Contacts of the strand formed by residues 45 - 51 (chain F) in PDB entry 3KYM
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 LEU 45 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36E TYR* 6.2 1.3 - - + -
38E GLN* 5.0 0.9 - - - +
44E PRO* 4.9 8.3 - - + -
87E TYR* 3.8 37.2 - - + -
98E PHE* 3.0 50.1 + - + +
99E GLY 4.9 2.0 + - - -
37F VAL* 3.6 18.4 - - + -
38F ARG 3.5 17.7 - - - +
39F GLN* 3.8 24.1 - - + +
43F LYS 3.7 1.8 + - - -
44F GLY* 1.3 71.4 - - - -
46F GLU* 1.3 57.5 - - - +
95F TYR* 4.0 15.7 - - + -
109F TRP* 4.3 20.0 - - + -
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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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98E PHE* 4.4 1.3 - - - -
37F VAL* 4.0 3.8 - - - -
38F ARG* 2.9 76.3 + - + +
40F ALA* 4.8 11.0 + - - +
43F LYS* 6.0 0.5 - - - +
44F GLY 3.4 14.6 + - - +
45F LEU* 1.3 74.7 - - - +
47F TRP* 1.3 66.8 + - - +
48F VAL* 3.9 1.5 - - + +
63F SER* 5.4 2.8 + - - -
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Residues in contact with TRP 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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94E TRP* 3.2 47.8 - + - -
95E PRO* 2.9 32.5 - - + -
96E LEU* 4.1 26.4 + - + +
98E PHE* 4.5 12.8 - - + -
35F PHE* 3.4 34.7 - + + -
36F TRP 4.0 4.9 - - - +
37F VAL* 4.4 5.8 - - + +
46F GLU* 1.3 79.7 - - - +
48F VAL* 1.3 70.2 + - - +
49F SER 3.3 24.3 - - - +
50F TRP* 4.1 2.6 - - - +
59F LYS* 5.0 0.9 - - + -
60F TYR* 3.7 3.4 - - - -
61F ALA* 3.6 44.4 - - + +
64F VAL* 5.5 0.2 - - - +
106F PHE* 5.0 6.5 - - + -
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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* 2.8 27.4 + - + +
37F VAL 4.3 0.4 - - - -
38F ARG* 3.7 48.0 - - + +
46F GLU* 3.9 2.2 - - + +
47F TRP* 1.3 82.5 - - - +
49F SER* 1.3 66.2 + - - +
60F TYR* 4.0 0.7 - - - -
61F ALA 3.4 21.0 + - - -
64F VAL* 3.8 18.2 - - + +
68F PHE* 3.9 29.8 - - + -
81F LEU* 4.3 7.6 - - + -
94F TYR* 4.2 4.0 - - + -
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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 PHE* 3.2 10.2 - - - -
36F TRP* 2.9 26.5 + - - -
47F TRP* 3.3 7.0 - - - +
48F VAL* 1.3 83.5 - - - +
50F TRP* 1.3 58.7 + - - +
59F LYS 3.7 5.8 - - - -
60F TYR* 3.4 12.4 - - - -
70F ILE* 2.8 41.3 - - - +
81F LEU* 3.9 23.1 - - - -
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Residues in contact with TRP 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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104B TRP* 5.7 11.0 - + - -
94E TRP* 5.8 2.7 - + + -
33F PRO* 3.6 13.0 - - + +
34F MET 3.6 8.1 - - - -
35F PHE* 3.4 42.6 - + + -
47F TRP* 4.2 5.4 - - + +
49F SER* 1.3 78.8 + - - +
51F ILE* 1.3 75.3 + - - +
52F GLY* 4.0 12.3 - - - -
57F ILE* 3.7 41.1 - - + -
58F THR* 3.4 2.6 - - - -
59F LYS* 2.9 59.1 + - + +
70F ILE* 3.8 4.9 - - - +
99F GLU* 3.2 19.8 + - - -
104F TRP* 4.1 19.5 - + - +
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Residues in contact with ILE 51 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33F PRO* 3.3 22.2 - - - +
34F MET 3.2 16.0 + - - +
50F TRP* 1.3 84.9 - - - +
52F GLY* 1.3 68.7 + - - +
55F GLY* 3.8 21.3 - - - +
57F ILE 3.5 10.5 - - - +
58F THR* 3.7 13.0 - - + -
70F ILE* 3.4 42.8 - - + +
71F SER* 4.2 4.3 - - - -
72F ARG* 3.3 34.5 - - + +
79F LEU* 4.2 7.0 - - + -
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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