Contacts of the strand formed by residues 55 - 61 (chain F) in PDB entry 5WFE
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 ASN 55 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27E ARG* 3.1 29.3 + - - +
7F VAL 4.0 0.5 - - - +
8F THR 4.0 0.9 - - - -
9F GLU* 2.8 53.2 + - - +
10F ASN* 4.3 6.6 + - - +
54F GLY* 1.3 73.9 - - - +
56F VAL* 1.3 63.5 + - - +
73F PHE 3.1 5.6 - - - +
74F GLY 4.1 0.4 - - - -
75F LEU 2.9 38.7 + - - +
76F ASN* 3.2 15.4 + - - +
13H T 5.2 1.0 + - - -
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Residues in contact with VAL 56 (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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27E ARG* 3.4 6.0 + - - -
6F VAL* 3.8 22.9 - - + -
7F VAL 3.2 13.0 - - - +
8F THR* 4.1 7.0 - - + -
11F VAL* 3.5 26.9 - - + -
15F LEU* 4.0 13.5 - - + -
19F LEU* 5.2 0.4 - - + -
44F TRP* 4.5 1.4 - - + -
47F ILE* 3.7 31.2 - - + -
51F ALA* 4.3 6.7 - - + -
55F ASN* 1.3 78.4 - - - +
57F VAL* 1.3 63.5 + - - +
71F GLN 4.4 0.2 - - - +
72F THR* 3.5 1.4 - - - -
73F PHE* 2.6 44.0 + - + +
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Residues in contact with VAL 57 (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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26E VAL* 4.8 14.4 - - + -
27E ARG* 3.2 36.3 - - + +
5F VAL 3.7 0.9 - - - +
6F VAL* 3.4 2.1 - - - -
7F VAL* 2.9 49.0 + - + +
56F VAL* 1.3 78.2 - - - +
58F MET* 1.3 67.8 + - - +
59F ALA* 4.2 2.7 - - + +
70F PHE* 4.1 18.4 - - + -
71F GLN 3.4 13.2 - - - +
72F THR* 3.6 15.7 - - + -
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Residues in contact with MET 58 (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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4F LEU* 3.5 32.1 - - + -
5F VAL 3.2 7.0 - - - +
6F VAL* 3.8 12.8 - - + -
40F ARG* 3.7 26.9 - - + +
41F GLU* 5.5 0.9 - - + -
43F ILE* 5.1 1.6 - - - -
44F TRP* 3.7 43.4 - - + -
47F ILE* 4.2 9.2 - - + -
57F VAL* 1.3 74.3 - - - +
59F ALA* 1.3 61.8 + - - +
60F TRP* 3.4 28.6 - - + -
70F PHE* 3.1 3.9 - - - +
71F GLN* 3.0 39.4 + - - +
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Residues in contact with ALA 59 (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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3E MET* 3.6 20.3 - - + +
26E VAL* 6.4 2.5 - - + -
32E VAL* 4.6 14.4 - - + -
4F LEU* 3.5 1.9 - - - +
5F VAL* 2.7 45.7 + - + +
57F VAL* 4.2 3.6 - - + -
58F MET* 1.3 73.9 - - - +
60F TRP* 1.3 60.9 + - - +
68F PHE* 4.8 3.6 - - + -
69F GLU 3.2 6.1 - - - +
70F PHE* 3.7 15.3 - - + -
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Residues in contact with TRP 60 (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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3E MET* 4.1 1.3 - - - -
3F MET 3.0 14.4 - - - +
4F LEU* 4.2 1.3 - - + -
40F ARG* 3.3 51.2 - - - +
58F MET* 3.4 48.5 - - + -
59F ALA* 1.3 74.4 - - - +
61F ALA* 1.3 58.8 + - - +
62F THR* 3.4 19.8 - - + +
68F PHE* 3.1 4.3 - - - -
69F GLU* 2.4 88.9 + - + +
70F PHE* 3.8 9.6 - - - -
71F GLN* 3.7 31.0 - - + -
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Residues in contact with ALA 61 (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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3E MET* 3.6 21.5 - - + +
34E ASP* 5.5 0.7 - - - +
2F SER* 3.2 23.1 + - - -
3F MET* 3.1 30.3 + - + +
60F TRP* 1.3 74.9 - - - +
62F THR* 1.3 64.5 + - - +
67F GLY 3.6 12.1 - - - +
68F PHE* 3.7 3.8 - - - +
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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