Contacts of the strand formed by residues 46 - 56 (chain L) in PDB entry 6BCH
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 TRP 46 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36L VAL* 3.7 22.9 - - + -
37L SER 3.4 7.6 - - - -
38L LYS* 3.2 42.6 - - + -
39L ASP 3.7 0.8 + - - +
42L ARG* 3.2 17.6 - - - +
44L THR* 3.2 24.7 + - - -
45L GLY* 1.3 89.0 + - - +
47L SER* 1.3 60.5 + - - +
48L VAL* 4.2 2.0 + - - +
127L HIS* 5.6 1.6 - - - +
128L LEU* 6.0 1.4 - - - +
133L LEU* 4.0 19.5 - - + +
150L GLU 5.6 1.1 - - - -
151L LEU* 3.6 24.9 - - + -
154L ALA* 3.7 17.9 - - + +
155L PHE* 3.1 37.7 - + - -
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Residues in contact with SER 47 (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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35L THR* 3.4 2.0 - - - +
36L VAL* 3.2 5.5 - - - +
37L SER* 2.9 50.4 + - - -
39L ASP* 4.0 10.1 + - - +
42L ARG* 3.8 30.7 - - - +
46L TRP* 1.3 73.5 - - - +
48L VAL* 1.3 61.3 + - - +
49L ARG* 6.0 2.1 - - - -
5O T 5.9 4.7 - - - -
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Residues in contact with VAL 48 (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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34L LEU* 5.1 3.6 - - + -
35L THR 3.3 4.3 - - - +
36L VAL* 3.6 21.8 - - + -
46L TRP 4.2 2.6 + - - +
47L SER* 1.3 78.0 - - - +
49L ARG* 1.3 68.1 + - - +
50L PRO* 4.6 1.2 - - - +
122L ILE* 3.9 20.1 - - + +
127L HIS* 4.3 26.4 + - + +
133L LEU* 3.6 31.6 - - + -
136L ILE* 3.7 35.2 - - + -
4O A 5.4 1.2 + - - -
5O T 5.5 2.2 - - - +
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Residues in contact with ARG 49 (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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33L MET 4.1 0.2 - - - +
34L LEU* 3.5 7.6 - - - -
35L THR* 2.9 51.2 + - - +
47L SER* 5.9 2.0 - - - +
48L VAL* 1.3 77.7 - - - +
50L PRO* 1.3 72.2 + - + +
51L ARG* 3.7 27.1 - - - +
87L GLU* 3.1 33.7 + - - +
5O T 3.8 44.4 - - + +
6O G 2.7 40.6 + - - -
7O C 4.0 0.4 - - - +
21P G 3.6 11.0 + - - -
22P C 4.2 4.6 - - - +
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Residues in contact with PRO 50 (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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33L MET 3.5 5.8 - - - +
34L LEU* 3.8 11.0 - - + -
49L ARG* 1.3 92.8 + - + +
51L ARG* 1.3 65.6 + - - +
87L GLU* 3.9 14.3 - - - +
89L LEU* 5.0 4.7 - - + -
92L LEU* 3.5 24.3 - - + +
115L PHE* 3.4 23.6 - - + -
119L PHE* 4.5 14.4 - - + -
122L ILE* 3.7 28.5 - - + -
5O T 5.8 2.9 - - - +
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Residues in contact with ARG 51 (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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31L SER 4.0 0.4 - - - +
32L PHE* 3.6 0.9 - - - -
33L MET* 2.9 67.6 + - + +
35L THR* 2.9 28.5 + - - +
49L ARG* 3.7 27.0 - - + +
50L PRO* 1.3 81.4 - - + +
52L PHE* 1.3 61.1 + - - +
53L ARG* 4.6 6.7 - - + +
86L PHE 3.6 7.4 - - - +
87L GLU* 3.0 32.1 + - + +
92L LEU* 4.6 0.2 - - - -
115L PHE* 3.3 11.2 - - - -
7O C 3.2 6.5 - - - +
20P A 3.6 19.1 + - - +
21P G 2.8 45.0 + - - -
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Residues in contact with PHE 52 (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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26L ALA* 4.4 3.8 - - + -
30L SER* 3.6 32.1 - - - -
31L SER 3.5 7.2 - - - -
32L PHE* 3.3 45.8 - + + -
51L ARG* 1.3 74.7 - - - +
53L ARG* 1.3 71.1 + - - +
54L ILE* 4.9 7.0 - - + -
85L ARG* 3.6 1.2 - - - +
86L PHE* 2.9 63.5 + + + +
92L LEU* 3.8 18.8 - - + +
95L VAL* 3.8 18.8 - - + -
99L PHE* 3.7 20.0 - + - -
115L PHE* 4.7 0.2 - - + -
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Residues in contact with ARG 53 (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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30L SER* 3.4 4.1 - - - -
31L SER* 2.9 35.9 + - - -
33L MET* 3.6 30.8 - - + +
51L ARG* 4.6 7.5 - - + +
52L PHE* 1.3 80.8 - - - +
54L ILE* 1.3 67.9 + - - +
55L GLY* 4.2 1.1 - - - +
83L ARG* 3.0 39.3 - - + +
84L ILE 3.3 17.3 - - - +
85L ARG* 4.1 18.6 - - + +
87L GLU* 5.1 4.2 + - - -
8O T 4.9 2.6 + - - -
18P G 3.0 34.4 + - - -
19P G 3.1 29.9 + - - -
20P A 4.5 6.9 - - - +
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Residues in contact with ILE 54 (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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25L PHE* 3.3 50.7 - - + +
26L ALA* 4.1 13.7 - - + +
29L ASP* 4.4 4.7 - - + -
30L SER* 4.0 15.0 - - - +
52L PHE* 4.9 11.9 - - + -
53L ARG* 1.3 79.0 - - - +
55L GLY* 1.3 67.1 + - - +
56L LEU* 4.4 4.5 - - + -
64L LEU* 4.1 7.5 - - + +
67L ILE* 4.6 15.3 - - + -
83L ARG* 3.6 0.5 - - - -
84L ILE* 2.9 58.3 + - + +
86L PHE* 5.4 1.1 - - + -
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Residues in contact with GLY 55 (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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29L ASP* 4.1 4.6 + - - +
53L ARG* 4.2 2.0 - - - +
54L ILE* 1.3 73.7 - - - +
56L LEU* 1.3 77.3 + - - +
81L ASP* 5.5 1.8 - - - -
82L ALA 3.3 9.6 - - - -
83L ARG* 4.3 10.8 - - - -
16P T 2.5 32.5 - - - -
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Residues in contact with LEU 56 (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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25L PHE* 3.5 36.8 - - + -
29L ASP* 3.4 24.7 - - + +
54L ILE* 4.4 2.0 - - + -
55L GLY* 1.3 91.7 - - - +
57L HIS* 1.3 67.6 + - - +
60L ASP* 4.0 28.5 - - + +
63L ILE* 4.0 7.0 - - + -
64L LEU* 3.6 26.9 - - + -
81L ASP* 3.7 7.2 - - - +
82L ALA* 2.9 32.4 + - + +
16N T 4.0 4.9 - - - -
16P T 3.9 7.1 + - - +
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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