Contacts of the strand formed by residues 48 - 54 (chain A) in PDB entry 1X47
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 PHE 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A PHE 4.8 0.2 - - - -
46A GLU 3.1 0.6 - - - -
47A PRO* 1.3 100.3 - - + +
49A GLY* 1.3 59.5 + - - +
63A THR* 3.0 4.9 - - - -
64A ALA 2.8 36.9 + - - +
65A SER 2.6 28.5 - - - -
66A SER* 3.4 13.9 - - - +
67A LYS* 4.1 26.9 - - + +
70A ALA* 3.4 3.8 - - - +
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Residues in contact with GLY 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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38A PHE* 3.7 6.4 - - - +
39A PHE* 3.0 45.2 + - - +
40A GLU 5.4 0.9 - - - -
47A PRO 3.4 2.2 + - - -
48A PHE* 1.3 74.3 - - - +
50A ALA* 1.3 62.2 + - - +
62A GLY 3.5 0.9 - - - -
63A THR* 3.3 22.7 - - - -
67A LYS* 6.0 1.0 - - - +
70A ALA* 4.1 1.6 - - - -
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Residues in contact with ALA 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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36A TYR* 5.8 0.2 - - + -
37A ASN 3.3 5.8 - - - +
38A PHE* 3.6 25.4 - - + -
39A PHE* 3.3 7.8 - - - -
49A GLY* 1.3 75.6 - - - +
51A SER* 1.3 59.5 + - - +
61A SER* 3.5 0.2 - - - -
62A GLY 2.8 32.5 + - - +
67A LYS* 4.9 1.1 - - + +
70A ALA* 3.9 4.6 - - + +
71A LYS* 3.8 30.5 - - + +
74A ALA* 3.2 9.5 - - + +
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Residues in contact with SER 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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36A TYR* 3.3 7.3 - - - +
37A ASN* 2.5 54.0 + - - +
39A PHE* 3.0 19.2 - - - -
50A ALA* 1.3 74.2 - - - +
52A VAL* 1.3 64.6 + - - +
53A THR 3.9 0.2 - - - -
58A THR* 4.1 16.3 - - - +
60A GLY 3.7 1.1 - - - -
61A SER* 3.4 22.4 - - - -
74A ALA* 3.8 1.5 - - - +
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Residues in contact with VAL 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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22A LEU* 4.5 5.6 - - + -
34A PRO* 4.4 20.4 - - + -
35A VAL 3.9 2.9 - - - +
36A TYR* 3.8 21.3 - - + -
51A SER* 1.3 73.2 - - - +
53A THR* 1.3 62.2 + - - +
54A ILE* 3.7 3.5 + - + -
58A THR* 4.6 0.4 - - - +
59A TYR* 3.1 26.4 + - - +
60A GLY 2.9 9.2 + - - +
74A ALA* 3.3 34.8 - - + +
75A ALA* 3.5 8.1 - - - +
78A THR* 3.1 34.3 + - + +
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Residues in contact with THR 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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34A PRO* 3.8 1.2 - - - +
35A VAL* 2.4 60.3 + - - +
37A ASN* 3.2 34.9 + - + +
51A SER* 3.9 1.1 - - - -
52A VAL* 1.3 72.5 - - - +
54A ILE* 1.3 62.1 + - - +
55A ASP 3.5 3.2 + - - -
56A GLY* 3.8 20.9 - - - +
57A VAL 3.2 3.4 - - - -
58A THR* 3.2 33.7 - - + +
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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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26A MET* 3.5 44.0 - - + -
30A LEU* 4.0 15.5 - - + -
32A VAL* 4.4 9.6 - - + -
34A PRO* 4.4 5.6 - - + -
52A VAL* 4.5 6.1 - - + -
53A THR* 1.3 70.8 - - - +
55A ASP* 1.3 67.7 + - + +
56A GLY 2.9 7.6 + - - -
57A VAL* 2.5 26.6 + - - +
59A TYR* 3.3 50.9 - - + +
78A THR* 4.0 10.1 - - + -
82A LEU* 5.1 1.6 - - + -
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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