Contacts of the strand formed by residues 20 - 28 (chain F) in PDB entry 4KYI
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 CYS 20 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F ILE* 1.3 84.0 - - - +
21F GLN* 1.3 65.7 + - - +
22F PHE* 3.4 36.0 - - + -
68F THR* 5.0 10.5 - - - -
69F THR 3.4 8.2 + - - -
70F VAL* 3.8 7.7 - - + +
71F LYS* 3.1 21.2 + - - +
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Residues in contact with GLN 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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468E SER* 4.1 15.2 + - - +
469E SER* 3.5 29.6 + - - -
472E ASN* 3.9 13.9 - - + +
473E TYR* 4.6 2.6 + - - -
19F ILE* 4.3 11.6 + - + +
20F CYS* 1.3 70.5 - - - +
22F PHE* 1.3 72.3 + - - +
71F LYS* 3.4 42.3 - - - +
73F GLU* 3.7 24.0 - - - +
95F GLN* 4.7 6.4 + - - -
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Residues in contact with PHE 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 CYS* 3.4 42.8 - - + -
21F GLN* 1.3 83.0 + - - +
23F LYS* 1.3 55.8 + - - +
70F VAL* 3.7 23.3 - - + -
71F LYS 2.9 9.1 + - - -
72F PHE* 3.4 23.6 - + + -
73F GLU* 2.7 36.1 + - - +
95F GLN* 3.9 25.8 - - + -
96F ALA* 6.2 0.7 - - + -
179F ALA 5.5 0.4 - - - -
182F LEU* 3.5 47.1 - - + -
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Residues in contact with LYS 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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476E GLN* 4.4 19.4 + - - +
22F PHE* 1.3 72.9 - - - +
24F LEU* 1.3 61.6 + - - +
73F GLU* 3.6 17.2 - - - +
75F TRP* 3.9 29.8 - - + +
89F MET 3.8 15.4 + - - -
90F TYR* 3.1 28.0 + - - +
92F ARG* 4.4 1.0 - - - +
93F GLY* 3.7 35.0 - - - +
94F ALA* 3.5 6.6 - - + +
95F GLN* 2.9 43.8 + - - +
96F ALA* 3.3 7.3 + - - +
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Residues in contact with LEU 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 PHE 3.8 0.4 + - - -
23F LYS* 1.3 75.1 - - - +
25F VAL* 1.3 62.6 + - - +
26F LEU* 3.7 21.5 - - + -
72F PHE* 4.5 21.3 - - + -
73F GLU 2.8 17.2 + - - +
74F ILE* 3.4 9.6 - - + -
75F TRP* 2.8 27.8 + - - +
96F ALA* 3.6 28.9 - - + +
98F ILE* 4.0 13.5 - - + -
175F PHE* 3.7 31.0 - - + -
178F ILE* 3.8 26.5 - - + -
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Residues in contact with VAL 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 LEU* 1.3 77.5 - - - +
26F LEU* 1.3 69.3 + - - +
27F LEU* 3.8 15.1 + - + +
75F TRP* 3.8 6.5 - - + +
77F THR* 3.7 25.8 - - + -
90F TYR* 3.6 26.7 - - + +
91F TYR* 3.7 24.0 - - + +
94F ALA* 4.0 4.0 - - + -
96F ALA 3.4 14.6 + - - +
97F ALA* 3.3 11.0 - - + +
98F ILE 2.8 26.0 + - - +
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Residues in contact with LEU 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 LEU* 3.7 17.5 - - + -
25F VAL* 1.3 75.4 - - - +
27F LEU* 1.3 58.7 + - - +
34F LYS* 3.5 50.5 - - + +
37F LEU* 4.8 7.6 - - + -
38F VAL* 3.6 12.1 - - + -
74F ILE* 3.7 29.8 - - + -
75F TRP 3.3 9.6 + - - +
76F ASP* 4.5 6.1 - - - +
77F THR* 2.3 33.1 + - - +
98F ILE* 3.3 19.3 - - + +
100F VAL* 4.7 7.6 - - + -
175F PHE* 5.2 4.3 - - + -
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Residues in contact with LEU 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 VAL* 3.8 22.4 - - + +
26F LEU* 1.3 84.1 - - - +
28F GLY* 1.3 53.6 + - - +
34F LYS* 3.7 5.4 - - - +
77F THR* 3.7 14.6 - - + +
87F ALA* 4.8 5.6 - - + -
90F TYR* 5.5 0.2 - - + -
91F TYR* 4.1 14.1 - - + -
97F ALA* 5.3 1.3 - - + -
98F ILE 3.0 6.7 + - - +
99F VAL* 3.2 12.7 - - + -
100F VAL* 2.7 34.7 + - - +
115F TRP* 3.6 46.0 - - + -
119F LEU* 4.0 35.4 - - + -
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Residues in contact with GLY 28 (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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27F LEU* 1.3 76.7 - - - +
29F GLU* 1.3 63.9 + - - -
34F LYS* 2.4 25.3 + - - +
79F GLY* 3.2 10.4 - - - +
99F VAL* 4.9 1.3 - - - -
100F VAL 3.7 12.3 - - - -
108F THR 6.2 0.2 - - - -
111F ARG* 5.4 0.2 - - - -
112F ALA* 6.0 0.4 - - - -
115F TRP* 3.7 30.4 + - - +
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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