Contacts of the strand formed by residues 50 - 57 (chain A) in PDB entry 1X8E
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 VAL 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A VAL* 3.8 24.9 - - + -
25A ARG 4.1 2.7 - - - +
26A ARG* 3.2 33.5 - - + +
49A PRO* 1.3 75.0 - - - +
51A VAL* 1.3 62.1 + - - +
52A TYR 3.8 9.9 - - - +
53A GLU* 4.5 6.1 - - - +
74A TYR* 3.6 50.0 - - + +
83A PHE* 4.1 7.1 - - - -
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Residues in contact with VAL 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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25A ARG 3.0 11.6 + - - +
27A LEU* 3.6 44.9 - - + +
30A MET* 3.8 13.7 - - - -
34A PHE* 5.1 1.1 - - + -
49A PRO 3.6 1.3 + - - +
50A VAL* 1.3 76.2 - - - +
52A TYR* 1.3 68.6 + - + +
73A LEU* 3.2 13.5 - - + +
74A TYR* 2.9 25.4 + - - +
83A PHE* 4.0 24.9 - - + -
84A PHE 3.5 29.2 - - - +
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Residues in contact with TYR 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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23A SER 4.1 0.2 - - - +
24A VAL* 3.8 2.1 - - - +
25A ARG* 3.0 54.7 + - + +
30A MET* 3.9 15.3 - - - -
50A VAL* 3.8 9.8 - - - -
51A VAL* 1.3 93.7 - - + +
53A GLU* 1.3 58.5 + - - +
54A VAL* 3.7 26.6 - - + +
71A THR* 3.9 5.6 - - + -
72A VAL 3.1 14.1 - - - +
73A LEU* 3.8 10.5 - - + -
74A TYR* 4.3 0.2 - - - -
84A PHE 4.0 4.0 - - - -
85A THR* 3.7 30.5 - - + -
86A LYS* 3.2 41.4 + - - +
88A HIS* 6.3 1.8 - + - -
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Residues in contact with GLU 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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22A LYS* 5.0 6.5 - - + -
23A SER 3.4 4.9 - - - +
24A VAL* 4.2 27.2 - - + +
50A VAL* 4.5 7.1 - - - +
52A TYR* 1.3 73.7 - - - +
54A VAL* 1.3 63.9 + - - +
55A TYR* 3.8 28.5 + - + +
70A THR 3.8 0.2 - - - +
71A THR* 3.1 8.3 - - - +
72A VAL* 2.9 45.0 + - + +
74A TYR* 2.9 33.1 + - - -
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Residues in contact with VAL 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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21A LYS 3.7 1.1 - - - +
22A LYS* 3.5 6.8 - - - +
23A SER* 2.9 42.4 + - - +
25A ARG* 6.0 0.9 - - + -
52A TYR* 3.7 29.2 - - + +
53A GLU* 1.3 79.7 - - - +
55A TYR* 1.3 69.6 + - - +
56A ALA* 3.9 8.1 - - + +
69A ALA* 4.3 17.9 - - + -
70A THR 3.4 9.2 - - - +
71A THR* 3.8 12.1 - - - +
152A TYR* 5.7 0.4 - - - +
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Residues in contact with TYR 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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15A GLY 3.2 25.8 - - - -
16A ILE* 3.3 39.0 - - + +
17A ILE* 3.7 32.8 - - + +
20A ALA* 3.9 10.5 - - + -
21A LYS 4.0 2.7 - - - -
22A LYS* 3.7 32.8 - - + +
53A GLU* 3.8 23.9 + - + +
54A VAL* 1.3 78.2 - - - +
56A ALA* 1.3 61.1 + - - +
69A ALA* 3.6 3.1 - - - -
70A THR* 2.9 40.4 + - - +
72A VAL* 4.2 17.0 - - + -
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Residues in contact with ALA 56 (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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20A ALA* 3.5 1.0 - - - +
21A LYS* 3.2 39.1 + - + +
54A VAL* 3.9 6.9 - - + -
55A TYR* 1.3 73.2 - - - +
57A VAL* 1.3 64.4 + - - +
58A GLU* 3.6 30.9 + - + +
68A PHE 3.6 7.4 - - - +
69A ALA* 4.3 4.0 - - + +
152A TYR* 4.3 9.2 - - - +
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Residues in contact with VAL 57 (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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6A PHE* 3.9 26.5 - - + -
8A VAL* 5.1 3.4 - - + -
17A ILE* 4.2 13.9 - - + -
20A ALA* 4.1 17.5 - - + -
56A ALA* 1.3 77.7 - - - +
58A GLU* 1.3 60.5 + - - +
59A GLN* 4.2 6.8 + - - +
66A LEU 4.8 0.3 - - - +
67A ASN* 3.6 2.9 - - - -
68A PHE* 2.8 74.7 + - + +
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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