Contacts of the helix formed by residues 56 - 62 (chain A) in PDB entry 1PBH
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 ALA 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ARG* 4.4 6.0 - - - +
31A ALA* 4.2 3.9 - - - +
32A PHE* 3.3 42.0 - - + -
35A VAL* 3.7 26.0 - - + -
54A VAL 3.3 5.1 + - - -
55A SER* 1.3 72.3 - - - +
57A GLU* 1.3 56.9 + - - +
59A LEU* 4.2 0.9 - - - +
60A LEU* 2.9 32.4 + - - +
91A GLY 4.1 3.6 + - - -
103A TYR* 4.5 6.8 - - + +
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Residues in contact with GLU 57 (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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55A SER* 2.9 9.4 - - - +
56A ALA* 1.3 78.2 - - - +
58A ASP* 1.3 65.6 + - - +
60A LEU* 4.2 4.3 - - - -
61A THR* 2.9 36.7 + - - +
101A ARG* 3.5 38.3 + - + +
102A PRO 4.3 2.5 - - - +
103A TYR* 3.2 22.2 - - - +
104A SER* 2.8 46.2 + - - -
105A ILE 4.4 0.7 + - - -
126A PRO* 3.5 19.3 - - - +
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Residues in contact with ASP 58 (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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55A SER* 2.7 30.3 + - - +
57A GLU* 1.3 74.1 - - - +
59A LEU* 1.3 56.9 + - - +
62A CYS* 3.0 35.6 + - - +
82A PHE* 4.1 2.9 - - - -
87A GLY 4.1 5.2 - - - +
88A LEU* 3.7 11.7 - - + +
89A VAL* 3.3 28.0 + - + +
101A ARG* 3.0 20.4 + - - +
140A TYR* 2.9 39.5 + - - -
144A LYS* 4.1 2.6 - - - -
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Residues in contact with LEU 59 (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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30A TRP* 4.0 3.3 - - + -
31A ALA* 3.7 20.0 - - + +
34A ALA* 4.1 1.8 - - + -
35A VAL* 3.6 23.3 - - + -
55A SER 3.5 8.7 + - - +
56A ALA 4.2 2.0 - - - +
57A GLU 3.2 0.2 - - - -
58A ASP* 1.3 78.2 - - - +
60A LEU* 1.3 69.2 + - - +
63A CYS* 3.2 26.7 + - - +
67A CYS* 4.0 9.4 - - - -
79A ALA* 3.5 41.7 - - + +
82A PHE* 3.2 29.4 - - + -
88A LEU* 3.7 20.6 - - + +
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Residues in contact with LEU 60 (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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26A CYS* 3.5 22.0 - - - -
28A SER* 3.5 20.9 - - - -
30A TRP* 4.3 15.8 - - + -
31A ALA* 4.4 4.0 - - + -
56A ALA 2.9 18.5 + - - +
57A GLU* 3.6 4.3 - - - +
59A LEU* 1.3 80.0 - - - +
61A THR* 1.3 68.6 + - + +
63A CYS* 4.4 2.8 + - - +
64A GLY 5.2 2.1 + - - -
70A GLY* 3.5 42.3 - - - +
71A CYS* 3.8 4.0 - - - +
103A TYR* 3.5 22.2 - - + -
105A ILE* 4.1 8.5 - - + -
125A THR* 4.1 10.3 - - + +
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Residues in contact with THR 61 (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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57A GLU* 2.9 28.3 + - - +
60A LEU* 1.3 89.0 - - + +
62A CYS* 1.3 60.1 + - - -
63A CYS 3.6 0.6 + - - -
64A GLY 5.3 0.9 + - - -
101A ARG* 2.8 28.4 + - - +
125A THR* 4.3 4.3 - - - +
126A PRO* 3.1 48.1 - - + +
128A CYS* 3.1 20.8 + - - +
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Residues in contact with CYS 62 (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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58A ASP* 3.0 16.6 + - - +
61A THR* 1.3 77.2 + - - +
63A CYS* 1.3 67.7 + - - +
82A PHE* 3.7 17.4 - - + -
101A ARG* 3.0 33.0 - - - -
128A CYS* 2.0 47.0 - - - -
130A LYS* 4.5 4.7 - - + -
140A TYR* 4.1 14.4 - - - +
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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