Contacts of the strand formed by residues 47 - 51 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B LEU* 3.8 31.0 - - + -
38B ALA 3.3 18.8 - - - +
39B ALA* 3.7 17.7 - - + +
45B ARG 5.2 0.2 - - - +
46B LEU* 1.3 90.6 - - - +
48B PHE* 1.3 60.7 + - - +
135B VAL* 3.5 32.3 - - - -
136B GLY* 4.8 3.4 - - - -
137B LEU 5.8 0.2 - - - -
191B VAL* 5.3 11.8 + - - +
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Residues in contact with PHE 48 (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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37B LEU* 3.5 7.2 - - - +
38B ALA* 3.0 50.7 + - + -
39B ALA 5.7 0.2 - - - -
40B GLU* 5.1 18.6 - - + -
44B ASN* 5.8 2.9 - - + -
46B LEU 5.0 4.5 - - - -
47B CYS* 1.3 76.8 - - - +
49B LEU* 1.3 82.0 + - + +
50B GLU* 5.4 4.7 - - + -
64B ILE* 5.8 5.6 - - + -
190B GLN* 6.3 0.2 - - - +
191B VAL* 5.9 0.7 - - - -
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Residues in contact with LEU 49 (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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35B LEU* 3.8 24.9 - - + -
36B CYS 3.3 7.6 - - - +
37B LEU* 5.3 1.6 - - - -
48B PHE* 1.3 93.5 - - - +
50B GLU* 1.3 64.2 + - - +
51B PRO* 4.3 4.1 - - - +
182B LEU* 3.7 30.5 - - + -
189B LEU* 3.3 43.5 + - + +
190B GLN* 3.8 1.3 - - - -
191B VAL* 3.7 32.1 - - + +
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Residues in contact with GLU 50 (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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35B LEU* 3.9 0.7 - - - -
36B CYS* 2.5 48.7 + - + +
38B ALA* 4.9 11.2 - - + -
48B PHE* 5.3 5.6 - - + -
49B LEU* 1.3 78.8 - - - +
51B PRO* 1.3 91.0 - - - +
52B THR* 3.2 2.5 + - - -
58B VAL* 6.0 2.1 - - - +
60B PRO* 3.9 28.1 - - + +
61B ASP* 5.1 6.7 - - + +
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Residues in contact with PRO 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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33B LEU* 6.0 5.4 - - + -
34B LYS 3.7 12.8 - - - +
35B LEU* 3.7 8.7 - - + -
49B LEU* 4.3 4.7 - - + +
50B GLU* 1.3 113.6 - - - +
52B THR* 1.3 60.9 + - - +
53B SER* 3.5 4.0 - - - +
54B ASN* 4.7 9.7 + - + +
58B VAL 5.8 0.2 - - - +
60B 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