Contacts of the helix formed by residues 25 - 29 (chain B) in PDB entry 1PRX
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 PHE 25 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B ALA* 3.6 25.6 - - + -
12B PRO* 3.2 28.3 - - + +
13B ASN* 3.6 1.0 + - - -
14B PHE* 2.8 51.5 + + + +
23B ILE* 3.9 8.7 - - + +
24B ARG* 1.3 70.7 - - - +
26B HIS* 1.3 65.0 + + - +
28B PHE* 3.3 9.5 + + - +
29B LEU* 3.1 54.0 + - + +
34B GLY 6.3 0.2 - - - -
36B LEU* 4.7 9.6 - - + -
69B ILE* 4.4 22.0 - - + -
137B PHE* 3.7 26.9 - + - -
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Residues in contact with HIS 26 (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 VAL* 4.1 11.9 - - + -
11B ALA* 2.8 28.0 + - + -
12B PRO 4.3 2.9 - - - -
13B ASN* 3.0 46.6 + - + +
25B PHE* 1.3 83.8 - + - +
27B ASP* 1.3 60.0 + - - +
29B LEU* 3.4 0.6 + - - -
30B GLY* 2.9 26.0 + - - -
141B LYS* 3.5 47.0 - - + +
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Residues in contact with ASP 27 (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 ASN* 4.8 1.2 + - - +
24B ARG* 3.0 52.9 + - + +
26B HIS* 1.3 81.8 - - - +
28B PHE* 1.3 63.1 - - - +
30B GLY* 3.2 14.7 + - - -
67B LYS* 4.9 1.2 + - - -
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Residues in contact with PHE 28 (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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23B ILE* 4.5 22.0 - - + -
24B ARG 3.0 11.9 + - - +
25B PHE* 3.6 11.9 - + - +
27B ASP* 1.3 76.9 - - - +
29B LEU* 1.3 76.1 + - + +
67B LYS* 2.9 59.0 + - + +
68B LEU 3.5 21.8 - - - -
69B ILE* 3.9 33.0 - - + -
101B PRO* 4.0 22.9 - - + -
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Residues in contact with LEU 29 (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* 5.3 0.7 - - + -
25B PHE* 3.1 49.9 + - + +
26B HIS* 3.8 3.8 - - + +
28B PHE* 1.3 98.5 - - + +
30B GLY* 1.3 64.6 - - - +
31B ASP 3.1 0.3 + - - -
32B SER* 2.9 33.2 + - - +
33B TRP 4.4 2.7 - - - +
34B GLY* 3.7 29.8 - - - +
67B LYS* 3.6 4.0 + - + -
69B ILE* 5.8 0.9 - - + -
137B PHE* 4.5 17.0 - - + -
138B GLY 5.1 2.2 - - - +
141B LYS* 4.0 26.0 - - + -
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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