Contacts of the strand formed by residues 42 - 46 (chain T) in PDB entry 2BWE
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 GLN 42 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28T LYS* 3.1 75.4 + - + +
31T ILE* 3.4 22.0 - - - +
32T ASN* 3.5 14.6 - - - +
37T ILE* 3.2 25.0 + - + +
38T PRO 3.8 8.1 - - - +
39T VAL* 3.0 12.7 + - - +
41T ASN* 1.3 74.8 - - - +
43T ARG* 1.3 61.4 + - - +
44T LEU* 4.0 2.6 - - + +
70T LEU* 3.5 25.6 - - + -
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Residues in contact with ARG 43 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362D GLN 5.3 1.8 + - - -
365D LEU* 5.2 2.5 - - - +
366D ASP* 3.3 41.4 + - - +
369D LEU* 4.8 7.1 - - - +
345E PHE* 4.6 12.3 - - - -
28T LYS* 5.0 1.3 - - - +
41T ASN 3.4 1.4 + - - -
42T GLN* 1.3 71.7 - - - +
44T LEU* 1.3 60.0 + - - +
45T ILE* 3.9 11.6 + - + +
50T ILE* 3.4 34.2 - - + +
69T HIS 3.8 0.3 - - - +
70T LEU* 3.8 0.7 - - - +
71T VAL* 2.9 62.5 + - + +
73T SER* 3.5 26.6 + - - +
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Residues in contact with LEU 44 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7T ILE* 5.4 0.7 - - + -
24T VAL* 4.8 2.9 - - + -
27T PHE* 3.7 36.1 - - + -
28T LYS* 4.0 31.1 - - + +
31T ILE* 3.8 26.7 - - + -
42T GLN* 3.8 5.3 + - + +
43T ARG* 1.3 71.1 - - - +
45T ILE* 1.3 62.3 + - - +
50T ILE* 3.5 6.2 - - - +
51T LEU* 2.7 46.1 + - + +
68T VAL* 4.1 10.1 - - + -
69T HIS 3.3 11.2 - - - +
70T LEU* 3.9 25.4 - - + -
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Residues in contact with ILE 45 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342D MET* 3.7 45.6 - - + +
344D PHE* 4.1 9.6 - - + -
365D LEU* 3.1 44.2 - - + -
369D LEU* 4.1 11.4 - - + -
43T ARG* 4.7 7.2 - - + +
44T LEU* 1.3 79.4 - - - +
46T TYR* 1.3 61.6 + - - +
49T LYS 3.2 14.8 - - - +
50T ILE* 4.4 10.8 - - + -
67T SER 5.1 0.2 - - - +
68T VAL* 3.9 2.4 - - - -
69T HIS* 2.8 41.1 + - - +
71T VAL* 4.2 6.1 - - + -
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Residues in contact with TYR 46 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342D MET* 4.3 1.1 - - - +
349K ARG* 5.6 2.7 + - - -
371K GLY* 5.2 2.2 - - - -
44T LEU 4.1 1.4 + - - -
45T ILE* 1.3 72.8 - - - +
47T SER* 1.3 91.0 + - - +
48T GLY 3.3 2.0 - - - -
49T LYS* 3.0 22.1 + - + +
51T LEU* 4.0 18.2 - - + +
60T TYR* 3.6 26.2 - + + -
61T HIS 4.1 3.1 + - - -
62T ILE* 3.6 35.8 - - + -
63T GLN* 3.9 0.7 + - - +
66T HIS* 2.5 46.0 + - + -
67T SER 3.4 26.0 - - - -
68T VAL* 3.9 11.9 - - + -
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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
------------------------------------------------------------
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