Contacts of the strand formed by residues 47 - 52 (chain A) in PDB entry 3C6M
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 TYR 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A GLY* 3.9 13.5 - - - -
20A GLU* 3.7 46.2 + - + +
23A LEU* 4.3 27.1 - - + -
39A VAL* 4.5 2.9 - - + -
40A HIS 3.6 3.4 - - - +
41A THR* 3.5 35.4 - - + -
42A TRP* 3.7 6.3 - - - -
46A GLY* 1.3 85.4 - - - -
48A LEU* 1.3 61.8 + - - +
49A ALA 4.2 0.7 - - - +
61A LEU 4.2 0.9 - - - +
62A ARG* 3.1 10.6 + - - +
63A ILE* 2.9 48.3 + - + -
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Residues in contact with LEU 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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38A SER 3.7 0.9 - - - +
39A VAL* 3.3 5.4 - - - -
40A HIS* 2.8 41.4 + - + +
42A TRP* 3.7 13.7 - - + -
47A TYR* 1.3 74.3 - - - +
49A ALA* 1.3 65.2 + - - +
50A THR* 4.1 5.8 + - - +
60A ASN* 3.8 27.8 - - + +
61A LEU 3.5 7.9 - - - +
62A ARG* 4.6 2.0 - - - +
50B THR* 3.7 19.7 - - + -
52B THR* 3.8 16.8 - - + -
58B PHE* 3.5 47.3 - - + -
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Residues in contact with ALA 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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23A LEU* 3.9 16.6 - - + -
37A GLU* 3.9 9.4 - - - +
38A SER 3.5 4.3 - - - -
39A VAL* 4.4 3.4 - - + +
47A TYR* 4.2 0.4 - - - +
48A LEU* 1.3 75.1 - - - +
50A THR* 1.3 64.3 + - - +
51A TYR* 3.4 33.5 - - + +
59A ALA 3.6 3.1 - - - +
60A ASN* 3.6 1.0 - - - -
61A LEU* 2.9 40.0 + - + +
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Residues in contact with THR 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 ALA 3.3 0.9 - - - +
37A GLU* 3.2 5.9 - - - -
38A SER* 2.9 42.2 + - - -
48A LEU* 4.1 8.7 + - - +
49A ALA* 1.3 72.7 - - - +
51A TYR* 1.3 65.2 + - - +
52A THR* 4.5 10.5 - - + +
58A PHE* 4.8 0.2 - - + -
59A ALA 3.4 7.4 - - - +
60A ASN* 3.0 21.1 + - - +
40B HIS* 6.5 0.2 - - + -
48B LEU* 4.0 27.6 - - + -
50B THR* 4.0 16.0 + - - +
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Residues in contact with TYR 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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23A LEU* 3.8 6.4 - - - +
27A GLN* 3.5 20.4 - - + +
30A PHE* 3.4 50.3 - + + -
31A GLN 5.2 0.4 - - - -
35A MET* 3.4 27.2 - - + +
36A ALA 3.0 6.5 - - - +
37A GLU* 2.7 50.4 + - + -
49A ALA* 3.4 27.8 - - + +
50A THR* 1.3 74.3 - - - +
52A THR* 1.3 62.4 + - - +
58A PHE* 3.1 10.2 - - - +
59A ALA* 3.0 43.1 + - + -
61A LEU* 4.1 6.2 - - + +
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Residues in contact with THR 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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34A GLY 4.1 1.6 - - - +
35A MET* 2.9 23.4 - - - -
36A ALA* 3.0 28.1 + - - +
50A THR* 4.5 15.0 - - + +
51A TYR* 1.3 79.9 - - - +
53A ASN* 1.3 59.4 - - - +
54A LYS 4.5 0.2 + - - -
57A SER 3.9 2.2 - - - -
58A PHE* 4.5 2.5 - - + -
40B HIS* 3.1 53.3 + - + +
42B TRP* 4.1 15.7 - - + -
48B LEU* 4.6 1.8 - - + -
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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