Contacts of the helix formed by residues 42 - 56 (chain A) in PDB entry 1PY1
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 GLU 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ASP* 3.0 19.0 - - - +
41A PHE* 1.3 114.5 - - + +
43A GLY* 1.3 66.8 + - - +
44A PRO 3.6 1.1 - - - -
45A PRO* 2.9 18.4 - - + +
46A LEU* 3.4 13.5 + - + +
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Residues in contact with GLY 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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10A LEU* 4.0 18.4 - - - -
37A LEU* 3.6 11.9 - - - -
40A ASP* 3.4 12.5 + - - -
42A GLU* 1.3 77.7 - - - +
44A PRO* 1.3 62.6 - - - +
46A LEU* 2.7 6.9 + - - -
47A ALA* 2.7 36.2 + - - +
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Residues in contact with PRO 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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37A LEU* 3.0 35.4 - - + +
38A ASN* 4.6 2.5 - - - +
40A ASP 3.5 8.5 - - - +
41A PHE* 4.3 5.4 - - - +
42A GLU 3.7 0.4 - - - -
43A GLY* 1.3 88.5 - - - +
45A PRO* 1.3 72.6 - - + +
47A ALA* 3.9 1.8 - - + +
48A THR* 3.2 20.3 + - - +
80A ARG* 3.8 37.9 - - + +
81A PHE* 4.4 6.1 - - + -
84A GLU* 3.4 15.0 - - + +
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Residues in contact with PRO 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 PHE 4.4 5.6 - - - +
42A GLU* 2.9 28.9 - - + +
44A PRO* 1.3 90.5 - - + +
46A LEU* 1.3 58.2 + - - +
48A THR* 3.1 13.3 + - - -
49A ARG* 3.5 26.5 + - - +
84A GLU* 3.1 31.0 - - + +
89A ARG* 6.2 0.2 - - - -
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Residues in contact with LEU 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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10A LEU* 3.7 26.9 - - + -
11A GLU* 4.2 15.9 - - - +
42A GLU* 3.4 13.5 + - + +
43A GLY* 2.7 15.8 + - - +
45A PRO* 1.3 73.0 - - - +
47A ALA* 1.3 62.1 + - - +
49A ARG* 3.2 33.5 + - + +
50A LEU* 3.1 47.9 + - + +
58B PRO* 5.8 4.0 - - + -
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Residues in contact with ALA 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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10A LEU* 4.0 11.0 - - + -
33A PHE* 3.5 31.6 - - + -
37A LEU* 4.0 10.3 - - + -
43A GLY 2.7 18.1 + - - +
44A PRO 3.9 3.8 - - - +
46A LEU* 1.3 73.7 - - - +
48A THR* 1.3 59.5 + - - +
50A LEU* 3.2 3.9 + - - +
51A LEU* 2.9 35.5 + - - +
81A PHE* 4.3 10.5 - - + -
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Residues in contact with THR 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 PRO 3.2 13.4 + - - +
45A PRO* 3.1 14.9 + - - +
47A ALA* 1.3 77.1 - - - +
49A ARG* 1.3 59.6 + - - +
51A LEU* 4.5 2.7 - - - -
52A ALA* 3.0 23.9 + - - +
81A PHE* 4.0 17.7 - - + -
84A GLU* 3.7 34.7 + - + +
85A VAL* 4.2 9.4 - - + -
89A ARG* 5.9 3.8 - - - +
90A PHE* 3.3 35.4 - - + +
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Residues in contact with ARG 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 PRO* 3.5 23.7 + - - +
46A LEU* 3.2 38.4 + - + +
48A THR* 1.3 78.8 + - - +
50A LEU* 1.3 67.0 + - - +
52A ALA* 3.6 5.6 + - - +
53A HIS* 3.2 22.5 + - - +
89A ARG* 5.7 9.6 - - + +
58B PRO* 4.1 18.3 - - + +
106B ARG* 3.1 45.4 - - - +
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Residues in contact with LEU 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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10A LEU* 4.0 8.1 - - + -
11A GLU* 3.8 44.0 - - + +
14A ILE* 4.1 16.6 - - + -
33A PHE* 4.7 4.5 - - + -
46A LEU* 3.1 44.1 + - + +
47A ALA* 3.7 6.1 - - - +
49A ARG* 1.3 78.5 - - - +
51A LEU* 1.3 61.8 + - - +
53A HIS* 3.4 5.9 + - + +
54A LYS* 3.1 29.3 + - - +
58B PRO* 4.2 23.6 - - + -
59B GLN* 4.3 15.3 - - + +
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Residues in contact with LEU 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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14A ILE* 3.5 27.8 - - + -
33A PHE* 4.4 11.2 - - + -
47A ALA 2.9 22.0 + - - +
48A THR* 3.9 6.5 - - - +
50A LEU* 1.3 75.8 - - - +
52A ALA* 1.3 56.0 + - - +
54A LYS* 3.1 3.8 + - - +
55A ILE* 2.7 45.2 + - + +
66A ALA* 3.8 18.8 - - + +
69A VAL* 3.6 16.8 - - + -
70A LEU* 3.9 28.3 - - + -
73A CYS* 5.6 0.2 - - - -
81A PHE* 4.1 20.6 - - + -
90A PHE* 4.3 6.7 - - + -
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Residues in contact with ALA 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 THR 3.0 18.6 + - - +
49A ARG* 4.0 6.7 - - - +
50A LEU 3.4 0.2 - - - -
51A LEU* 1.3 77.8 - - - +
53A HIS* 1.3 60.7 + - - +
55A ILE* 3.5 6.1 + - - +
56A GLN* 2.9 34.6 + - - +
90A PHE* 3.9 10.2 - - + -
93A GLU* 3.5 38.4 - - + -
94A LEU* 6.2 0.2 - - - -
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Residues in contact with HIS 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 ARG 3.2 15.3 + - - +
50A LEU 3.8 4.2 + - - +
51A LEU 3.2 0.6 - - - -
52A ALA* 1.3 79.8 - - - +
54A LYS* 1.3 70.8 + - + +
56A GLN* 3.3 14.6 + - - +
53B HIS* 2.7 85.3 + + - -
54B LYS* 5.0 0.4 - - - -
56B GLN* 4.0 11.2 - - + -
57B SER* 3.4 32.3 + - - -
58B PRO* 3.5 20.5 - - + +
59B GLN* 5.9 1.0 + - - -
62B GLU* 4.6 7.2 + - - -
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Residues in contact with LYS 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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14A ILE* 4.1 16.6 - - + -
15A ASN* 3.1 30.0 + - - +
18A THR* 3.5 25.3 + - + +
50A LEU* 3.1 15.5 + - - +
51A LEU* 3.1 6.3 + - - +
53A HIS* 1.3 88.1 + - + +
55A ILE* 1.3 63.2 + - - +
57A SER* 3.0 24.2 + - - -
62A GLU* 3.3 28.0 + - + +
63A ALA* 3.3 9.0 + - - -
66A ALA* 3.5 20.4 - - + -
20B PRO* 5.8 0.6 - - - +
53B HIS* 4.7 0.4 - - - -
54B LYS* 5.7 1.2 - - - +
59B GLN* 4.4 9.3 - - - +
62B GLU* 4.7 12.9 + - - -
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Residues in contact with ILE 55 (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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51A LEU* 2.7 33.5 + - + +
52A ALA* 3.9 6.7 - - - +
54A LYS* 1.3 71.4 - - - +
56A GLN* 1.3 57.1 + - + +
57A SER 3.3 1.0 + - - +
63A ALA* 3.3 21.1 - - - +
66A ALA* 3.9 14.4 - - + +
67A LEU* 3.5 39.5 - - + -
70A LEU* 3.7 21.3 - - + -
90A PHE* 4.2 6.3 - - + -
93A GLU 5.7 0.4 - - - +
94A LEU* 3.9 16.2 - - + -
97A VAL* 4.1 17.0 - - + +
111A VAL* 4.5 2.0 - - + +
115A ILE* 4.0 18.4 - - + -
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Residues in contact with GLN 56 (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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52A ALA* 2.9 23.0 + - - +
53A HIS* 3.3 12.1 + - - +
54A LYS 3.1 1.4 - - - -
55A ILE* 1.3 77.5 - - + +
57A SER* 1.3 63.2 + - - +
58A PRO* 3.7 3.6 - - - +
93A GLU* 3.0 49.2 + - + +
96A LYS* 4.5 9.5 - - - +
97A VAL* 3.7 19.8 - - + +
103A LEU* 4.1 22.8 - - + +
53B HIS* 3.5 12.6 - - + -
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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