Contacts of the helix formed by residues 36 - 54 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B SER* 4.2 0.9 - - - -
35B SER* 1.3 76.7 - - - +
37B LYS* 1.3 64.6 + - - +
38B SER* 4.1 15.7 - - - +
39B SER* 3.0 22.2 + - - +
40B ILE* 3.2 10.3 + - - +
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Residues in contact with LYS 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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26B LEU* 4.2 21.5 - - + +
27B THR* 4.1 26.2 - - - +
30B SER* 3.7 18.4 - - - +
35B SER 3.6 1.0 + - - -
36B ALA* 1.3 71.6 - - - +
38B SER* 1.3 57.0 + - - +
40B ILE* 3.2 12.3 + - - +
41B SER* 2.9 31.4 + - - -
64B GLY 5.9 2.9 - - - -
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Residues in contact with SER 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ALA* 4.1 11.5 - - - +
37B LYS* 1.3 78.8 - - - +
39B SER* 1.3 65.2 + - - +
41B SER* 3.5 9.5 + - - -
42B GLU* 3.2 29.4 + - - +
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Residues in contact with SER 39 (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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5B ARG* 4.3 0.4 + - - -
8B ARG* 4.0 19.5 + - - -
35B SER* 4.6 7.4 - - - -
36B ALA* 3.0 21.4 + - - +
38B SER* 1.3 79.8 + - - +
40B ILE* 1.3 65.2 + - - +
42B GLU* 3.2 15.9 + - - +
43B ASP* 3.0 28.2 + - - +
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Residues in contact with ILE 40 (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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8B ARG* 4.0 18.4 - - + +
12B LEU* 4.5 6.7 - - + -
26B LEU* 4.5 8.5 - - + +
29B PHE* 3.7 24.9 - - + +
30B SER* 4.1 20.2 - - - +
33B TYR* 3.7 26.5 - - + -
35B SER* 4.1 12.8 - - - -
36B ALA 3.6 10.8 - - - +
37B LYS* 3.2 9.4 + - - +
39B SER* 1.3 77.6 - - - +
41B SER* 1.3 57.0 + - - +
43B ASP* 3.1 6.9 + - - +
44B LEU* 2.8 45.1 + - + +
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Residues in contact with SER 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 3.5 22.7 - - - +
37B LYS 2.9 16.6 + - - -
38B SER* 3.7 11.7 - - - -
39B SER 3.2 0.2 - - - -
40B ILE* 1.3 75.5 - - - +
42B GLU* 1.3 56.7 + - - +
44B LEU* 3.2 11.9 + - - +
45B THR* 3.0 30.1 + - - -
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Residues in contact with GLU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ARG* 4.4 15.6 + - - +
38B SER* 3.2 18.5 + - - +
39B SER* 3.2 15.4 + - - +
41B SER* 1.3 72.0 - - - +
43B ASP* 1.3 66.0 + - - +
45B THR* 3.3 10.3 + - - -
46B ILE* 3.2 27.6 + - + +
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Residues in contact with ASP 43 (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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5B ARG* 2.3 39.3 + - - +
8B ARG* 2.5 46.0 + - - +
9B LEU* 3.8 18.3 + - + +
12B LEU* 3.7 16.3 - - + +
39B SER 3.0 9.6 + - - +
40B ILE* 3.2 10.9 - - - +
42B GLU* 1.3 76.8 - - - +
44B LEU* 1.3 61.4 + - - +
46B ILE* 3.3 6.8 + - - +
47B ILE* 3.2 26.2 + - - +
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Residues in contact with LEU 44 (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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12B LEU* 3.8 29.4 - - + -
16B LEU* 3.9 20.9 - - + -
26B LEU* 3.7 30.1 - - + -
29B PHE* 5.1 0.7 - - + -
40B ILE* 2.8 30.7 + - + +
41B SER* 3.2 10.0 + - - +
43B ASP* 1.3 72.1 - - - +
45B THR* 1.3 57.3 + - - +
47B ILE* 3.3 1.9 + - + +
48B LYS* 2.9 32.4 + - - +
59B LEU* 3.3 13.2 - - + +
61B THR* 5.2 10.1 - - + -
69B VAL* 3.8 25.4 - - + -
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Residues in contact with THR 45 (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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41B SER 3.0 13.2 + - - -
42B GLU* 3.5 13.5 - - - +
44B LEU* 1.3 77.2 - - - +
46B ILE* 1.3 62.9 + - + +
48B LYS* 3.7 10.7 - - + +
49B GLN* 3.1 44.3 + - - +
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Residues in contact with ILE 46 (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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4A ARG* 4.8 8.7 - - - +
6A SER* 3.9 39.3 - - - +
7A GLY 4.4 2.2 - - - +
10A VAL* 4.4 4.7 - - + -
5B ARG* 3.4 36.6 - - - +
9B LEU* 4.2 13.2 - - + -
42B GLU* 3.2 16.1 + - + +
43B ASP* 3.3 7.6 + - - +
45B THR* 1.3 80.5 - - + +
47B ILE* 1.3 62.0 + - - +
49B GLN* 3.4 11.1 + - - +
50B THR* 3.1 28.0 + - - +
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Residues in contact with ILE 47 (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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10A VAL* 3.9 25.4 - - + -
9B LEU* 4.1 9.0 - - + +
12B LEU* 3.8 37.0 - - + -
13B THR* 3.9 11.4 - - - +
16B LEU* 3.9 10.1 - - + -
43B ASP 3.2 15.9 + - - +
44B LEU* 3.8 7.2 - - + +
46B ILE* 1.3 73.2 - - - +
48B LYS* 1.3 55.3 + - - +
50B THR* 3.2 1.6 + - - -
51B PHE* 2.6 77.3 + - + +
59B LEU* 3.9 10.5 - - + -
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Residues in contact with LYS 48 (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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44B LEU 2.9 22.4 + - - +
45B THR* 3.7 9.6 - - - +
47B ILE* 1.3 71.8 - - - +
49B GLN* 1.3 57.1 + - + +
51B PHE* 3.2 5.7 + - - +
52B GLU* 2.8 70.3 + - - +
58B THR* 4.9 1.8 - - - -
59B LEU* 3.6 45.6 + - + +
60B LEU* 5.9 2.0 - - - +
61B THR* 5.6 6.1 - - + -
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Residues in contact with GLN 49 (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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45B THR* 3.1 35.9 + - - +
46B ILE* 3.7 10.8 - - - +
47B ILE 3.3 0.2 - - - -
48B LYS* 1.3 80.2 - - + +
50B THR* 1.3 58.0 + - - +
52B GLU* 3.3 9.9 + - - +
53B GLN* 2.8 32.4 + - - +
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Residues in contact with THR 50 (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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3A PHE* 5.1 3.8 - - + -
7A GLY* 3.3 42.0 - - - +
10A VAL* 4.1 12.8 - - + +
11A ASP* 4.0 13.5 - - + +
46B ILE* 3.1 16.4 + - - +
47B ILE 3.7 2.9 - - - -
49B GLN* 1.3 74.7 - - - +
51B PHE* 1.3 69.1 + - + +
53B GLN* 4.4 9.3 + - - +
54B GLN* 2.8 46.1 + - + +
56B ILE* 5.4 0.9 - - + -
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Residues in contact with PHE 51 (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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10A VAL* 3.6 18.6 - - + -
14A ASN* 5.0 1.3 - - + -
13B THR* 4.0 17.7 - - + -
16B LEU* 4.7 4.9 - - + -
17B LEU* 3.7 23.6 - - + -
47B ILE* 2.6 45.6 + - + +
48B LYS* 3.6 5.6 - - - +
50B THR* 1.3 72.3 - - - +
52B GLU* 1.3 58.3 + - - +
55B GLY 3.1 6.2 + - - -
56B ILE* 2.8 52.9 + - + -
57B GLY 3.3 17.2 + - - +
58B THR* 4.7 0.7 - - - +
59B LEU* 3.7 21.5 - - + -
71B TYR* 3.7 34.3 - + - -
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Residues in contact with GLU 52 (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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48B LYS* 2.8 54.9 + - - +
49B GLN* 3.8 7.8 - - - +
51B PHE* 1.3 75.9 - - - +
53B GLN* 1.3 62.1 + - - +
54B GLN 3.3 0.5 + - - -
55B GLY* 3.3 2.5 + - - -
57B GLY 3.6 15.0 - - - +
58B THR* 3.8 20.3 - - + +
76B LYS* 2.9 31.1 + - - +
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Residues in contact with GLN 53 (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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2A LYS* 3.5 25.8 + - - +
3A PHE* 4.5 13.7 - - - -
49B GLN 2.8 18.4 + - - +
50B THR* 3.9 9.8 + - - +
52B GLU* 1.3 76.9 - - - +
54B GLN* 1.3 79.5 + - - +
76B LYS* 3.3 14.4 + - - +
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Residues in contact with GLN 54 (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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3A PHE* 3.5 29.1 - - + -
11A ASP* 3.1 31.2 - - - +
32A ARG* 3.6 15.7 + - - +
50B THR* 2.8 30.3 + - + +
53B GLN* 1.3 107.1 + - + +
55B GLY* 1.3 62.5 + - - +
56B ILE* 3.5 17.1 + - + +
76B LYS* 4.7 0.4 - - - -
79B GLU* 5.5 0.9 - - - +
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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