Contacts of the helix formed by residues 10 - 17 (chain B) in PDB entry 1PG3
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 PRO 10 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ALA 3.4 9.8 - - - +
9B ILE* 1.3 88.4 - - + +
11B ALA* 1.3 65.4 + - - +
12B ASN* 3.0 20.4 - - - +
13B ILE* 2.9 16.7 + - + +
14B ALA* 3.0 10.6 + - - +
405B GLU 5.8 1.1 - - - +
406B LYS* 4.1 23.6 - - + +
407B CYS 5.4 0.2 - - - -
408B PRO* 3.9 27.6 - - + -
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Residues in contact with ALA 11 (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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9B ILE 3.5 3.3 + - - -
10B PRO* 1.3 70.8 - - - +
12B ASN* 1.3 57.9 + - - +
14B ALA* 3.2 6.5 + - - +
15B ASP* 2.8 42.2 + - - +
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Residues in contact with ASN 12 (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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10B PRO* 3.0 26.2 - - - +
11B ALA* 1.3 79.0 + - - +
13B ILE* 1.3 77.9 + - - +
15B ASP* 3.6 11.8 + - - +
16B ARG* 3.5 21.6 + - - +
381B ARG* 4.8 15.6 + - - +
406B LYS* 4.4 10.6 + - - +
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Residues in contact with ILE 13 (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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9B ILE* 4.0 4.0 - - + -
10B PRO* 2.9 13.0 + - + +
12B ASN* 1.3 101.5 - - - +
14B ALA* 1.3 60.3 + - - +
16B ARG* 3.2 10.5 + - + +
17B CYS* 2.8 30.0 + - + +
294B ASP* 5.0 6.3 - - - +
381B ARG* 4.0 11.9 - - + +
382B ILE* 3.5 26.0 - - + -
406B LYS 5.0 0.2 - - - +
408B PRO* 3.7 21.1 - - + -
427B PRO* 3.6 38.8 - - + +
428B GLY* 3.7 6.7 - - - +
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Residues in contact with ALA 14 (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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9B ILE* 4.1 15.5 - - + +
10B PRO 3.0 12.1 + - - +
11B ALA* 3.2 10.5 + - - +
13B ILE* 1.3 77.3 - - - +
15B ASP* 1.3 64.6 + - - +
16B ARG 3.1 1.0 + - - -
17B CYS* 3.5 23.9 + - - +
428B GLY 5.5 1.3 - - - +
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Residues in contact with ASP 15 (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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11B ALA* 2.8 30.4 + - - +
12B ASN* 3.8 9.2 - - - +
13B ILE 3.2 0.6 - - - -
14B ALA* 1.3 77.5 - - - +
16B ARG* 1.3 58.5 + - + +
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Residues in contact with ARG 16 (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 ASN* 3.5 18.2 - - - +
13B ILE* 3.8 9.0 - - + +
14B ALA 3.1 0.2 - - - -
15B ASP* 1.3 78.5 - - + +
17B CYS* 1.3 70.9 + - - +
18B LEU* 4.5 1.0 - - - +
294B ASP* 4.3 7.0 - - - +
296B HIS* 2.8 70.0 + - + +
299B ASP* 4.6 1.4 + - - -
381B ARG* 2.8 40.7 - - - +
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Residues in contact with CYS 17 (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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13B ILE* 2.8 14.5 + - + +
14B ALA* 3.5 19.9 - - - +
16B ARG* 1.3 83.1 - - - +
18B LEU* 1.3 60.7 + - - +
19B ILE 3.6 14.8 - - - +
20B ASN* 4.0 10.5 - - - -
294B ASP* 3.3 18.4 - - - +
428B GLY* 3.5 39.3 - - - +
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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