Contacts of the helix formed by residues 36 - 54 (chain D) in PDB entry 1P4A
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 ALA 36 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30D SER* 4.3 1.1 - - - -
35D SER* 1.3 77.4 - - - +
37D LYS* 1.3 65.8 + - - +
38D SER* 3.2 16.2 - - - +
39D SER* 3.0 20.6 + - - +
40D ILE* 3.1 12.5 + - - +
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Residues in contact with LYS 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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26D LEU* 4.1 30.1 - - + +
27D THR* 3.4 33.6 - - + +
30D SER* 4.0 17.4 + - - +
35D SER 3.7 0.8 + - - -
36D ALA* 1.3 72.7 - - - +
38D SER* 1.3 58.2 + - - +
40D ILE* 3.1 12.6 + - - +
41D SER* 2.9 31.3 + - - -
65D ALA 5.4 4.0 + - - -
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Residues in contact with SER 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D ALA* 4.1 11.1 - - - +
37D LYS* 1.3 80.8 - - - +
39D SER* 1.3 59.2 + - - +
41D SER* 3.6 9.5 + - - -
42D GLU* 3.4 20.3 + - - +
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Residues in contact with SER 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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8D ARG* 4.1 16.3 + - - -
35D SER* 4.4 7.1 - - - -
36D ALA* 3.0 23.4 + - - +
38D SER* 1.3 79.6 + - - +
40D ILE* 1.3 65.5 + - - +
42D GLU* 3.4 13.7 + - - +
43D ASP* 3.3 20.4 + - - +
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Residues in contact with ILE 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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8D ARG* 3.9 17.0 - - - +
12D LEU* 4.6 7.9 - - + -
26D LEU* 4.5 6.7 - - + +
29D PHE* 3.7 26.9 - - + +
30D SER* 4.2 16.6 - - - +
33D TYR* 3.8 26.5 - - + -
35D SER* 4.1 13.7 - - - -
36D ALA 3.1 13.1 + - - +
37D LYS* 3.1 9.8 + - - +
39D SER* 1.3 77.2 - - - +
41D SER* 1.3 63.2 + - - +
43D ASP* 2.9 10.7 + - - +
44D LEU* 2.9 40.5 + - + +
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Residues in contact with SER 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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26D LEU* 3.6 21.7 - - - +
37D LYS 2.9 17.1 + - - -
38D SER* 3.7 10.7 - - - -
39D SER 3.3 0.4 - - - -
40D ILE* 1.3 78.0 - - - +
42D GLU* 1.3 59.6 + - - +
44D LEU* 3.8 10.7 - - - +
45D THR* 3.0 29.5 + - - -
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Residues in contact with GLU 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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5D ARG* 3.2 25.0 + - - +
38D SER 3.4 9.5 + - - +
39D SER* 3.4 9.8 + - - +
40D ILE 3.2 0.8 - - - -
41D SER* 1.3 76.8 - - - +
43D ASP* 1.3 70.9 + - - +
45D THR* 3.4 9.1 + - - -
46D ILE* 3.3 29.5 + - + +
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Residues in contact with ASP 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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5D ARG* 3.9 16.5 + - - +
8D ARG* 2.6 49.1 + - - +
9D LEU* 4.0 19.3 + - + +
12D LEU* 3.5 18.4 - - + +
39D SER 3.3 11.1 + - - +
40D ILE* 2.9 9.1 + - - +
42D GLU* 1.3 82.0 - - - +
44D LEU* 1.3 57.5 + - - +
46D ILE* 3.1 8.9 + - - +
47D ILE* 3.0 32.0 + - - +
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Residues in contact with LEU 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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12D LEU* 3.9 28.3 - - + -
16D LEU* 4.0 9.6 - - + -
26D LEU* 3.6 26.2 - - + -
29D PHE* 4.7 1.8 - - + -
40D ILE* 2.9 29.0 + - + +
41D SER* 3.8 8.7 - - - +
43D ASP* 1.3 73.6 - - - +
45D THR* 1.3 57.8 + - - +
47D ILE* 4.4 2.0 - - + +
48D LYS* 2.8 32.3 + - - +
59D LEU* 3.4 23.7 - - + +
69D VAL* 3.6 35.4 - - + -
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Residues in contact with THR 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 SER* 3.0 15.1 + - - -
42D GLU* 3.5 12.5 - - - -
44D LEU* 1.3 74.4 - - - +
46D ILE* 1.3 55.3 + - + +
48D LYS* 3.6 11.2 + - + +
49D GLN* 2.7 52.8 + - - +
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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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4C ARG* 3.4 23.3 - - - +
6C SER* 3.6 31.6 - - - +
7C GLY* 4.0 10.1 - - - +
10C VAL* 4.4 6.3 - - + -
5D ARG* 2.8 35.4 - - - +
9D LEU* 4.7 5.2 - - + -
42D GLU* 3.3 19.0 + - + +
43D ASP* 3.1 10.7 + - - +
45D THR* 1.3 77.7 - - + +
47D ILE* 1.3 63.7 + - - +
49D GLN* 3.4 8.9 + - - +
50D THR* 3.0 32.2 + - - +
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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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10C VAL* 4.0 18.2 - - + -
9D LEU* 4.0 7.4 - - + -
12D LEU* 3.7 42.2 - - + -
13D THR* 3.7 19.1 - - - +
16D LEU* 4.0 10.8 - - + -
43D ASP 3.0 11.2 + - - +
44D LEU* 3.8 6.7 - - + +
46D ILE* 1.3 77.5 - - - +
48D LYS* 1.3 53.9 + - - +
50D THR* 3.3 0.9 + - - -
51D PHE* 2.8 70.0 + - + +
59D LEU* 3.9 11.9 - - + -
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Residues in contact with LYS 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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44D LEU 2.8 18.0 + - - +
45D THR* 3.7 11.0 - - + +
47D ILE* 1.3 77.6 - - - +
49D GLN* 1.3 63.3 + - - +
51D PHE* 3.4 2.1 + - - +
52D GLU* 3.0 54.7 + - - +
57D GLY 5.0 0.2 - - - +
58D THR* 5.2 2.8 - - - +
59D LEU* 3.1 44.3 + - + +
60D LEU* 5.1 5.9 - - - +
61D THR* 5.4 7.8 + - - +
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Residues in contact with GLN 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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4C ARG* 3.4 29.8 + - - -
45D THR* 2.7 39.3 + - - +
46D ILE* 3.4 13.7 - - - +
48D LYS* 1.3 77.9 - - - +
50D THR* 1.3 57.2 + - - +
52D GLU* 3.4 6.1 + - - +
53D GLN* 3.0 31.8 + - - +
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Residues in contact with THR 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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3C PHE* 4.9 3.6 - - + -
7C GLY* 3.4 42.2 - - - +
10C VAL* 3.8 19.7 - - + +
11C ASP* 4.0 14.4 - - + +
46D ILE* 3.0 20.0 + - - +
47D ILE 3.7 2.9 - - - -
49D GLN* 1.3 76.3 - - - +
51D PHE* 1.3 61.0 + - + +
53D GLN* 3.4 6.4 + - + -
54D GLN* 2.9 42.6 + - + +
56D ILE* 5.1 0.9 - - + -
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Residues in contact with PHE 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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10C VAL* 3.7 18.6 - - + -
14C ASN* 5.1 0.7 - - + -
13D THR* 4.1 13.5 - - + -
16D LEU* 4.6 8.5 - - + -
17D LEU* 3.8 26.5 - - + -
47D ILE* 2.8 47.2 + - + +
48D LYS* 3.8 5.2 - - - +
50D THR* 1.3 73.5 - - - +
52D GLU* 1.3 60.6 + - - +
55D GLY 3.2 1.9 + - - -
56D ILE* 2.8 53.7 + - + -
57D GLY 3.3 16.1 + - - +
59D LEU* 4.8 9.2 - - + +
71D TYR* 3.7 41.3 - + + -
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Residues in contact with GLU 52 (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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48D LYS* 3.0 54.1 + - - +
49D GLN* 3.9 6.1 - - - +
51D PHE* 1.3 77.0 - - - +
53D GLN* 1.3 61.3 + - - +
55D GLY* 3.4 9.0 + - - -
57D GLY 3.9 8.5 - - - +
58D THR* 4.2 23.1 - - - +
76D LYS* 3.4 15.1 - - - -
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Residues in contact with GLN 53 (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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2C LYS 5.9 0.4 + - - -
3C PHE* 3.4 23.7 - - + -
49D GLN 3.0 17.9 + - - +
50D THR* 3.9 9.6 - - - +
52D GLU* 1.3 78.3 - - - +
54D GLN* 1.3 86.3 + - + +
55D GLY 3.2 0.4 - - - -
76D LYS* 2.8 18.8 + - - +
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Residues in contact with GLN 54 (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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3C PHE* 3.2 17.3 - - + -
11C ASP* 3.0 33.0 - - - +
32C ARG* 3.2 22.2 + - - +
50D THR* 2.9 28.8 + - + +
53D GLN* 1.3 115.7 + - + +
55D GLY* 1.3 63.7 + - - +
56D ILE* 3.4 16.6 + - + +
76D LYS* 4.2 2.5 - - - -
79D GLU* 5.7 0.3 - - - +
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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