Contacts of the helix formed by residues 76 - 82 (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 ASN 76 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B ASP 4.9 0.2 + - - -
49B ILE* 4.2 8.3 - - + +
75B LEU* 1.3 80.5 - - - +
77B LEU* 1.3 63.3 + - - +
78B ALA* 2.9 22.6 - - - +
79B ALA* 2.9 40.2 + - + +
80B ASN* 3.2 27.2 + - - +
153B ALA 4.0 3.7 - - - +
154B ARG* 3.1 24.6 - - - +
250B PRO* 3.9 17.0 - - + +
251B GLU 3.0 23.3 - - - +
253B MET* 4.2 5.7 - - - +
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Residues in contact with LEU 77 (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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76B ASN* 1.3 70.4 - - - +
78B ALA* 1.3 67.5 + - - +
80B ASN* 3.3 1.9 + - - +
81B CYS* 3.0 25.9 + - - -
150B LEU* 4.0 7.6 - - + -
153B ALA* 3.9 22.3 + - + +
253B MET* 5.6 0.8 - - - +
259B LEU* 3.3 39.7 - - + -
278B THR* 4.5 12.5 - - + +
281B TYR* 4.7 0.4 - - + -
282B LEU* 3.5 43.3 - - + +
318B TYR* 3.6 37.9 - - + -
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Residues in contact with ALA 78 (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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76B ASN* 2.9 12.7 - - - +
77B LEU* 1.3 84.0 - - - +
79B ALA* 1.3 54.5 + - - +
81B CYS* 4.6 2.0 - - - -
82B LEU* 2.7 50.2 + - + +
83B ASP* 3.9 1.6 - - - -
150B LEU* 3.7 13.7 - - - +
153B ALA* 4.9 1.6 - - - +
154B ARG* 3.5 37.7 - - + +
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Residues in contact with ALA 79 (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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47B ASP* 6.2 2.5 - - + -
49B ILE* 6.2 1.1 - - + -
76B ASN* 2.9 28.9 - - + +
77B LEU 3.2 0.2 - - - -
78B ALA* 1.3 77.8 - - - +
80B ASN* 1.3 61.2 + - - +
83B ASP* 3.3 23.5 + - + +
84B ARG* 3.0 31.2 + - + +
154B ARG* 4.4 0.2 - - - +
250B PRO* 4.3 12.1 - - + -
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Residues in contact with ASN 80 (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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46B LEU* 3.2 17.7 - - + -
47B ASP* 2.7 51.5 + - - +
75B LEU* 4.1 11.3 - - - +
76B ASN 3.2 23.8 + - - +
77B LEU 3.7 7.6 - - - +
78B ALA 3.2 0.2 - - - -
79B ALA* 1.3 80.7 - - - +
81B CYS* 1.3 57.2 + - - +
82B LEU 3.5 0.2 - - - -
84B ARG* 3.0 33.1 + - - +
85B HIS* 3.1 13.7 + - - -
282B LEU* 4.0 13.9 - - + +
322B ALA* 3.5 6.8 - - + -
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Residues in contact with CYS 81 (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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77B LEU* 3.0 35.6 + - - +
78B ALA 4.0 1.3 - - - +
80B ASN* 1.3 78.2 - - - +
82B LEU* 1.3 65.7 + - + +
85B HIS* 3.5 3.5 - - - -
110B TYR* 3.2 24.1 - - - -
150B LEU* 4.0 15.9 - - + -
282B LEU* 4.6 2.2 - - - -
318B TYR* 3.6 32.8 - - - -
321B LEU* 3.6 21.1 - - + +
322B ALA* 3.7 11.7 - - - -
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Residues in contact with LEU 82 (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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78B ALA* 2.7 20.6 + - + +
80B ASN 3.5 1.4 - - - -
81B CYS* 1.3 93.7 - - + +
83B ASP* 1.3 70.0 + - - +
84B ARG 3.4 1.8 - - - -
85B HIS* 3.0 19.9 + - - +
86B LEU* 3.6 9.1 + - - +
110B TYR* 4.4 11.1 - - + +
113B LEU* 3.6 38.6 - - + -
114B HIS* 4.1 19.3 - - + +
117B VAL* 3.6 42.0 - - + -
150B LEU* 4.1 13.2 - - + -
154B ARG* 4.7 3.1 - - - +
321B LEU* 5.1 0.7 - - + -
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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