Contacts of the helix formed by residues 24 - 38 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A TYR 5.7 0.2 - - - +
411A LEU 6.1 0.2 - - - +
412A LEU 6.0 0.4 - - - +
413A GLY* 3.8 28.9 - - - +
20D GLU 3.5 15.9 - - - +
21D ILE 3.0 11.3 + - - +
23D TYR* 1.3 82.9 - - + +
25D ARG* 1.3 58.6 + - - +
26D ASP 3.4 2.5 - - - -
27D ALA* 3.3 14.3 + - + +
28D VAL* 2.9 32.1 + - + +
246D LEU* 4.2 0.2 - - - -
256D VAL* 3.9 37.2 - - + +
259D ASN* 5.4 6.1 - - + -
260D ALA* 5.9 3.4 - - + +
411D LEU* 4.6 16.4 - - + -
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Residues in contact with ARG 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ILE 4.0 1.2 + - - -
22D THR* 3.3 40.3 + - - +
23D TYR 3.4 1.4 - - - -
24D LEU* 1.3 76.5 - - - +
26D ASP* 1.3 67.0 + - - +
28D VAL* 3.4 4.3 + - - +
29D LYS* 3.0 37.9 + - + +
244D SER 5.2 0.3 - - - +
245D GLU* 3.3 32.5 + - - +
246D LEU* 4.1 18.7 - - + +
247D GLU* 4.2 17.2 + - - -
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Residues in contact with ASP 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 4.0 28.2 - - + +
34A ALA* 4.5 15.2 - - - +
39A THR* 5.0 4.0 + - - -
23D TYR 4.9 3.0 + - - +
24D LEU 3.4 0.6 - - - -
25D ARG* 1.3 77.9 + - - +
27D ALA* 1.3 65.5 + - - +
29D LYS* 3.2 23.3 + - - +
30D VAL* 3.1 29.1 + - - +
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Residues in contact with ALA 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ALA* 5.4 9.4 - - + -
30A VAL* 5.0 4.7 - - - +
24D LEU* 3.3 19.5 + - + +
26D ASP* 1.3 76.9 - - - +
28D VAL* 1.3 62.8 + - - +
30D VAL* 3.1 10.9 - - + +
31D THR* 3.1 28.9 + - - -
411D LEU* 4.1 17.3 - - + -
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Residues in contact with VAL 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D LEU* 2.9 24.4 + - + +
25D ARG* 3.7 6.5 - - - +
27D ALA* 1.3 77.0 - - - +
29D LYS* 1.3 56.1 + - - +
31D THR 3.4 0.3 + - - -
32D HIS* 2.8 28.8 + - - +
244D SER 4.1 10.3 - - - +
246D LEU* 4.0 15.0 - - + -
252D TYR* 3.5 35.4 - - + -
256D VAL* 3.6 29.4 - - + -
407D MSE 3.6 21.9 - - + +
411D LEU* 4.6 2.9 - - + -
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Residues in contact with LYS 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ARG* 3.0 32.6 + - + +
26D ASP* 3.2 23.9 + - - +
28D VAL* 1.3 75.7 - - - +
30D VAL* 1.3 63.8 + - + +
32D HIS* 3.2 7.2 + - - +
33D HIS* 3.1 37.8 + - + +
244D SER* 3.4 32.8 - - - +
245D GLU* 5.0 10.2 + - - +
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Residues in contact with VAL 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ASP* 4.5 20.1 - - + +
27A ALA* 4.4 22.7 - - + +
30A VAL* 3.7 28.5 - - + -
26D ASP 3.1 12.7 + - - +
27D ALA* 3.1 21.1 - - - +
29D LYS* 1.3 76.1 - - + +
31D THR* 1.3 70.9 + - - +
33D HIS* 3.3 12.8 + - + +
34D ALA* 3.1 19.4 + - - +
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Residues in contact with THR 31 (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 ALA 3.1 16.1 + - - -
28D VAL 3.8 0.2 - - - -
30D VAL* 1.3 80.5 - - - +
32D HIS* 1.3 66.6 + - - +
34D ALA* 3.0 8.0 + - + +
35D ILE* 2.9 23.7 + - + +
407D MSE 3.7 27.5 - - + -
410D TYR* 3.3 47.1 + - + +
411D LEU* 4.5 6.1 - - - +
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Residues in contact with HIS 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D VAL 2.8 18.2 + - - +
29D LYS 3.2 5.6 + - - +
31D THR* 1.3 76.1 - - - +
33D HIS* 1.3 75.8 + + - +
35D ILE* 3.3 3.5 + - - +
36D HIS* 3.1 56.8 + + + -
242D GLY 3.2 27.2 + - - -
243D THR 3.5 2.2 - - - -
244D SER* 3.3 38.4 + - - -
252D TYR* 2.9 30.9 + - + +
407D MSE 3.9 6.5 - - - +
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Residues in contact with HIS 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D LYS* 3.1 31.7 + - + +
30D VAL* 3.6 11.0 - - + +
31D THR 3.2 0.2 - - - -
32D HIS* 1.3 90.2 - + - +
34D ALA* 1.3 58.0 + - - +
36D HIS* 5.1 1.8 - - - -
37D GLU* 2.8 60.5 + - - +
39D THR* 4.6 0.9 - - - -
244D SER* 4.8 8.4 - - - -
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Residues in contact with ALA 34 (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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26A ASP* 5.1 8.1 - - - +
30D VAL 3.1 13.0 + - - +
31D THR* 3.0 15.8 + - + +
33D HIS* 1.3 76.6 - - - +
35D ILE* 1.3 56.1 + - - +
38D LYS* 2.9 24.4 + - - -
39D THR* 3.1 27.4 + - - +
40D GLY* 4.1 15.5 + - - +
46D LEU* 4.3 1.9 - - - +
410D TYR* 5.0 9.8 + - + -
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Residues in contact with ILE 35 (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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31D THR* 2.9 23.4 + - + +
32D HIS* 3.6 5.8 - - - +
34D ALA* 1.3 78.6 - - - +
36D HIS* 1.3 66.5 + - + +
38D LYS* 3.5 6.6 + - - +
46D LEU* 3.5 29.0 - - + +
49D VAL* 4.1 25.5 - - + +
252D TYR* 4.4 9.4 - - + +
403D LYS* 4.1 18.6 - - + -
406D ALA* 4.0 23.8 - - + -
407D MSE 4.2 26.5 - - + +
410D TYR* 3.7 19.5 - - + -
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Residues in contact with HIS 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D HIS* 3.1 55.0 + + + +
33D HIS* 4.4 2.2 - - - +
35D ILE* 1.3 82.9 - - + +
37D GLU* 1.3 64.9 + - + +
38D LYS* 3.7 15.8 + - - +
49D VAL* 4.0 15.5 - - + +
50D ASP* 5.1 0.2 + - - -
238D ARG* 3.8 33.2 + - - -
242D GLY* 4.5 3.6 - - - -
399D TYR* 5.4 0.4 - - - -
403D LYS* 3.0 35.1 + - - -
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Residues in contact with GLU 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D HIS* 2.8 43.2 + - - +
36D HIS* 1.3 76.4 - - + +
38D LYS* 1.3 73.3 + - - +
39D THR* 3.4 21.3 + - + +
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Residues in contact with LYS 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D ALA 2.9 11.0 + - - -
35D ILE 3.5 6.6 + - - +
36D HIS* 3.3 18.6 + - - +
37D GLU* 1.3 80.0 - - - +
39D THR* 1.3 60.7 + - - +
43D ASN* 3.2 39.5 + - + +
46D LEU* 3.7 41.4 + - + -
47D GLY* 5.8 0.9 - - - -
49D VAL* 5.4 3.6 - - - +
50D ASP* 4.4 17.8 + - - +
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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