Contacts of the strand formed by residues 55 - 60 (chain B) in PDB entry 1PR1
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 ARG 55 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ALA* 4.9 0.2 - - - +
14B ASP* 2.3 35.8 + - - -
15B VAL* 3.3 21.1 - - - +
51B THR* 2.9 3.8 - - - -
52B TYR 2.6 39.9 + - - +
53B LYS 3.0 2.5 + - - +
54B GLY* 1.3 77.4 - - - +
56B LYS* 1.3 81.7 + - - +
57B ILE* 3.4 20.8 + - + +
232B VAL* 4.2 5.1 - - - +
233B LEU* 3.7 19.5 - - + -
236B ASP* 2.5 54.3 + - - -
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Residues in contact with LYS 56 (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 GLY* 2.9 29.8 + - - -
12B PHE 3.4 16.3 + - - -
13B ALA* 3.2 19.9 - - + +
49B THR* 3.8 22.7 - - + -
50B GLY 3.3 11.9 - - - +
51B THR* 3.9 8.3 - - + +
54B GLY 3.9 2.4 + - - -
55B ARG* 1.3 92.7 + - - +
57B ILE* 1.3 63.2 + - - +
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Residues in contact with ILE 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ALA* 3.7 3.8 - - - -
15B VAL* 4.3 15.0 - - + +
17B LEU* 4.4 10.1 - - + -
33B LEU* 3.7 19.6 - - + +
49B THR* 3.4 1.2 - - - +
50B GLY 2.7 37.3 + - - +
52B TYR* 4.1 14.8 - - + -
55B ARG* 3.4 33.8 + - + +
56B LYS* 1.3 83.8 - - - +
58B SER* 1.3 77.0 + - - +
59B VAL* 4.5 2.2 - - + -
229B LEU* 4.1 21.3 - - + +
232B VAL* 3.8 20.6 - - + -
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Residues in contact with SER 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 3.4 18.5 - - - -
13B ALA* 2.8 31.2 + - - +
15B VAL 3.3 10.6 + - - -
16B VAL* 3.4 10.3 - - - -
17B LEU 2.9 22.3 + - - -
48B PHE 3.0 8.5 - - - -
49B THR* 2.8 18.9 + - - +
57B ILE* 1.3 76.7 - - - +
59B VAL* 1.3 69.5 + - - +
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Residues in contact with VAL 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 5.9 0.2 - - - -
17B LEU* 3.3 18.2 - - + +
19B PRO* 4.1 2.5 - - + -
25B ALA* 4.0 16.8 - - - +
28B ILE* 3.8 48.0 - - + -
29B ALA* 4.8 2.0 - - + +
33B LEU* 3.6 27.6 - - + -
47B GLY* 3.3 1.0 - - - -
48B PHE* 2.7 44.4 + - + +
57B ILE* 4.5 5.2 - - + -
58B SER* 1.3 81.0 - - - +
60B MET* 1.3 62.5 + - - +
229B LEU* 6.0 0.2 - - + -
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Residues in contact with MET 60 (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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5B ILE* 3.9 10.8 - - + -
12B PHE* 4.0 22.0 - - + -
16B VAL* 4.2 7.3 - - + +
17B LEU 3.1 7.3 + - - -
18B MET* 3.3 36.4 - - + +
19B PRO* 3.9 4.7 - - - -
25B ALA* 3.8 1.8 - - - -
40B ASN* 4.0 11.9 - - - +
45B MET* 3.9 14.1 - - + +
46B LEU 3.4 15.5 - - - +
47B GLY* 3.6 7.6 - - - -
59B VAL* 1.3 77.3 - - - +
61B GLY* 1.3 70.8 + - - +
72B TYR* 3.8 28.3 - - + -
76B LEU* 3.8 29.4 - - + -
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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