Contacts of the strand formed by residues 19 - 27 (chain F) 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 GLU 19 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18F ASP* 1.3 71.6 - - - +
20F VAL* 1.3 62.5 + - - +
66F CYS* 5.4 4.5 - - + -
67F PHE 3.3 9.9 - - - +
68F VAL* 4.2 12.5 - - + +
204F PRO* 3.8 2.9 - - - +
205F ILE* 3.0 47.3 + - + +
206F CYS* 3.0 22.5 + - + +
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Residues in contact with VAL 20 (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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14F LEU* 5.1 12.8 - - + -
18F ASP* 3.9 12.6 - - + +
19F GLU* 1.3 80.0 - - - +
21F VAL* 1.3 67.7 + - - +
22F LEU 5.6 0.2 - - - +
66F CYS* 4.4 0.2 - - - -
67F PHE* 2.5 58.0 + - + +
68F VAL* 4.9 4.5 - - - -
69F LEU* 4.7 12.1 - - + +
109F LEU* 6.1 0.9 - - + -
202F MET* 3.6 22.7 - - + -
204F PRO* 4.3 17.3 - - + -
205F ILE* 4.5 0.6 - - - +
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Residues in contact with VAL 21 (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 VAL* 1.3 82.9 - - - +
22F LEU* 1.3 63.5 + - - +
23F GLN* 4.0 4.3 + - + +
36F CYS* 3.7 27.8 - - - -
62F LEU* 5.5 3.1 - - + +
65F CYS* 3.7 27.6 - - + +
66F CYS* 4.7 2.2 - - - -
67F PHE* 4.9 1.1 - - - -
201F ASN 4.3 0.3 - - - +
202F MET* 3.2 13.5 - - - +
203F ASN* 3.4 19.8 + - - +
205F ILE* 3.8 34.5 - - + -
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Residues in contact with LEU 22 (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 VAL* 5.6 0.2 - - - +
21F VAL* 1.3 73.6 - - - +
23F GLN* 1.3 61.1 + - - +
24F CYS* 6.2 0.4 - - + -
36F CYS* 3.2 24.9 - - - -
37F LEU* 4.2 20.7 + - + +
67F PHE* 4.6 19.2 - - + -
109F LEU* 5.9 6.7 - - + -
171F LEU* 5.7 9.9 - - + -
200F TRP* 3.9 25.6 - - + -
201F ASN 3.3 20.2 - - - +
202F MET* 3.6 24.2 - - + +
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Residues in contact with GLN 23 (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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21F VAL* 5.0 4.3 - - + +
22F LEU* 1.3 80.0 - - - +
24F CYS* 1.3 64.8 + - - +
34F LYS* 3.4 24.1 - - + +
35F LEU 3.4 15.5 - - - +
36F CYS* 5.0 4.5 - - + +
37F LEU 5.7 0.2 - - - +
52F THR* 3.5 26.0 - - + +
53F SER* 5.2 0.6 + - - +
200F TRP* 3.8 1.6 - - - +
201F ASN* 2.7 53.6 + - + +
203F ASN* 6.1 1.2 - - - +
268F SER* 4.9 8.7 + - - -
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Residues in contact with CYS 24 (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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22F LEU* 6.2 0.4 - - + -
23F GLN* 1.3 76.2 - - - +
25F ASN* 1.3 60.9 + - - +
26F ALA 4.2 0.2 + - - -
34F LYS* 3.3 7.7 - - - +
35F LEU* 3.2 30.9 + - - +
49F LEU* 6.2 0.2 - - + -
182F LEU* 4.0 35.1 - - + +
198F THR* 5.8 1.1 - - + -
199F LEU* 4.5 12.8 - - - +
200F TRP* 4.9 6.5 - - + +
201F ASN* 4.8 3.4 - - - +
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Residues in contact with ASN 25 (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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24F CYS* 1.3 78.0 - - - +
26F ALA* 1.3 85.6 + - - +
27F THR* 4.0 2.3 + - - -
32F GLN* 4.4 15.9 - - - +
33F LEU 3.2 18.6 + - - +
34F LYS* 4.2 8.7 - - + +
182F LEU* 5.1 3.2 - - - +
198F THR* 5.6 6.1 - - - +
199F LEU* 5.3 12.5 + - + +
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Residues in contact with ALA 26 (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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24F CYS 4.2 0.6 + - - -
25F ASN* 1.3 78.6 + - - +
27F THR* 1.3 61.1 + - - +
28F VAL* 3.0 9.9 + - + +
33F LEU* 2.8 35.3 + - + +
35F LEU* 5.9 4.5 - - + +
49F LEU* 6.4 0.7 - - + -
182F LEU* 4.9 15.5 - - + -
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Residues in contact with THR 27 (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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25F ASN* 4.0 4.5 + - - -
26F ALA* 1.3 67.2 - - - +
28F VAL* 1.3 65.6 + - - +
31F GLU 4.9 1.3 - - - -
32F GLN* 5.1 4.9 - - - +
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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