Contacts of the strand formed by residues 43 - 52 (chain F) in PDB entry 3E8C
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 PHE 43 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295A LYS* 5.2 2.6 + - - -
38F ALA* 3.8 18.4 - - + -
39F HIS 3.3 23.1 - - - -
40F LEU* 3.2 15.9 + - + +
41F ASP* 3.2 0.9 - - - -
42F GLN* 1.3 82.4 - - + +
44F GLU* 1.3 60.5 + - - +
45F ARG* 3.8 6.0 + - + +
60F VAL* 4.3 20.9 - - + -
61F LYS 3.5 2.2 - - - +
62F HIS* 3.2 45.1 - + + -
63F MET* 3.3 12.8 - - - +
69F TYR* 4.4 1.8 - + - -
71F MET* 3.7 23.3 - - + -
108F PHE* 3.8 22.2 - + - -
110F PHE* 3.8 9.6 - + - -
119F VAL* 3.9 21.3 - - + -
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Residues in contact with GLU 44 (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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43F PHE* 1.3 69.8 - - - +
45F ARG* 1.3 64.9 + - - +
46F ILE* 3.5 7.9 + - + +
60F VAL* 3.2 7.6 - - - -
61F LYS* 2.8 67.3 + - + +
63F MET* 3.5 28.0 - - + +
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Residues in contact with ARG 45 (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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263A SER* 6.2 1.0 - - - -
40F LEU* 5.5 13.9 - - + -
43F PHE* 3.8 6.0 + - + +
44F GLU* 1.3 73.4 - - - +
46F ILE* 1.3 61.4 + - - +
58F MET* 3.8 36.1 - - + +
59F LEU 4.1 4.7 - - - -
60F VAL* 4.4 9.9 - - + -
71F MET* 5.6 3.8 - - - -
73F ILE* 5.0 3.1 - - - -
332F GLU* 5.7 0.4 + - - -
333F GLU 3.8 10.9 + - - -
334F GLU* 3.5 28.9 + - - +
335F ILE* 3.5 44.9 + - - +
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Residues in contact with ILE 46 (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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44F GLU* 3.8 14.8 - - + +
45F ARG* 1.3 78.0 - - - +
47F LYS* 1.3 74.6 + - + +
58F MET* 4.4 2.0 - - - -
59F LEU* 3.0 31.3 + - + +
60F VAL 4.5 0.9 - - - -
61F LYS* 4.1 16.4 - - + -
68F HIS* 3.6 34.8 - - + +
322F GLY 5.8 0.2 - - - +
332F GLU* 5.1 1.2 - - - +
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Residues in contact with LYS 47 (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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46F ILE* 1.3 91.2 - - + +
48F THR* 1.3 70.8 + - - +
49F LEU* 3.6 0.4 + - - +
58F MET* 3.4 13.7 - - - +
59F LEU* 2.6 39.6 + - + +
324F THR* 3.3 35.2 + - + +
327F PHE* 5.0 0.4 + - - +
328F ASP 4.4 3.0 + - - -
329F ASP* 2.6 39.0 + - - +
330F TYR 5.3 0.4 - - - +
332F GLU* 4.1 12.1 - - - +
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Residues in contact with THR 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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47F LYS* 1.3 82.9 + - - +
49F LEU* 1.3 64.0 + - - +
50F GLY 3.3 26.9 - - - +
51F THR* 5.2 0.2 - - - -
56F ARG* 3.2 32.3 + - - +
57F VAL 3.6 6.7 - - - +
58F MET* 4.0 7.0 - - - +
327F PHE* 5.8 0.2 - - - +
328F ASP 4.2 5.0 - - - +
330F TYR* 3.7 32.6 + - + -
332F GLU* 3.1 31.4 + - - +
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Residues in contact with LEU 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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47F LYS* 3.6 1.3 + - + +
48F THR* 1.3 75.8 - - - +
50F GLY* 1.3 57.1 + - - +
57F VAL* 2.8 10.3 + - + +
58F MET 3.9 5.8 - - - +
59F LEU* 3.6 29.8 - - + +
70F ALA* 4.4 6.3 - - + -
122F TYR* 3.5 38.4 - - + +
324F THR* 3.8 30.5 - - + -
327F PHE* 3.9 31.3 - - + +
328F ASP 5.1 0.2 + - - -
330F TYR* 3.3 16.1 + - - -
351F G96 3.5 29.8 - - + +
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Residues in contact with GLY 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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48F THR* 3.3 12.6 - - - +
49F LEU* 1.3 80.9 - - - +
51F THR* 1.3 60.1 + - - -
56F ARG* 3.5 1.6 - - - +
57F VAL* 2.9 33.5 + - - +
330F TYR* 3.8 12.6 - - - -
351F G96 3.9 12.2 - - - +
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Residues in contact with THR 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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48F THR* 5.2 1.3 - - - -
50F GLY* 1.3 73.9 - - - -
52F GLY* 1.3 64.9 + - - +
55F GLY 4.1 7.4 + - - -
56F ARG* 4.3 15.0 + - - +
330F TYR* 4.0 31.4 + - + +
351F G96 4.1 15.1 - - - +
18L ARG* 5.5 5.2 + - - -
20L ASN* 5.5 2.9 - - - +
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Residues in contact with GLY 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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51F THR* 1.3 80.7 + - - +
53F SER* 1.3 66.0 + - - -
54F PHE 3.3 2.7 - - - -
55F GLY 3.0 21.9 + - - +
351F G96 3.7 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