Contacts of the helix formed by residues 51 - 56 (chain I) in PDB entry 1PP9
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 51 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A VAL* 4.7 3.8 - - + +
136A GLN* 2.7 31.9 - - + +
137A GLU* 4.2 13.5 - - - -
140A GLU* 2.8 13.1 + - - +
306B PRO* 4.1 9.6 - - - -
49I VAL* 3.6 3.9 - - - +
50I LEU* 1.3 75.5 - - - +
52I ARG* 1.3 64.9 + - - +
53I GLU* 3.2 16.6 - - - +
54I SER* 3.0 38.7 + - - -
55I LEU* 3.2 22.3 + - - +
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Residues in contact with ARG 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A GLN* 4.6 0.4 - - - +
296B TYR* 3.2 29.6 + - - +
300B ALA* 4.8 9.3 + - - +
303B VAL 4.2 3.6 + - - -
304B HIS* 3.2 26.9 + - - +
305B GLN 2.7 31.9 + - - -
306B PRO* 3.5 17.2 - - + +
307B PHE* 3.4 32.9 - - - +
51I CYS* 1.3 75.2 - - - +
53I GLU* 1.3 70.7 + - - +
55I LEU* 3.4 4.0 + - - +
56I ARG* 3.2 21.8 + - - +
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Residues in contact with GLU 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LYS* 5.5 3.7 + - - +
130A GLU* 5.5 2.4 - - - +
133A VAL* 3.7 40.1 - - + +
136A GLN* 5.4 0.3 + - - -
137A GLU* 4.7 3.1 - - - +
287B ARG* 3.9 48.6 + - + +
288B GLY 5.6 1.0 - - - +
51I CYS* 3.2 10.7 - - - +
52I ARG* 1.3 83.7 + - - +
54I SER* 1.3 60.6 + - - +
55I LEU 3.1 5.4 + - - -
56I ARG* 3.4 20.8 + - - +
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Residues in contact with SER 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A GLU* 4.2 9.5 + - - +
140A GLU* 2.7 39.7 + - - -
49I VAL* 3.9 18.9 - - - +
51I CYS* 3.0 12.6 - - - -
53I GLU* 1.3 76.4 - - - +
55I LEU* 1.3 59.1 + - - +
56I ARG 4.6 2.1 - - - +
58I GLN* 4.1 8.3 + - - +
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Residues in contact with LEU 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B LEU* 4.5 14.6 - - + -
254B HIS* 6.0 0.2 - - - +
306B PRO* 4.2 11.4 - - + +
307B PHE* 3.8 30.1 - - - +
308B ASP* 2.9 26.3 - - + +
327B ILE* 3.8 29.2 - - + +
328B SER* 5.6 0.2 - - - -
49I VAL* 3.8 20.4 - - + -
51I CYS 3.2 13.6 + - - +
52I ARG* 3.7 7.0 - - - +
53I GLU 3.1 0.6 - - - -
54I SER* 1.3 78.8 - - - +
56I ARG* 1.3 63.1 + - - +
58I GLN* 3.0 33.3 + - + +
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Residues in contact with ARG 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B GLY* 4.8 1.0 - - - -
281B ALA 4.7 2.8 - - - +
282B GLY* 3.3 34.2 + - - +
283B PRO* 3.6 30.1 - - + +
285B VAL 6.1 0.4 - - - +
287B ARG* 6.4 1.3 - - - -
288B GLY 5.1 5.6 - - - +
290B ASN* 3.0 40.0 + - - +
293B SER* 4.5 12.7 + - - -
296B TYR* 3.7 11.2 - - - +
307B PHE 5.4 0.2 - - - -
308B ASP* 2.7 37.6 + - - +
309B VAL 2.9 21.9 + - - -
310B SER* 4.2 7.3 - - - -
52I ARG 3.2 12.7 + - - +
53I GLU* 3.4 17.1 + - - +
54I SER 4.6 2.4 - - - +
55I LEU* 1.3 76.0 - - - +
57I GLY* 1.3 61.7 + - - +
58I GLN* 5.3 0.3 - - - +
59I ALA* 5.2 0.2 - - - +
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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