Contacts of the strand formed by residues 47 - 55 (chain A) in PDB entry 1D5C
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 ASP 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A ILE* 1.3 80.3 - - - +
48A PHE* 1.3 103.6 + - - +
49A LEU* 3.8 23.6 - - + +
64A LEU 3.8 0.6 - - - +
66A ASP* 3.0 45.8 + - + +
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Residues in contact with PHE 48 (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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46A ILE* 4.2 27.8 - - + -
47A ASP* 1.3 104.9 + - - +
49A LEU* 1.3 76.6 + - - +
63A GLN* 5.7 7.0 - - + +
64A LEU 3.5 3.1 - - - +
65A TRP* 3.5 57.0 - + + -
66A ASP 5.1 2.2 - - - -
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Residues in contact with LEU 49 (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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28A ILE* 4.2 20.6 - - + -
29A THR* 6.0 2.2 - - - +
32A MSE 3.7 24.2 - - + -
33A TYR* 3.9 27.1 - - + +
47A ASP* 3.8 22.7 - - + +
48A PHE* 1.3 84.5 - - - +
50A SER* 1.3 56.1 + - - +
63A GLN* 4.7 2.2 - - - +
64A LEU* 2.6 50.0 + - + +
66A ASP* 6.5 0.4 - - + -
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Residues in contact with SER 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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32A MSE 3.7 12.4 - - - +
49A LEU* 1.3 75.8 - - - +
51A LYS* 1.3 61.2 + - - +
61A ARG* 3.3 33.5 + - - -
62A LEU 2.9 15.9 - - - -
63A GLN* 4.0 14.1 - - - -
64A LEU* 5.0 0.2 - - - -
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Residues in contact with LYS 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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31A PHE* 3.0 59.0 + - + +
32A MSE 3.8 32.5 + - + +
50A SER* 1.3 77.2 - - - +
52A THR* 1.3 71.1 + - - +
53A LEU* 3.9 10.0 + - - +
60A VAL 3.8 0.7 - - - +
61A ARG* 3.6 8.2 - - - +
62A LEU* 2.8 36.0 + - + +
64A LEU* 5.4 1.0 - - + +
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Residues in contact with THR 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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51A LYS* 1.3 84.5 - - - +
53A LEU* 1.3 65.6 + - - +
54A TYR* 3.6 44.2 - - + +
59A PRO* 4.0 16.8 - - + -
60A VAL 3.5 10.3 - - - +
61A ARG* 2.9 37.3 + - + +
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Residues in contact with LEU 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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31A PHE* 3.7 33.2 - - + -
51A LYS* 3.9 10.5 + - - +
52A THR* 1.3 79.1 - - - +
54A TYR* 1.3 63.2 + - - +
55A LEU* 3.7 12.5 + - + -
59A PRO* 3.4 1.4 - - - +
60A VAL* 2.7 43.4 + - + +
62A LEU* 3.7 25.4 - - + -
165A PHE 3.9 22.4 - - - +
166A LYS* 4.5 5.8 - - + +
169A ALA* 4.0 9.6 - - + -
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Residues in contact with TYR 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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52A THR* 3.6 37.4 - - + +
53A LEU* 1.3 75.2 - - - +
55A LEU* 1.3 64.7 + - - +
56A ASP 4.3 0.2 + - - -
58A GLY 5.5 0.2 - - - -
59A PRO* 3.9 23.8 - - + -
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Residues in contact with LEU 55 (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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53A LEU* 3.7 10.5 + - + +
54A TYR* 1.3 81.2 - - - +
56A ASP* 1.3 54.0 + - - +
57A GLU* 2.4 26.6 + - + +
58A GLY* 2.7 28.2 + - - +
60A VAL* 3.7 16.2 - - + -
166A LYS* 4.2 30.3 - - + +
169A ALA* 3.3 36.3 - - + +
170A SER* 3.5 20.0 - - - +
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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