Contacts of the strand formed by residues 46 - 55 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A VAL* 3.6 23.1 - - + -
37A SER 3.4 7.6 - - - -
38A LYS* 3.2 42.4 - - + -
39A ASP* 3.7 1.3 + - - +
42A ARG* 3.2 17.3 - - - +
44A THR* 3.2 25.1 + - - -
45A GLY* 1.3 90.2 + - - +
47A SER* 1.3 60.5 + - - +
48A VAL* 4.2 1.8 + - - +
127A HIS* 5.6 1.4 - - - +
128A LEU* 6.0 1.6 - - - +
133A LEU* 3.9 19.2 - - + +
150A GLU 5.5 0.7 - - - -
151A LEU* 3.6 26.2 - - + -
154A ALA* 3.7 18.2 - - + -
155A PHE* 3.1 38.4 - + - -
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Residues in contact with SER 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A THR* 3.3 2.1 - - - +
36A VAL* 3.2 5.9 - - - +
37A SER* 2.8 50.4 + - - -
39A ASP* 4.0 9.5 + - - +
42A ARG* 3.8 31.0 - - - +
46A TRP* 1.3 74.6 - - - +
48A VAL* 1.3 61.2 + - - +
49A ARG* 6.0 2.0 - - - -
5C T 5.9 4.7 - - - -
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Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 5.1 3.1 - - + -
35A THR 3.2 4.0 - - - +
36A VAL* 3.6 20.6 - - + -
46A TRP 4.2 2.6 + - - +
47A SER* 1.3 78.5 - - - +
49A ARG* 1.3 67.7 + - - +
50A PRO* 4.6 1.2 - - - +
122A ILE* 3.8 20.0 - - + +
127A HIS* 4.3 25.7 + - + +
133A LEU* 3.5 31.6 - - + -
136A ILE* 3.7 35.7 - - + -
4C A 5.4 1.2 + - - -
5C T 5.5 2.9 - - - +
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Residues in contact with ARG 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 3.4 8.5 - - - -
35A THR* 2.9 51.2 + - - +
47A SER* 6.0 1.8 - - - -
48A VAL* 1.3 78.1 - - - +
50A PRO* 1.3 72.0 + - + +
51A ARG* 3.5 28.0 - - - +
87A GLU* 3.1 34.7 + - - +
5C T 4.1 40.4 - - + +
6C G 2.8 39.8 + - - -
7C C 3.6 0.8 - - - +
21X G 3.3 16.7 + - - -
22X C 4.1 5.1 - - - +
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Residues in contact with PRO 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A MET 3.5 5.6 - - - +
34A LEU* 3.8 11.4 - - + -
48A VAL 4.6 0.2 - - - +
49A ARG* 1.3 92.5 + - + +
51A ARG* 1.3 64.3 + - - +
87A GLU* 3.9 14.8 - - - +
89A LEU* 5.0 4.9 - - + -
92A LEU* 3.5 25.1 - - + +
115A PHE* 3.5 22.7 - - + -
119A PHE* 4.5 15.0 - - + -
122A ILE* 3.8 27.6 - - + -
5C T 5.7 2.9 - - - +
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Residues in contact with ARG 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A SER 4.5 0.2 - - - -
32A PHE* 3.6 1.0 - - - -
33A MET* 2.9 66.4 + - + +
35A THR* 2.8 28.8 + - - +
49A ARG* 3.5 27.7 - - - +
50A PRO* 1.3 81.6 - - + +
52A PHE* 1.3 61.3 + - - +
53A ARG* 4.7 6.7 - - + +
86A PHE 3.6 7.6 - - - +
87A GLU* 3.1 32.5 + - + +
115A PHE* 3.2 12.5 - - - -
7C C 3.4 5.1 - - - +
8C T 4.6 0.2 + - - -
20X A 3.6 19.0 + - - +
21X G 2.9 45.0 + - - -
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Residues in contact with PHE 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ALA* 4.4 1.3 - - + -
30A SER* 3.6 31.4 - - - -
31A SER 3.5 6.5 - - - -
32A PHE* 3.3 45.3 - + + -
51A ARG* 1.3 75.1 - - - +
53A ARG* 1.3 67.7 + - - +
54A ILE* 4.2 18.2 - - + -
85A ARG* 3.5 1.6 - - - +
86A PHE* 2.9 68.2 + + + +
92A LEU* 3.8 17.7 - - + +
95A VAL* 3.8 17.7 - - + -
99A PHE* 3.8 18.8 - + - -
115A PHE* 4.7 0.2 - - + -
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Residues in contact with ARG 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A SER* 3.4 5.0 - - - -
31A SER* 2.9 36.0 + - - +
33A MET* 3.6 31.0 - - + +
51A ARG* 4.7 7.9 - - + +
52A PHE* 1.3 79.8 - - - +
54A ILE* 1.3 74.2 + - - +
55A GLY* 5.0 0.4 - - - +
83A ARG* 2.9 39.4 - - + +
84A ILE 3.4 12.6 - - - +
85A ARG* 4.3 17.3 - - + +
87A GLU* 5.3 3.6 + - - -
8C T 4.9 3.0 + - - -
18X G 2.8 35.4 + - - -
19X G 2.8 31.9 + - - -
20X A 4.4 8.1 - - - +
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Residues in contact with ILE 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ILE* 5.8 2.2 - - + +
25A PHE* 4.4 8.1 - - + +
26A ALA* 4.5 12.3 - - + +
29A ASP* 5.2 4.5 - - + +
30A SER* 3.6 21.1 - - - +
52A PHE* 4.2 21.1 - - + -
53A ARG* 1.3 83.5 - - - +
55A GLY* 1.3 60.8 + - - +
56A LEU* 3.6 30.7 - - + -
64A LEU* 3.8 10.8 - - + +
67A ILE* 4.1 25.8 - - + -
82A ALA 3.7 0.3 - - - +
83A ARG* 3.1 6.1 - - - +
84A ILE* 2.9 50.4 + - + -
86A PHE* 5.7 0.4 - - + -
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Residues in contact with GLY 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ASP* 4.2 5.9 + - - +
53A ARG* 4.4 0.8 - - - +
54A ILE* 1.3 73.2 - - - +
56A LEU* 1.3 76.3 + - - +
81A ASP* 5.1 4.5 - - - -
82A ALA 3.2 10.5 - - - -
83A ARG* 4.2 10.1 - - - -
16X T 2.4 27.8 - - - -
17X A 6.4 1.3 - - - -
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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