Contacts of the strand formed by residues 47 - 51 (chain D) in PDB entry 6X34
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 CYS 47 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37D LEU* 3.8 30.5 - - + -
38D ALA 3.3 18.2 - - - +
39D ALA* 3.7 17.9 - - + +
46D LEU* 1.3 88.8 - - - +
48D PHE* 1.3 60.8 + - - +
135D VAL* 3.5 32.1 - - - -
136D GLY* 4.8 3.4 - - - -
137D LEU 5.8 0.2 - - - -
191D VAL* 5.3 11.8 + - - +
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Residues in contact with PHE 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LEU* 3.5 7.4 - - - +
38D ALA* 3.0 47.8 + - + -
39D ALA 5.7 0.2 - - - -
40D GLU* 5.1 18.8 - - + -
44D ASN* 5.8 3.1 - - + -
46D LEU 5.0 4.3 - - - -
47D CYS* 1.3 77.6 - - - +
49D LEU* 1.3 81.9 + - + +
50D GLU* 5.4 4.9 - - + -
64D ILE* 5.8 5.8 - - + -
190D GLN* 6.3 0.7 - - - +
191D VAL* 5.9 0.9 - - - -
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Residues in contact with LEU 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D CYS* 6.2 0.2 - - + -
35D LEU* 3.8 24.2 - - + -
36D CYS 3.3 8.7 - - - +
37D LEU* 5.3 1.6 - - - -
48D PHE* 1.3 92.8 - - - +
50D GLU* 1.3 64.9 + - - +
51D PRO* 4.3 4.1 - - + +
182D LEU* 3.7 29.8 - - + -
189D LEU* 3.3 44.2 + - + +
190D GLN* 3.8 0.9 - - - -
191D VAL* 3.7 32.8 - - + +
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Residues in contact with GLU 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D LEU* 3.9 0.9 - - - -
36D CYS* 2.5 47.9 + - + +
38D ALA* 4.9 11.4 - - + -
48D PHE* 5.3 5.5 - - + -
49D LEU* 1.3 77.6 - - - +
51D PRO* 1.3 92.1 - - - +
52D THR* 3.2 2.5 + - - -
58D VAL* 6.0 2.1 - - - +
60D PRO* 3.9 26.5 - - + +
61D ASP* 5.1 7.2 - - + +
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Residues in contact with PRO 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LEU* 6.0 4.9 - - + -
34D LYS 3.7 12.1 - - - +
35D LEU* 3.7 8.5 - - + -
49D LEU 4.3 4.0 - - - +
50D GLU* 1.3 112.9 - - - +
52D THR* 1.3 62.2 + - - +
53D SER* 3.5 5.1 + - - +
54D ASN* 4.7 8.7 + - + +
60D PRO* 4.6 1.9 - - - +
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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