Contacts of the helix formed by residues 35 - 50 (chain D) in PDB entry 2PI8
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 35 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ALA* 6.2 0.7 - - + -
33D PRO* 4.4 3.4 - - - +
34D ILE* 1.3 73.9 + - - +
36D ALA* 1.3 58.9 + - - +
37D GLY 3.7 0.9 - - - -
38D ASP* 3.4 25.4 - - + +
39D PHE* 3.2 21.0 + - - +
255D ARG 3.2 26.1 + - - -
256D ALA* 3.9 9.9 - - - +
290D LEU 4.1 0.3 - - - +
291D ARG* 3.3 30.6 - - - +
292D LEU* 3.0 39.8 + - - +
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Residues in contact with ALA 36 (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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34B ILE* 3.6 25.2 - - + +
32D ALA* 6.3 1.1 - - + -
33D PRO* 4.1 10.7 + - + +
34D ILE 3.6 4.2 + - - -
35D ASN* 1.3 71.7 - - - +
37D GLY* 1.3 66.1 + - - +
38D ASP* 3.1 1.5 + - - -
39D PHE* 3.1 17.8 + - - +
40D ALA* 3.4 6.1 + - - +
65D GLN* 5.1 0.3 + - - -
68D LEU* 4.0 44.4 - - + +
69D ARG* 4.7 5.8 + - - +
292D LEU* 5.5 0.2 - - - -
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Residues in contact with GLY 37 (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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34B ILE* 3.2 35.5 + - - +
291B ARG* 5.6 1.6 - - - -
36D ALA* 1.3 79.3 - - - +
38D ASP* 1.3 59.9 + - - +
39D PHE 3.2 0.2 - - - -
40D ALA* 3.4 19.7 + - - +
41D GLU* 3.6 6.9 + - - +
69D ARG* 4.8 6.5 - - - -
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Residues in contact with ASP 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE 3.1 18.8 - - - +
35B ASN* 5.1 0.9 - - - -
36B ALA* 4.2 5.9 + - - +
37B GLY* 3.8 23.4 + - - -
38B ASP* 4.8 6.6 + - - +
34D ILE 4.1 1.4 - - - +
35D ASN* 3.4 33.6 - - + +
36D ALA 3.1 0.2 - - - -
37D GLY* 1.3 75.9 - - - +
39D PHE* 1.3 64.6 + - - +
41D GLU* 3.5 13.4 + - - +
42D GLN* 3.4 18.9 + - - +
253D VAL* 4.3 8.3 - - + +
254D GLY 5.7 2.5 - - - +
256D ALA* 4.2 10.4 - - + +
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Residues in contact with PHE 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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35D ASN* 3.2 19.7 + - - +
36D ALA* 3.1 8.2 + - - +
38D ASP* 1.3 75.8 - - - +
40D ALA* 1.3 62.9 + - - +
42D GLN* 3.3 6.3 + - + +
43D ILE* 3.1 51.4 + - + +
61D TYR* 4.7 1.3 - + - -
64D VAL* 3.5 26.0 - - + -
65D GLN* 3.6 15.5 - - - -
68D LEU* 4.1 3.8 - - + -
256D ALA* 4.8 6.5 - - - -
270D THR* 3.7 26.2 - - + -
292D LEU* 3.5 48.2 - - + +
293D MSE 4.7 0.7 - - - -
294D VAL* 3.6 25.4 - - + -
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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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36D ALA 3.4 4.4 + - - +
37D GLY* 3.4 16.8 + - - +
38D ASP 3.2 0.2 - - - -
39D PHE* 1.3 80.4 - - - +
41D GLU* 1.3 56.2 + - - +
43D ILE* 3.3 4.3 + - - +
44D ASN* 2.9 29.2 + - - +
65D GLN* 3.8 27.4 - - - +
69D ARG* 4.9 8.1 - - - +
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Residues in contact with GLU 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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37D GLY 3.6 7.1 + - - +
38D ASP* 3.5 14.4 + - - +
39D PHE 3.3 0.2 - - - -
40D ALA* 1.3 74.5 - - - +
42D GLN* 1.3 65.4 + - - +
44D ASN* 3.2 10.4 + - + +
45D HIS* 3.2 49.8 + - + +
253D VAL* 3.7 25.1 - - - +
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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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38D ASP 3.4 9.0 + - - +
39D PHE* 3.3 12.5 + - + +
40D ALA 3.3 0.2 - - - -
41D GLU* 1.3 79.1 - - - +
43D ILE* 1.3 63.6 + - + +
45D HIS* 3.4 12.4 + - - +
46D ILE* 3.4 12.1 + - - +
250D VAL* 4.8 0.2 - - - +
251D PRO 3.4 22.2 + - - -
252D LEU* 4.1 0.4 - - - +
253D VAL* 3.5 33.5 - - + +
256D ALA* 3.2 28.0 - - + +
257D SER* 3.9 5.8 - - - -
294D VAL* 3.5 18.4 - - - +
296D LEU* 3.1 35.7 - - - +
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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 PHE* 3.1 50.6 + - + +
40D ALA* 3.6 7.6 - - - +
42D GLN* 1.3 75.0 - - - +
44D ASN* 1.3 65.0 + - - +
46D ILE* 2.9 18.9 + - + +
47D ARG* 3.2 10.4 + - - +
54D TYR* 4.4 9.5 - - + -
61D TYR* 3.5 49.4 - - + -
65D GLN* 4.6 6.7 - - + +
294D VAL* 3.6 20.6 - - + -
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Residues in contact with ASN 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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40D ALA 2.9 17.8 + - - +
41D GLU* 3.2 11.1 + - - +
43D ILE* 1.3 75.8 - - - +
45D HIS* 1.3 71.0 + - - +
47D ARG* 3.3 35.3 + - - +
48D ASN* 3.4 24.9 + - - +
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Residues in contact with HIS 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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41D GLU* 3.2 39.2 + - + +
42D GLN 3.5 8.1 - - - +
43D ILE 3.1 0.6 - - - -
44D ASN* 1.3 83.8 + - - +
46D ILE* 1.3 59.3 + - - +
48D ASN* 4.0 3.7 + - - +
49D SER* 2.9 37.0 + - - -
243D PRO* 6.1 0.9 - - + -
250D VAL* 3.9 3.8 - - + -
251D PRO* 3.5 41.4 - - + +
253D VAL* 3.8 21.7 - - + +
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Residues in contact with ILE 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* 3.4 22.9 - - - +
43D ILE* 2.9 20.7 + - + +
45D HIS* 1.3 76.3 - - - +
47D ARG* 1.3 56.7 + - - +
50D SER* 2.7 37.7 + - - +
53D LEU* 4.0 28.3 - - + -
54D TYR* 3.8 15.9 - - + +
61D TYR* 3.6 25.8 - - + +
250D VAL* 3.9 19.3 - - + -
294D VAL* 3.7 21.5 - - + -
296D LEU* 4.0 8.7 - - + -
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Residues in contact with ARG 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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111A THR* 4.8 21.0 - - - +
43D ILE 3.2 7.3 + - - +
44D ASN* 3.3 28.8 + - - +
45D HIS 3.1 0.4 - - - -
46D ILE* 1.3 79.0 - - - +
48D ASN* 1.3 71.7 + - - +
51D PRO* 3.6 22.3 - - - +
54D TYR* 3.0 57.9 + - + +
62D ASN* 5.3 1.6 + - - -
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Residues in contact with ASN 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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110A HIS* 3.4 52.3 + - + +
111A THR* 5.3 1.0 - - - +
147A LEU* 5.8 4.0 - - - +
44D ASN* 3.4 36.6 + - - +
45D HIS* 3.4 5.4 + - - +
47D ARG* 1.3 90.4 - - - +
49D SER* 1.3 64.3 + - - +
50D SER 3.5 0.4 - - - -
51D PRO* 4.2 6.9 - - - +
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Residues in contact with SER 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 HIS* 2.9 18.2 + - - -
48D ASN* 1.3 79.9 - - - +
50D SER* 1.3 60.9 + - - +
51D PRO* 3.7 4.5 - - - +
245D LYS* 4.7 6.4 + - - -
248D SER 5.2 0.7 - - - +
249D ALA* 3.8 20.2 - - - +
250D VAL* 4.0 5.4 - - - -
251D PRO* 3.1 34.3 - - - +
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Residues in contact with SER 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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46D ILE 2.7 19.6 + - - +
49D SER* 1.3 80.9 - - - +
51D PRO* 1.3 58.9 - - - +
52D ARG* 3.1 5.8 + - - +
53D LEU* 3.0 40.5 + - - +
54D TYR 3.1 5.5 + - - -
248D SER 4.7 5.3 + - - -
250D VAL* 3.7 22.0 - - - -
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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