Contacts of the strand formed by residues 27 - 33 (chain B) in PDB entry 1E8O
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 TYR 27 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A VAL* 6.0 6.5 - - + -
29A LEU 3.1 6.3 - - - +
30A LYS* 2.9 62.7 + - + -
25B SER* 4.0 18.6 - - - -
26B VAL* 1.3 74.2 - - - +
28B ILE* 1.3 62.2 + - - +
29B THR* 4.3 7.6 - - + -
60B ALA* 2.9 27.3 - - - +
61B THR* 2.8 37.8 + - + +
62B ASP 4.8 8.3 - - - -
63B GLY* 4.8 5.2 - - - -
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Residues in contact with ILE 28 (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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27A VAL 3.8 1.0 - - - +
28A VAL* 3.3 1.7 - - - -
29A LEU* 2.8 49.9 + - + +
66A HIS* 4.6 5.5 + - - +
9B PHE* 5.7 0.9 - - + -
13B LEU* 4.3 9.0 - - + -
17B PHE* 3.8 21.5 - - + -
26B VAL* 3.9 10.1 - - + -
27B TYR* 1.3 81.0 - - - +
29B THR* 1.3 65.6 + - - +
58B LEU* 4.5 17.3 - - + -
59B ARG 3.2 9.4 - - - +
60B ALA* 4.0 9.0 - - + -
83B TYR* 3.7 19.3 - - + +
87B LEU* 3.6 30.7 - - + -
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Residues in contact with THR 29 (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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26A ARG* 5.4 11.2 + - - +
27A VAL 3.1 7.0 - - - -
28A VAL* 3.0 32.3 - - + -
27B TYR* 5.1 6.1 - - + -
28B ILE* 1.3 80.6 - - - +
30B LEU* 1.3 61.0 + - - +
31B LYS* 6.4 0.2 - - - -
57B LEU 3.9 0.5 - - - +
58B LEU* 3.5 7.5 - - - +
59B ARG* 2.6 64.1 + - - +
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Residues in contact with LEU 30 (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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26A ARG* 3.7 3.4 - - - -
27A VAL* 2.9 49.3 + - + +
66A HIS* 4.2 26.5 - - + +
69A LEU* 4.0 23.1 - - + -
70A MET* 4.2 10.5 - - + +
73A MET* 3.3 19.8 - - + +
29B THR* 1.3 74.4 - - - +
31B LYS* 1.3 62.5 + - - +
56B CYS* 3.2 35.0 - - - -
57B LEU 3.6 3.6 - - - +
58B LEU* 3.6 21.5 - - + -
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Residues in contact with LYS 31 (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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23A MET 3.6 16.6 - - - +
24A LYS* 3.4 25.5 + - - +
25A ALA 3.6 11.4 - - - +
26A ARG* 3.3 42.4 - - + +
45A ASP* 4.6 3.0 + - - -
73A MET* 3.3 11.0 - - - -
29B THR* 6.4 0.4 - - - -
30B LEU* 1.3 76.6 - - - +
32B LYS* 1.3 68.5 + - + +
56B CYS* 3.5 1.2 - - - -
57B LEU* 2.7 47.1 + - + +
59B ARG* 6.0 2.9 - - - +
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Residues in contact with LYS 32 (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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18A TYR* 3.7 18.3 + - + +
22A PRO* 3.5 30.0 + - - +
23A MET* 3.7 39.9 - - + +
25A ALA 5.0 0.8 + - - -
72A LEU 5.4 1.8 + - - -
73A MET* 3.2 41.4 + - + +
31B LYS* 1.3 82.7 - - + +
33B TYR* 1.3 66.4 + - - +
34B ASP* 3.8 2.7 + - - -
54B ASN* 3.5 22.7 + - - +
55B LYS 3.7 9.4 - - - +
56B CYS* 4.3 0.4 - - - +
57B LEU* 5.3 0.2 - - - -
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Residues in contact with TYR 33 (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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3B LEU* 4.1 14.0 - - + +
31B LYS 3.3 3.0 + - - -
32B LYS* 1.3 76.5 - - - +
34B ASP* 1.3 81.5 + - - +
54B ASN* 5.2 1.9 - - - +
55B LYS* 3.4 31.7 + - + +
56B CYS 4.0 9.4 - - - +
57B LEU* 3.8 43.5 - - + +
70B VAL* 4.1 31.2 - - + -
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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