Contacts of the strand formed by residues 47 - 50 (chain B) in PDB entry 2P1Q
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 LYS 47 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B GLN* 2.8 39.9 + - - +
23B LEU* 4.7 1.2 - - - +
24B ASP* 3.3 31.6 + - - +
45B ARG* 3.4 22.1 + - - +
46B ARG* 1.3 82.4 - - + +
48B VAL* 1.3 67.8 + - - +
49B PHE* 5.2 4.7 - - + -
68B VAL* 4.6 0.4 - - - -
70B SER* 3.2 26.5 - - - +
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Residues in contact with VAL 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A PHE* 4.4 4.7 - - + -
24B ASP* 5.1 0.9 - - - -
45B ARG* 4.0 9.2 - - - +
47B LYS* 1.3 82.8 - - - +
49B PHE* 1.3 61.1 - - - +
50B ILE* 4.1 14.1 - - + -
61B VAL* 4.2 16.4 - - + -
65B PHE* 3.6 33.7 - - + -
68B VAL* 3.9 16.2 - - + -
70B SER 3.0 3.7 + - - +
71B VAL* 3.7 32.0 - - + -
72B GLU* 3.1 26.0 + - - +
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Residues in contact with PHE 49 (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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158A ALA 3.4 6.4 - - - +
159A PHE* 3.5 13.9 + - - +
160A GLU* 3.7 33.5 + - - -
24B ASP* 3.3 26.3 + - - +
47B LYS* 5.2 5.4 - - + -
48B VAL* 1.3 75.2 - - - +
50B ILE* 1.3 66.1 + - - +
51B GLY* 3.9 20.7 + - - -
72B GLU* 3.7 42.4 - - + +
74B LYS* 4.0 12.3 - - + -
484B ARG* 6.0 0.4 - - - -
509B ARG* 4.2 5.6 - - - -
801B IHP 3.6 28.9 - - - -
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Residues in contact with ILE 50 (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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158A ALA* 3.0 28.0 - - - +
159A PHE* 3.2 31.6 - - + -
48B VAL* 4.2 16.4 - - + -
49B PHE* 1.3 79.3 - - - +
51B GLY* 1.3 59.3 + - - +
52B ASN 3.3 23.4 + - - +
53B CYS* 4.1 1.8 - - - -
55B ALA* 5.5 0.2 - - + -
56B VAL* 3.8 18.6 - - + -
61B VAL* 4.6 3.6 - - + -
71B VAL* 5.3 1.1 - - + -
72B GLU 2.9 16.2 + - - +
73B LEU* 3.3 26.8 - - + -
74B LYS* 3.1 24.4 + - - +
96B TRP* 4.4 9.0 - - + -
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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