Contacts of the strand formed by residues 47 - 52 (chain F) in PDB entry 3SZ9
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 47 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38F PRO* 3.8 26.7 - - + -
39F THR 3.6 5.2 - - - +
40F VAL* 4.2 9.9 - - + +
45F GLY 5.7 0.4 - - - +
46F GLU* 1.3 75.6 + - - +
48F ILE* 1.3 63.9 + - - +
49F CYS* 3.6 27.1 - - - +
50F GLN* 5.1 4.5 - - + +
6911F EDO 3.9 8.4 - - - -
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Residues in contact with ILE 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F VAL* 4.0 17.3 - - + +
39F THR* 2.8 15.2 + - + +
40F VAL 3.7 3.1 - - - +
41F ASN* 3.6 25.1 - - + +
47F VAL* 1.3 74.9 - - - +
49F CYS* 1.3 62.6 + - - +
108F LEU* 3.8 35.2 - - + +
109F ASP* 3.5 30.3 - - + +
199F LEU* 3.9 18.4 - - + -
6911F EDO 3.8 21.5 - - - +
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Residues in contact with CYS 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F VAL* 4.0 25.6 - - + -
20F ASN* 4.6 6.1 - - - +
38F PRO* 3.5 2.6 - - - +
39F THR* 3.0 27.8 + - - +
47F VAL* 3.6 6.9 - - - +
48F ILE* 1.3 83.8 - - + +
50F GLN* 1.3 76.1 + - - +
51F VAL* 4.3 0.2 - - - -
199F LEU* 3.9 31.6 - - - -
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Residues in contact with GLN 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F ASN* 2.9 27.4 + - - +
36F THR* 2.7 39.7 + - + +
37F PHE* 3.3 18.1 - - - -
38F PRO* 3.5 26.8 - - + +
47F VAL* 5.1 4.8 - - + +
49F CYS* 1.3 77.5 - - - +
51F VAL* 1.3 64.5 + - - +
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Residues in contact with VAL 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F ASN* 3.5 11.7 - - + +
36F THR* 3.1 5.4 - - - -
37F PHE* 2.7 48.2 + - + +
39F THR* 4.0 18.2 - - + -
49F CYS* 4.3 1.1 - - - -
50F GLN* 1.3 81.3 - - - +
52F ALA* 1.3 80.4 + - - +
198F PRO* 3.9 20.6 - - + -
199F LEU* 4.0 13.9 - - + -
202F LEU* 4.1 10.8 - - + -
222F PRO* 3.8 24.0 - - + -
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Residues in contact with ALA 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F ASN 3.0 9.8 + - - +
21F GLN* 3.8 26.9 - - + -
22F ILE* 3.8 19.1 - - + +
29F HIS 4.2 1.6 - - - +
30F ASP* 4.6 3.6 - - - +
31F ALA 4.1 15.7 - - - +
35F LYS 3.6 7.2 - - - -
36F THR* 4.2 7.2 - - + +
37F PHE* 3.5 6.1 - - - -
51F VAL* 1.3 71.9 - - - +
53F GLU* 1.3 60.8 + - - +
54F GLY 3.5 2.0 + - - -
222F PRO* 3.4 20.4 - - - +
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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