Contacts of the strand formed by residues 50 - 57 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B VAL* 3.5 34.8 - - + -
25B ARG 4.0 4.5 - - - +
26B ARG* 4.0 23.6 - - - +
48B ASP 5.4 0.2 - - - +
49B PRO* 1.3 76.7 - - + +
51B VAL* 1.3 62.9 + - - +
52B TYR 3.8 10.3 - - - +
53B GLU* 3.6 26.2 - - + +
74B TYR* 3.4 29.3 - - + +
83B PHE* 5.2 1.2 - - - -
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ARG 3.2 10.7 + - - +
27B LEU* 3.8 40.8 - - + +
30B MET* 3.7 11.4 - - - -
34B PHE* 5.5 0.2 - - + -
49B PRO* 3.2 3.1 + - + +
50B VAL* 1.3 73.2 - - - +
52B TYR* 1.3 80.2 + - + +
73B LEU* 3.3 9.4 - - + +
74B TYR* 2.9 25.9 + - - +
83B PHE* 4.2 31.2 - - + -
84B PHE 3.4 17.5 - - - +
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Residues in contact with TYR 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B SER 3.8 0.5 - - - +
25B ARG* 3.1 58.2 + - + +
30B MET* 4.1 9.6 - - - -
50B VAL* 3.4 2.5 - - - +
51B VAL* 1.3 97.0 - - + +
53B GLU* 1.3 64.9 + - - +
54B VAL* 3.8 27.4 - - + -
71B THR* 4.0 9.0 - - + -
72B VAL 3.2 13.7 - - - +
73B LEU* 3.8 12.6 - - + -
74B TYR* 4.2 2.2 - - - -
84B PHE 3.8 8.5 - - - -
85B THR* 3.6 30.6 - - + -
86B LYS* 3.3 31.1 + - - +
87B GLY 5.1 0.2 + - - -
160B TYR* 5.4 3.1 - - - -
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Residues in contact with GLU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LYS* 3.9 28.3 - - + +
23B SER 3.2 6.7 - - - +
24B VAL* 4.3 11.5 - - + +
50B VAL* 3.6 24.6 - - + +
52B TYR* 1.3 73.1 - - - +
54B VAL* 1.3 65.2 + - - +
55B TYR* 4.3 19.3 + - + -
71B THR* 3.2 8.1 - - - +
72B VAL* 3.0 38.9 + - + +
74B TYR* 2.8 34.5 + - + -
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Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LYS 3.6 2.6 - - - +
22B LYS* 3.4 5.3 - - - -
23B SER* 3.0 41.7 + - - +
52B TYR* 3.8 26.9 - - + -
53B GLU* 1.3 80.2 - - - +
55B TYR* 1.3 62.6 + - - +
56B ALA* 3.8 9.6 + - + +
69B ALA* 4.0 19.3 - - + -
70B THR 3.4 10.8 - - - +
71B THR* 4.0 13.0 - - - +
152B TYR* 5.8 0.4 - - - +
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Residues in contact with TYR 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLY 3.9 6.5 - - - -
16B ILE* 3.4 47.0 - - + +
17B ILE* 3.2 43.4 - - + +
20B ALA* 4.1 4.7 - - + -
21B LYS 4.1 3.8 - - - -
22B LYS* 3.1 53.1 - - + +
53B GLU* 4.3 19.9 + - + -
54B VAL* 1.3 72.5 - - - +
56B ALA* 1.3 59.8 + - - +
69B ALA* 3.2 1.8 - - - -
70B THR* 3.0 40.8 + - - +
72B VAL* 4.6 12.3 - - + -
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Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ALA* 2.6 25.1 + - - +
21B LYS 3.5 12.5 + - - +
23B SER* 6.0 1.8 - - - +
54B VAL* 4.4 10.1 - - + +
55B TYR* 1.3 73.7 - - - +
57B VAL* 1.3 63.0 + - - +
58B GLU* 3.8 23.3 + - + +
69B ALA* 3.8 15.7 - - + -
152B TYR* 4.8 1.8 - - - +
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Residues in contact with VAL 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B PHE* 3.8 26.5 - - + -
8B VAL* 4.7 7.4 - - + -
17B ILE* 4.1 10.1 - - + -
20B ALA* 4.1 19.5 - - + -
56B ALA* 1.3 75.5 - - - +
58B GLU* 1.3 61.5 + - - +
59B GLN* 4.3 8.0 + - - +
67B ASN* 3.5 4.3 - - - +
68B PHE* 2.9 73.0 + - + +
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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