Contacts of the strand formed by residues 41 - 46 (chain L) in PDB entry 1DH6
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 LEU 41 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4L MET* 3.7 30.1 - - + -
23L CYS* 4.3 3.4 - - - -
25L SER* 5.5 0.2 - - - -
31L VAL* 4.3 4.0 - - + +
39L ASN 3.4 0.2 + - - -
40L TYR* 1.4 74.3 - - - +
42L ALA* 1.4 63.2 + - - +
43L TRP* 3.4 38.8 - - + +
57L TYR* 3.7 0.5 - - - -
58L TRP 3.0 42.8 + - - +
67L ALA* 4.9 3.8 - - - -
89L PHE* 3.8 47.6 - - + -
106L CYS* 4.6 3.1 - - + -
107L GLN 3.7 11.7 - - - +
108L GLN* 4.6 3.6 - - + +
109L HIS* 3.1 11.5 + - - -
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Residues in contact with ALA 42 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41L LEU* 1.4 77.3 - - - +
43L TRP* 1.4 60.5 + - - +
44L TYR* 3.9 26.8 - - + +
54L LEU* 5.0 6.3 - - + -
56L ILE 3.6 9.4 - - - +
57L TYR* 4.7 7.0 - - + -
105L TYR 4.3 0.2 - - - +
106L CYS* 3.7 1.4 - - - -
107L GLN* 2.8 45.1 + - + +
109L HIS* 3.5 15.4 + - + +
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Residues in contact with TRP 43 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L GLN* 4.3 5.4 - - - -
21L ILE* 3.9 28.7 - - + -
22L ASN 4.3 0.2 - - - -
23L CYS* 3.5 30.1 - - + -
41L LEU* 3.4 24.2 - - + +
42L ALA* 1.4 70.7 - - - +
44L TYR* 1.4 61.2 + - - +
54L LEU* 3.7 4.7 - - - +
55L LEU* 2.9 30.9 + - + -
56L ILE* 2.8 38.8 + - + +
67L ALA 4.5 9.0 + - - -
80L GLY* 5.3 0.2 - - - -
89L PHE* 4.4 2.3 - - + +
90L THR* 3.4 36.2 + - - -
91L LEU* 3.6 28.7 - - + -
104L TYR* 5.0 8.3 - - + -
105L TYR 3.6 20.4 - - - -
106L CYS* 3.7 17.9 - - + -
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Residues in contact with TYR 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42L ALA* 3.9 20.1 - - + +
43L TRP* 1.4 73.5 - - - +
45L GLN* 1.4 58.3 + - - +
46L GLN 4.2 0.2 - - - -
52L PRO* 4.1 29.8 - - + -
53L LYS 3.4 10.5 - - - +
54L LEU* 3.9 30.3 - - + +
55L LEU* 4.2 6.7 - - - +
104L TYR* 3.5 8.5 - - - +
105L TYR* 2.8 46.9 + - + +
107L GLN* 2.8 43.1 + - + -
109L HIS* 6.0 0.2 - - - -
139L PHE* 4.1 16.6 - + - -
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Residues in contact with GLN 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44L TYR* 1.4 72.1 - - - +
46L GLN* 1.4 56.9 + - - +
47L LYS* 2.5 42.7 + - + +
51L PRO 3.8 1.4 - - - +
52L PRO* 4.2 1.1 - - - -
53L LYS* 2.8 58.5 + - + +
55L LEU* 3.7 24.7 - - + +
78L PHE* 4.4 9.0 - - - -
100L ASP* 4.2 1.6 - - - -
102L ALA* 3.9 10.6 - - + +
104L TYR* 3.3 40.4 + - + -
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Residues in contact with GLN 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44L TYR 4.2 0.8 - - - -
45L GLN* 1.4 70.6 - - - +
47L LYS* 1.4 64.0 + - - +
48L PRO* 4.0 0.3 - - - +
49L GLY 5.7 1.2 - - - +
50L GLN 3.0 28.2 + - - +
51L PRO* 4.2 1.3 - - - +
52L PRO* 4.1 23.9 - - + +
102L ALA* 4.0 2.2 - - - -
103L VAL* 2.8 50.8 + - + +
105L TYR* 2.8 41.3 + - + -
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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