Contacts of the helix formed by residues 36 - 54 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A SER* 4.3 0.9 - - - -
35A SER* 1.3 75.9 - - - +
37A LYS* 1.3 65.9 + - - +
38A SER* 3.2 16.4 - - - +
39A SER* 3.0 23.4 + - - +
40A ILE* 3.0 12.3 + - - +
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Residues in contact with LYS 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 4.0 35.5 - - + +
27A THR* 4.1 26.8 - - + +
30A SER* 3.7 20.9 - - - +
35A SER 3.7 0.2 + - - -
36A ALA* 1.3 73.9 - - - +
38A SER* 1.3 57.4 + - - +
40A ILE* 3.2 10.9 + - - +
41A SER* 2.9 32.4 + - - -
65A ALA* 4.9 9.5 + - - +
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Residues in contact with SER 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA* 3.9 11.6 - - - +
37A LYS* 1.3 79.5 - - - +
39A SER* 1.3 63.0 + - - +
41A SER* 3.6 8.3 + - - -
42A GLU* 3.5 25.6 + - - +
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Residues in contact with SER 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG* 4.1 15.7 + - - -
35A SER* 4.7 5.6 - - - -
36A ALA* 3.0 24.4 + - - +
38A SER* 1.3 77.9 + - - +
40A ILE* 1.3 66.7 + - - +
42A GLU* 3.4 9.7 + - - +
43A ASP* 3.2 24.3 + - - +
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Residues in contact with ILE 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG* 3.6 33.2 - - - +
12A LEU* 4.7 7.2 - - + -
26A LEU* 4.5 7.9 - - + +
29A PHE* 3.9 21.5 - - + -
30A SER* 4.2 21.8 - - - +
33A TYR* 3.8 12.8 - - + -
35A SER* 4.0 13.7 - - - -
36A ALA 3.0 16.4 + - - +
37A LYS* 3.5 9.6 - - - +
39A SER* 1.3 76.7 - - - +
41A SER* 1.3 57.3 + - - +
43A ASP* 3.1 6.9 + - - +
44A LEU* 3.0 45.5 + - + +
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Residues in contact with SER 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 3.7 19.9 - - - +
37A LYS 2.9 19.1 + - - -
38A SER* 3.8 10.0 - - - -
39A SER 3.2 0.4 - - - -
40A ILE* 1.3 76.0 - - - +
42A GLU* 1.3 58.6 + - - +
44A LEU* 3.3 11.3 + - - +
45A THR* 3.0 31.3 + - - -
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Residues in contact with GLU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ARG* 5.5 5.1 + - - +
38A SER 3.5 14.1 + - - +
39A SER* 3.4 10.7 + - - +
40A ILE 3.2 0.4 - - - -
41A SER* 1.3 76.9 - - - +
43A ASP* 1.3 66.0 + - - +
45A THR* 3.3 15.6 + - - -
46A ILE* 3.3 20.6 + - + +
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Residues in contact with ASP 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ARG* 3.7 24.9 + - - +
8A ARG* 2.7 48.4 + - - +
9A LEU* 3.8 16.7 + - + +
12A LEU* 3.7 16.6 - - + -
39A SER 3.2 10.9 + - - +
40A ILE* 3.1 10.4 + - - +
42A GLU* 1.3 77.6 - - - +
44A LEU* 1.3 57.0 + - - +
46A ILE* 3.1 10.0 + - - +
47A ILE* 3.0 31.1 + - - +
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Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 4.0 27.1 - - + -
16A LEU* 4.1 9.4 - - + -
26A LEU* 3.7 31.0 - - + -
29A PHE* 4.6 2.0 - - + -
40A ILE* 3.0 28.1 + - + +
41A SER* 3.7 7.4 - - - +
42A GLU 3.3 0.2 - - - -
43A ASP* 1.3 74.2 - - - +
45A THR* 1.3 60.6 + - - +
47A ILE* 4.4 3.1 - - + +
48A LYS* 2.8 32.5 + - - +
59A LEU* 3.5 23.2 - - + +
61A THR* 6.0 0.7 - - - +
69A VAL* 3.7 29.6 - - + -
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Residues in contact with THR 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A SER 3.0 16.1 + - - -
42A GLU* 3.5 12.9 - - - +
43A ASP 3.2 0.2 - - - -
44A LEU* 1.3 77.6 - - - +
46A ILE* 1.3 63.0 + - + +
48A LYS* 3.8 8.6 - - + +
49A GLN* 2.9 55.9 + - + +
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Residues in contact with ILE 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ARG* 2.7 36.1 - - - +
9A LEU* 4.4 5.6 - - + -
42A GLU* 3.3 13.9 + - + +
43A ASP* 3.1 9.9 + - - +
45A THR* 1.3 76.8 - - + +
47A ILE* 1.3 65.3 + - - +
49A GLN* 3.3 9.4 + - - +
50A THR* 3.0 32.8 + - - +
6B SER* 3.8 39.7 - - - +
7B GLY* 4.3 2.9 - - - +
10B VAL* 4.4 7.0 - - + -
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Residues in contact with ILE 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 4.0 7.6 - - + -
12A LEU* 3.8 41.1 - - + -
13A THR* 3.8 20.2 - - - +
16A LEU* 3.9 10.1 - - + -
43A ASP 3.0 17.3 + - - +
44A LEU* 3.4 6.5 + - - +
46A ILE* 1.3 76.2 - - - +
48A LYS* 1.3 53.1 + - - +
50A THR* 3.3 0.7 + - - -
51A PHE* 2.7 67.3 + - + +
59A LEU* 3.7 16.6 - - + -
10B VAL* 3.8 18.2 - - + -
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Residues in contact with LYS 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU 2.8 23.0 + - - +
45A THR* 3.8 9.2 - - + +
47A ILE* 1.3 72.8 - - - +
49A GLN* 1.3 68.6 + - + +
51A PHE* 3.4 2.9 + - - +
52A GLU* 3.1 53.4 + - - +
57A GLY 4.9 0.3 - - - +
58A THR* 4.7 4.6 - - - +
59A LEU* 2.8 48.3 + - + +
60A LEU* 5.0 3.2 - - - +
61A THR* 5.4 6.3 - - - +
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Residues in contact with GLN 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A THR* 2.9 41.8 + - + +
46A ILE* 3.9 8.6 - - - +
48A LYS* 1.3 82.1 - - + +
50A THR* 1.3 63.2 + - - +
52A GLU* 3.5 7.5 + - - +
53A GLN* 3.1 27.4 + - - +
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Residues in contact with THR 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE* 3.0 20.1 + - - +
47A ILE 3.8 2.2 - - - -
49A GLN* 1.3 74.3 - - - +
51A PHE* 1.3 66.1 + - + +
53A GLN* 3.4 7.2 + - - +
54A GLN* 3.0 39.5 + - + +
56A ILE* 5.2 0.9 - - + -
3B PHE* 4.8 4.7 - - + -
7B GLY* 3.5 39.9 - - - +
10B VAL* 3.8 20.1 - - + +
11B ASP* 4.1 7.6 - - + +
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Residues in contact with PHE 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A THR* 4.0 15.0 - - + -
16A LEU* 4.5 9.4 - - + -
17A LEU* 3.7 26.5 - - + -
47A ILE* 2.7 47.4 + - + +
48A LYS* 3.7 6.1 - - - +
50A THR* 1.3 72.5 - - - +
52A GLU* 1.3 59.8 + - - +
55A GLY 3.3 1.9 + - - -
56A ILE* 2.7 57.1 + - + -
57A GLY 3.2 17.1 + - - +
59A LEU* 4.8 8.1 - - + +
71A TYR* 3.6 41.7 - + + -
10B VAL* 3.9 18.8 - - + -
14B ASN* 5.0 0.7 - - + -
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Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LYS* 3.1 55.0 + - - +
49A GLN* 3.8 7.4 - - - +
51A PHE* 1.3 75.8 - - - +
53A GLN* 1.3 63.2 + - - +
55A GLY* 3.2 5.1 + - - -
57A GLY 3.9 9.0 - - - +
58A THR* 4.3 19.1 + - - +
76A LYS* 3.1 29.0 + - - +
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Residues in contact with GLN 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLN 3.1 18.6 + - - +
50A THR* 4.0 6.1 - - - +
52A GLU* 1.3 76.2 - - - +
54A GLN* 1.3 81.4 + - - +
55A GLY 3.6 0.3 + - - -
76A LYS* 4.3 6.7 + - - +
2B LYS 6.1 0.6 - - - +
3B PHE* 3.5 27.5 - - - +
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Residues in contact with GLN 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A THR* 3.0 30.9 + - + +
53A GLN* 1.3 119.3 + - + +
55A GLY* 1.3 63.8 + - - +
56A ILE* 3.2 16.3 + - + +
79A GLU* 5.6 0.9 - - - +
3B PHE* 3.3 20.3 - - + -
11B ASP* 3.2 29.6 - - - +
32B ARG* 3.6 18.2 + - - +
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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