Contacts of the helix formed by residues 44 - 54 (chain C) in PDB entry 1PL8
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 CYS 44 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ILE* 1.3 76.2 - - - +
45C GLY* 1.3 70.4 + - - +
46C SER* 3.0 31.7 + - - -
47C ASP* 3.1 17.1 + - - +
48C VAL* 3.3 12.5 + - - +
69C HIS* 3.7 0.7 - - - -
70C GLU* 3.4 5.1 + - - +
182C PRO* 6.0 2.5 - - + -
337C PHE* 3.7 12.8 - - - -
344C LYS* 3.7 6.7 - - - +
400C NAD 5.4 14.4 - - - +
402C ZN 2.4 35.2 - - - -
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Residues in contact with GLY 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C CYS* 1.3 76.3 - - - +
46C SER* 1.3 51.2 + - - +
48C VAL* 3.6 1.1 - - - +
49C HIS* 2.7 37.7 + - - +
337C PHE* 3.4 24.1 - - - -
400C NAD 5.2 5.9 + - - -
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Residues in contact with SER 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C CYS* 3.0 9.3 - - - -
45C GLY* 1.3 76.1 - - - +
47C ASP* 1.3 72.6 + - - +
49C HIS* 3.2 0.9 + - - -
50C TYR* 3.0 35.8 + - - -
56C ILE* 3.5 21.3 - - - +
69C HIS* 3.0 30.9 - - - -
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Residues in contact with ASP 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C GLY 4.3 1.6 - - - +
43C ILE* 3.5 12.8 - - + +
44C CYS 3.1 26.3 + - - +
46C SER* 1.3 81.2 + - - +
48C VAL* 1.3 63.3 + - - +
50C TYR* 3.2 7.6 + - - +
51C TRP* 3.1 20.6 + - - +
67C LEU* 4.0 15.9 - - + +
68C GLY* 3.1 28.8 + - - -
69C HIS* 3.4 25.2 + - - -
120C ALA* 3.8 7.3 - - - +
334C PHE* 4.0 21.3 - - + -
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Residues in contact with VAL 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ILE* 4.9 2.9 - - + -
44C CYS 3.3 12.7 + - - +
45C GLY 3.8 5.6 - - - +
47C ASP* 1.3 76.1 - - + +
49C HIS* 1.3 58.1 + - - +
51C TRP* 3.3 21.6 + - + +
52C GLU* 3.0 41.7 + - - +
334C PHE* 4.0 26.0 - - + +
337C PHE* 3.6 44.4 - - + -
338C LYS* 5.4 5.4 - - + -
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Residues in contact with HIS 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C GLY 2.7 22.4 + - - +
46C SER 3.6 5.2 - - - +
47C ASP 3.2 0.4 - - - -
48C VAL* 1.3 70.6 - - - +
50C TYR* 1.3 60.8 + - - +
52C GLU* 4.7 3.4 - - - -
53C TYR* 2.8 68.1 + + + +
54C GLY 3.6 0.2 + - - -
55C ARG* 2.6 31.5 + - + -
56C ILE* 3.5 22.0 - - + +
57C GLY 5.5 0.7 - - - -
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Residues in contact with TYR 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C VAL* 3.5 9.8 - - + +
46C SER* 3.0 30.2 + - - -
47C ASP* 3.6 9.2 - - - +
49C HIS* 1.3 77.3 - - - +
51C TRP* 1.3 58.8 + - - +
54C GLY* 2.7 30.3 + - - +
55C ARG* 3.7 15.9 - - - +
56C ILE* 3.4 27.9 - - + +
59C PHE* 3.2 47.7 - - - +
61C VAL* 3.9 13.0 - - + -
65C MET* 4.0 9.0 - - + -
67C LEU* 4.2 12.1 - - + -
120C ALA 3.2 24.7 - - - -
121C THR* 3.9 9.5 + - - +
122C PRO* 3.4 17.5 - - + +
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Residues in contact with TRP 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C VAL* 4.0 15.4 - - + +
15C GLY 3.6 1.6 - - - +
16C PRO* 3.5 2.1 - - - +
17C GLY* 2.6 53.9 + - - -
18C ASP 4.1 1.6 - - - -
19C LEU* 3.5 35.2 - - + +
47C ASP 3.1 12.4 + - - +
48C VAL* 3.4 24.5 - - + +
50C TYR* 1.3 81.2 - - - +
52C GLU* 1.3 60.8 + - + +
67C LEU* 4.8 0.2 - - + -
331C LEU* 4.2 16.1 - - + +
334C PHE* 3.6 48.7 - + + -
335C GLU* 3.1 30.1 - - + -
338C LYS* 4.2 17.3 - - + -
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Residues in contact with GLU 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C PRO* 3.6 15.6 - - - +
17C GLY* 3.8 5.9 + - - +
48C VAL* 3.0 32.9 + - - +
49C HIS* 4.7 1.4 - - - -
51C TRP* 1.3 93.2 - - + +
53C TYR* 1.3 89.7 + - + +
338C LYS* 3.4 26.4 - - - +
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Residues in contact with TYR 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C PRO* 3.6 15.2 - - - +
49C HIS* 2.8 55.7 + + + +
52C GLU* 1.3 106.3 + - + +
54C GLY* 1.3 63.0 + - - +
55C ARG* 3.0 19.8 + - + +
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Residues in contact with GLY 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C GLY* 4.5 2.7 - - - -
16C PRO* 4.0 19.5 - - - +
50C TYR* 2.7 27.7 + - - -
52C GLU 3.6 1.2 - - - -
53C TYR* 1.3 73.2 - - - +
55C ARG* 1.3 59.1 + - - +
60C ILE* 3.9 4.0 - - - +
61C VAL* 3.0 39.9 + - - +
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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