Contacts of the strand formed by residues 45 - 51 (chain K) in PDB entry 6D6U
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 45 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37K VAL* 3.8 15.3 - - + -
38K LYS 3.8 2.0 - - - -
39K GLN* 3.7 36.8 - - + +
43K GLN 4.1 0.4 + - - -
44K GLY* 1.3 76.7 - - - +
46K GLU* 1.3 59.2 + - - +
95K TYR* 4.6 8.3 - - + -
108K TRP* 4.3 15.9 - - + -
36L TYR* 5.5 2.2 - - + -
38L GLN* 5.1 2.0 - - - +
44L PRO* 4.8 11.4 - - + -
87L HIS* 4.6 24.8 - - + +
96L THR* 5.6 0.3 + - - -
97L PHE* 3.5 59.5 + - + +
98L GLY 4.4 5.1 + - - +
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Residues in contact with GLU 46 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37K VAL* 3.4 5.6 - - - +
38K LYS* 3.1 47.6 + - + +
40K ARG* 4.4 19.6 + - - +
44K GLY 4.6 2.9 - - - +
45K LEU* 1.3 76.8 - - - +
47K TRP* 1.3 71.9 + - - +
61K ASP* 4.5 4.0 - - - +
63K LYS* 3.1 41.7 + - + +
64K PHE* 3.6 18.4 - - + -
96L THR* 6.1 0.7 - - - -
97L PHE* 5.0 2.5 - - - +
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Residues in contact with TRP 47 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K TYR* 3.3 18.5 - + - -
36K TRP 3.8 8.5 - - - -
37K VAL* 4.4 11.9 - - + -
46K GLU* 1.3 79.7 - - - +
48K ILE* 1.3 66.4 + - - +
49K GLY* 2.6 41.5 + - - -
50K ARG* 3.6 13.2 - - + -
59K LYS* 4.6 3.1 - - + -
60K TYR 4.3 8.3 - - - -
61K ASP* 3.1 54.1 + - + +
62K PRO* 5.6 1.8 - - + -
64K PHE* 4.1 2.1 - - - -
105K MET* 5.5 1.3 - - + -
94L TYR* 3.3 44.2 - + + -
95L PRO* 3.4 43.3 - - + +
96L THR* 5.1 5.3 + - - +
97L PHE* 5.1 5.4 - - + -
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Residues in contact with ILE 48 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36K TRP* 3.0 28.5 + - + +
37K VAL 4.1 1.6 - - - +
38K LYS* 3.8 20.9 - - + +
47K TRP* 1.3 76.7 - - - +
49K GLY* 1.3 62.8 + - - +
60K TYR* 3.6 5.6 - - + -
61K ASP* 2.9 27.9 + - - +
64K PHE* 3.6 31.9 - - + +
68K ALA* 4.4 21.5 - - + -
70K ILE* 5.0 5.4 - - + -
81K LEU* 4.8 8.7 - - + -
83K LEU* 6.5 0.4 - - + -
94K TYR* 3.6 37.7 - - + -
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Residues in contact with GLY 49 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K TYR* 3.7 5.0 - - - -
36K TRP* 3.7 11.5 + - - +
47K TRP* 2.6 31.2 + - - +
48K ILE* 1.3 83.4 - - - +
50K ARG* 1.3 61.0 + - - +
59K LYS 3.4 13.0 - - - -
60K TYR* 4.3 1.8 - - - -
70K ILE* 3.8 17.4 - - - +
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Residues in contact with ARG 50 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D ARG* 6.3 0.2 - - - +
174D GLU* 3.7 28.9 + - - -
177D ARG* 4.6 3.8 - - - +
33K TYR* 3.7 34.1 + - + -
34K MET 3.6 8.5 - - - +
35K TYR* 3.6 28.5 - - + +
47K TRP* 3.6 14.8 - - + -
49K GLY* 1.3 76.3 - - - +
51K ILE* 1.3 66.5 + - - +
52K ASP* 4.4 15.8 + - - +
57K ASP* 3.9 21.4 + - - +
58K THR* 3.3 6.2 - - - -
59K LYS* 3.1 62.8 + - + +
70K ILE* 4.0 6.2 - - - +
94L TYR* 4.3 4.4 - - - -
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Residues in contact with ILE 51 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33K TYR* 3.7 7.6 - - - +
34K MET* 3.1 49.5 + - + +
36K TRP* 5.1 1.8 - - + +
50K ARG* 1.3 78.2 - - - +
52K ASP* 1.3 70.2 + - - +
53K PRO* 3.8 3.6 - - + +
56K GLY* 4.8 5.2 - - - +
57K ASP 3.5 3.6 - - - +
58K THR* 3.7 13.9 - - + -
70K ILE* 3.5 46.2 - - + +
71K THR* 4.0 0.2 - - - -
72K THR* 3.8 35.7 - - + +
79K ALA* 5.1 5.8 - - + -
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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