Contacts of the strand formed by residues 47 - 53 (chain B) in PDB entry 5ELI
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 47 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B GLY 3.9 2.1 + - - +
46B ARG* 1.3 75.7 - - - +
48B LYS* 1.3 61.9 + - - +
62B ARG* 4.6 3.0 - - - +
65B SER* 2.7 37.2 + - - -
66B THR* 3.5 12.0 + - - +
67B HIS 3.4 15.4 + - - +
68B ASN* 3.3 48.3 + - - +
70B TRP* 4.3 19.1 - - + -
73B SER* 6.0 0.4 - - - -
86B ASP* 5.3 0.4 - - - -
112B SER* 3.5 4.3 - - - -
113B LEU* 2.9 47.3 + - + +
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Residues in contact with LYS 48 (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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38B TYR* 3.3 44.6 + - - -
43B HIS* 4.1 13.9 + - - -
46B ARG 2.7 23.8 + - - -
47B ARG* 1.3 78.3 - - - +
49B ALA* 1.3 61.3 + - - +
65B SER* 3.3 6.6 - - - -
66B THR* 2.9 32.6 + - - +
70B TRP* 4.4 3.6 - - - +
84B ILE* 4.4 1.3 - - - -
86B ASP* 3.2 29.4 + - - +
88B THR* 4.7 0.4 - - - +
93B LEU* 3.6 25.8 - - + -
111B GLN 3.0 8.1 - - - +
112B SER* 4.1 3.8 - - - -
113B LEU* 4.2 2.9 - - - +
121B LEU* 3.8 22.0 - - + -
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Residues in contact with ALA 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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48B LYS* 1.3 77.4 - - - +
50B TRP* 1.3 61.8 + - - +
51B CYS 4.2 0.4 - - - -
62B ARG* 3.5 40.6 - - - +
64B VAL 3.4 6.1 - - - +
65B SER* 4.0 0.4 - - - +
84B ILE* 4.4 5.6 - - - -
93B LEU* 4.6 1.7 - - - +
109B GLN 3.8 0.7 - - - +
110B CYS* 3.5 5.0 - - - +
111B GLN* 2.9 35.4 + - + +
113B LEU* 3.7 15.5 - - + -
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Residues in contact with TRP 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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34B VAL* 3.8 24.5 - - + -
49B ALA* 1.3 72.8 - - - +
51B CYS* 1.3 59.6 + - - +
62B ARG* 4.2 0.7 - - - -
63B VAL* 2.9 48.2 + - + +
64B VAL* 2.8 19.5 + - + +
82B THR* 4.1 10.0 - - + +
84B ILE* 4.4 0.9 - - + +
95B ILE* 3.4 49.1 - - + +
97B LEU* 4.5 17.2 - - + +
108B TYR* 3.3 53.9 - + + -
109B GLN 3.6 10.8 - - - -
110B CYS* 3.9 19.7 - - - -
124B VAL* 3.7 24.2 - - + -
126B VAL* 5.1 1.1 - - + -
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Residues in contact with CYS 51 (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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50B TRP* 1.3 75.1 - - - +
52B ARG* 1.3 59.9 + - - +
60B CYS* 2.1 44.6 - - - +
61B GLN 3.2 23.3 - - - +
62B ARG* 3.7 8.1 - - - +
63B VAL* 3.8 3.4 - - - +
108B TYR* 3.2 10.2 - - - +
109B GLN* 2.9 35.7 + - - -
111B GLN* 3.3 32.8 - - - +
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Residues in contact with ARG 52 (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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51B CYS* 1.3 75.6 - - - +
53B GLN* 1.3 63.1 + - - +
54B LEU* 3.4 28.5 - - + +
60B CYS* 3.2 4.8 - - - -
61B GLN* 2.9 31.4 + - + +
63B VAL* 4.1 6.2 - - + +
103B HIS* 3.4 19.2 + - - -
104B ASP* 4.3 5.5 + - - +
105B ALA 3.0 27.3 + - - -
106B GLY* 4.3 2.6 - - - -
107B LEU 3.4 13.7 - - - +
108B TYR* 3.1 43.9 + - + -
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Residues in contact with GLN 53 (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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51B CYS 4.2 0.2 + - - -
52B ARG* 1.3 73.8 - - - +
54B LEU* 1.3 69.9 + - - +
55B GLY 2.9 24.6 + - - +
56B GLU 2.9 17.2 + - - -
57B LYS 4.7 4.2 - - - -
58B GLY* 5.0 3.4 - - - -
59B PRO 3.7 10.8 - - - +
60B CYS* 4.0 10.0 - - + -
107B LEU* 2.9 49.2 + - + +
108B TYR* 5.2 0.4 - - - -
109B GLN* 3.0 27.3 + - + +
123B LYS* 3.4 28.3 + - - +
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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