Contacts of the strand formed by residues 45 - 51 (chain F) in PDB entry 4KRM
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 ARG 45 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37F PHE* 4.1 18.0 - - + -
38F ARG 3.7 7.4 - - - +
39F GLN* 3.8 24.7 + - + +
44F GLU* 1.3 76.4 - - - +
46F GLU* 1.3 58.9 + - - +
95F TYR* 3.4 48.1 + - + -
108F LEU* 3.6 30.6 - - + +
114F TRP* 3.5 50.1 - - - +
115F GLY 5.5 0.2 + - - -
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Residues in contact with GLU 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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37F PHE* 3.2 8.3 - - - -
38F ARG* 2.7 86.8 + - + +
40F ALA* 6.0 3.7 - - - +
43F LYS* 5.2 8.0 - - - +
44F GLU 3.4 7.8 + - - +
45F ARG* 1.3 74.4 - - - +
47F PHE* 1.3 67.5 + - - +
48F VAL* 4.1 0.2 - - - +
63F SER* 4.7 3.1 + - - -
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Residues in contact with PHE 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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36F TRP 4.1 0.9 - - - -
37F PHE* 3.5 25.8 - + + -
45F ARG 4.4 0.2 + - - -
46F GLU* 1.3 82.2 - - - +
48F VAL* 1.3 74.6 + - - +
49F SER* 3.2 36.8 - - - -
50F GLY* 3.4 7.6 - - - -
59F GLY 4.1 2.5 - - - -
60F TYR 4.0 6.7 - - - -
61F ALA* 3.3 34.5 - - + +
104F TRP* 3.9 18.2 - + - -
105F TYR 3.5 25.4 - - - -
106F GLY* 3.2 27.4 - - - +
111F TYR* 4.4 1.6 - - - -
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Residues in contact with VAL 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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36F TRP* 2.9 22.2 + - + +
37F PHE 3.8 3.4 - - - -
38F ARG* 3.7 45.5 - - + +
47F PHE* 1.3 79.0 - - - +
49F SER* 1.3 61.6 + - - +
60F TYR* 3.4 2.3 - - - -
61F ALA* 2.8 32.9 + - - +
64F VAL* 3.8 9.4 - - + +
68F PHE* 3.7 34.1 - - + -
81F LEU* 4.1 15.3 - - + -
94F TYR* 4.1 5.6 - - + -
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Residues in contact with SER 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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35F GLY* 3.3 0.2 - - - -
36F TRP* 2.7 29.5 + - - +
47F PHE* 3.2 14.5 - - - -
48F VAL* 1.3 84.2 - - - +
50F GLY* 1.3 59.3 + - - +
59F GLY 2.9 15.5 + - - -
60F TYR* 3.6 14.0 - - - -
70F ILE* 3.1 29.6 - - - +
81F LEU* 4.2 19.3 - - - -
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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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34F MET 3.4 9.0 - - - -
35F GLY* 4.0 1.3 - - - -
47F PHE* 3.4 10.6 - - - -
49F SER* 1.3 76.9 + - - +
51F ILE* 1.3 62.1 + - - +
58F THR* 3.3 5.5 - - - -
59F GLY 3.0 27.5 + - - +
70F ILE* 3.6 6.1 - - - +
104F TRP* 3.7 19.3 - - - -
111F TYR* 4.7 0.2 - - - -
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Residues in contact with ILE 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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33F GLY* 3.5 2.3 - - - -
34F MET* 2.7 53.5 + - + +
50F GLY* 1.3 75.8 - - - +
52F SER* 1.3 72.5 + - - +
55F GLY* 3.8 18.6 - - - +
57F SER 3.5 9.2 - - - +
58F THR* 3.9 15.5 - - + -
70F ILE* 3.5 17.3 - - + +
71F SER* 3.9 20.2 - - - +
72F ARG* 3.5 31.4 - - + +
79F VAL* 4.1 8.5 - - + -
104F TRP* 3.4 8.2 - - - +
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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