Contacts of the strand formed by residues 22 - 27 (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 THR 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B ASN 4.4 5.8 - - - +
21B THR* 1.3 82.4 - - - +
23B VAL* 1.3 63.8 + - - +
24B PHE* 4.4 2.2 - - - -
122B ARG* 3.1 36.3 + - - +
123B LYS 4.2 3.1 + - - -
124B VAL* 3.4 12.3 - - - +
125B LEU* 2.9 27.0 + - - +
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Residues in contact with VAL 23 (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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21B THR 5.5 0.4 - - - +
22B THR* 1.3 77.0 - - - +
24B PHE* 1.3 73.3 + - - +
25B GLN* 4.2 22.6 + - + +
125B LEU* 3.5 17.7 - - + +
127B GLU* 3.5 41.5 - - + +
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Residues in contact with PHE 24 (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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201A NAG 5.3 17.0 - - - -
22B THR* 4.4 3.8 - - - -
23B VAL* 1.3 81.7 - - - +
25B GLN* 1.3 63.0 - - - +
26B GLY 4.0 0.3 + - - -
32B LEU* 3.8 23.2 - - + +
33B GLN 3.7 20.2 - - - -
34B VAL* 3.4 31.2 - - + -
35B SER 4.5 2.0 - - - -
122B ARG* 3.8 23.1 - - - -
124B VAL* 3.6 34.5 - - + -
125B LEU 2.9 11.6 + - - +
126B VAL* 3.3 7.1 - - + +
127B GLU 2.9 24.8 + - - +
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Residues in contact with GLN 25 (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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23B VAL* 4.2 22.8 - - + +
24B PHE* 1.3 77.2 - - - +
26B GLY* 1.3 59.5 + - - +
32B LEU* 4.0 13.2 - - - +
127B GLU* 3.6 31.5 + - + +
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Residues in contact with GLY 26 (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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24B PHE 4.0 0.2 + - - -
25B GLN* 1.3 75.4 - - - +
27B VAL* 1.3 64.4 + - - -
30B GLN 5.9 0.2 - - - -
32B LEU* 4.5 8.0 - - - +
100B LEU* 3.6 18.8 - - - +
127B GLU 2.9 9.9 + - - -
128B VAL* 2.9 29.1 - - - +
129B LEU* 2.9 4.5 + - - -
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Residues in contact with VAL 27 (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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26B GLY* 1.3 73.5 - - - -
28B ALA* 1.3 78.4 + - - +
30B GLN* 3.3 46.7 + - + +
100B LEU* 3.9 1.8 - - - +
128B VAL* 4.4 0.2 - - - -
129B LEU* 3.3 23.8 - - + +
130B ALA 4.4 1.8 - - - +
131B ASP* 4.3 17.3 - - - +
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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