 20.8 + - - +
26C ASP* 4.4 21.4 - - + +
27C ALA* 4.4 22.4 - - + +
30C VAL* 4.1 24.0 - - + -
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Residues in contact with THR 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ALA 2.9 20.1 + - - -
28B VAL 3.7 2.9 - - - -
30B VAL* 1.3 76.4 - - - +
32B HIS* 1.3 66.3 + - - +
34B ALA* 3.1 7.3 + - + +
35B ILE* 3.0 23.7 + - + +
407B MSE 3.7 24.7 - - + -
410B TYR* 3.3 45.8 - - + +
411B LEU* 4.3 7.6 - - - +
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Residues in contact with HIS 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL 2.8 21.2 + - - +
29B LYS 3.4 4.9 - - - +
31B THR* 1.3 73.1 - - - +
33B HIS* 1.3 75.3 + + - +
35B ILE* 3.2 4.2 + - - +
36B HIS* 3.0 54.3 + + + +
242B GLY 3.2 30.1 + - - -
243B THR 3.7 5.4 + - - -
244B SER* 3.4 28.6 + - - -
252B TYR* 2.8 33.6 + - + +
407B MSE 3.9 5.8 - - - +
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Residues in contact with HIS 33 (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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29B LYS* 3.1 40.9 + - + +
30B VAL* 3.7 16.5 - - + +
31B THR 3.3 0.2 - - - -
32B HIS* 1.3 89.7 - + - +
34B ALA* 1.3 59.6 + - - +
36B HIS* 5.1 1.8 - - - -
37B GLU* 2.8 58.9 + - - +
39B THR* 4.8 0.7 - - - -
244B SER* 5.0 2.8 + - - -
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Residues in contact with ALA 34 (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 3.1 14.2 + - - +
31B THR* 3.1 15.0 + - + +
33B HIS* 1.3 74.8 - - - +
35B ILE* 1.3 60.5 + - + +
38B LYS* 2.9 23.9 + - - -
39B THR* 3.0 28.9 + - - +
40B GLY* 4.0 15.0 + - - +
46B LEU* 4.4 1.6 - - - +
410B TYR* 5.2 9.3 + - + -
26C ASP* 5.1 7.2 - - - +
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Residues in contact with ILE 35 (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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31B THR* 3.0 31.5 + - + +
32B HIS 3.2 5.6 + - - +
34B ALA* 1.3 78.0 - - - +
36B HIS* 1.3 74.6 + - + +
38B LYS* 3.3 10.6 + - - +
46B LEU* 3.6 25.4 - - + +
48B TRP* 5.2 2.5 - - + -
49B VAL* 4.2 24.2 - - + +
252B TYR* 4.3 11.7 - - + +
403B LYS* 4.3 11.4 - - + -
406B ALA* 4.1 21.5 - - + -
407B MSE 4.2 17.7 - - + +
410B TYR* 3.8 21.8 - - + -
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Residues in contact with HIS 36 (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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32B HIS* 3.0 50.4 + + + +
33B HIS* 4.4 2.0 - - - +
35B ILE* 1.3 85.7 - - + +
37B GLU* 1.3 63.2 + - + +
38B LYS* 3.7 10.8 + - - +
49B VAL* 3.8 19.6 - - + +
238B ARG* 3.5 40.0 + - - -
242B GLY* 4.4 2.8 - - - -
403B LYS* 2.8 29.1 + - - -
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Residues in contact with GLU 37 (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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33B HIS* 2.8 45.8 + - - +
36B HIS* 1.3 74.5 - - + +
38B LYS* 1.3 74.9 + - - +
39B THR* 3.4 20.0 + - + +
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Residues in contact with LYS 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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34B ALA 2.9 13.2 + - - -
35B ILE 3.7 10.2 + - - +
36B HIS* 3.3 9.2 + - - +
37B GLU* 1.3 82.6 - - - +
39B THR* 1.3 58.0 + - - +
43B ASN* 2.9 32.0 + - + +
46B LEU* 3.5 49.2 + - + +
47B GLY* 5.3 1.0 - - - -
49B VAL* 4.9 7.7 - - - +
50B ASP* 5.3 7.2 + - - +
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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
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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