Contacts of the strand formed by residues 49 - 54 (chain A) in PDB entry 3PE7
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 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A CYS 4.5 0.2 - - - -
43A PHE* 3.4 8.5 - - - -
44A THR* 3.1 46.5 + - + +
47A GLY 3.5 0.2 - - - -
48A SER* 1.3 101.7 + - - +
50A LEU* 1.3 62.2 - - - +
64A LEU* 4.0 29.2 - - + -
65A LEU 3.2 9.9 - - - +
66A ASP* 3.7 28.0 + - + -
67A LEU* 4.6 2.5 - - - +
393A ACT 5.9 1.8 - - - -
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Residues in contact with LEU 50 (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 LEU* 3.9 28.0 - - + -
42A CYS* 3.4 30.7 - - - +
43A PHE* 3.8 21.8 - - + -
49A LYS* 1.3 75.1 - - - +
51A LEU* 1.3 78.0 + - - +
52A PHE* 3.8 2.6 - - + -
63A TYR 3.8 0.3 - - - +
64A LEU* 3.5 4.4 - - - +
65A LEU* 2.7 48.8 + - + +
67A LEU* 4.4 10.8 - - + -
366A LEU* 3.7 25.4 - - + -
377A LEU* 4.0 12.1 - - + -
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Residues in contact with LEU 51 (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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35A ARG* 5.2 0.9 - - - -
36A ASN* 4.4 12.1 + - + +
41A LYS 4.3 5.8 - - - +
42A CYS* 2.8 28.4 + - - +
50A LEU* 1.3 84.4 - - - +
52A PHE* 1.3 64.3 + - - +
62A TYR* 3.6 28.5 - - + -
63A TYR 3.4 6.3 - - - +
64A LEU* 3.8 5.5 - - + +
75A LEU* 3.7 28.5 - - + -
86A GLY 4.0 20.6 - - - +
87A PHE* 4.2 7.6 - - - +
88A LEU* 4.3 15.9 - - + -
95A LEU* 3.7 26.0 - - + -
366A LEU* 5.6 0.2 - - - +
377A LEU* 5.2 0.5 - - - +
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Residues in contact with PHE 52 (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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9A LEU* 4.4 3.8 - - + -
27A THR* 4.0 12.1 - - + -
33A CYS* 4.0 19.5 - - - -
34A HIS 3.7 10.3 - - - +
35A ARG* 4.7 2.2 - - - +
36A ASN* 5.2 2.9 - - - +
50A LEU* 3.8 11.4 - - + -
51A LEU* 1.3 76.4 - - - +
53A GLY* 1.3 82.6 + - - +
54A GLY* 4.3 0.2 - - - -
56A PHE* 4.1 11.4 - + - -
62A TYR* 3.4 12.8 - - - -
63A TYR* 2.8 65.5 + + + -
65A LEU* 3.7 30.1 - - + -
72A ALA* 4.2 13.2 - - + -
83A THR 5.4 0.2 - - - -
377A LEU* 3.7 29.6 - - + -
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Residues in contact with GLY 53 (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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33A CYS* 3.1 3.3 - - - -
34A HIS* 2.8 57.4 + - - -
35A ARG 5.3 0.2 - - - -
52A PHE* 1.3 80.3 - - - +
54A GLY* 1.3 57.3 + - - -
60A TRP* 5.7 0.7 - - - -
61A ASN 3.2 9.0 - - - -
62A TYR* 4.6 0.2 - - - -
83A THR* 4.2 12.0 + - - -
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Residues in contact with GLY 54 (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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32A THR 3.5 8.5 - - - -
33A CYS* 3.9 11.4 - - - -
52A PHE* 4.3 1.8 - - - -
53A GLY* 1.3 73.9 - - - -
55A ALA* 1.3 61.2 + - - -
56A PHE* 3.5 4.5 - - - -
59A PRO 3.5 1.6 - - - +
60A TRP* 3.4 4.5 - - - +
61A ASN 2.9 30.8 + - - +
63A TYR* 3.4 21.2 + - - -
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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