Contacts of the strand formed by residues 96 - 102 (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 ALA 96 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22F PHE* 6.2 0.2 - - + -
23F LYS 3.3 6.1 + - - +
24F LEU* 3.7 16.8 - - + -
25F VAL 3.4 10.7 + - - -
72F PHE* 5.5 1.3 - - + -
94F ALA* 3.2 18.2 - - - +
95F GLN* 1.3 83.5 - - + +
97F ALA* 1.3 64.6 + - - +
127F ILE* 3.8 6.7 - - - +
128F VAL* 3.4 9.6 - - + +
178F ILE* 3.6 31.9 - - + -
182F LEU* 4.7 5.2 - - + -
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Residues in contact with ALA 97 (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* 4.6 0.6 - - - +
25F VAL* 3.3 23.8 - - + +
27F LEU* 5.3 2.0 - - + -
96F ALA* 1.3 79.4 - - - +
98F ILE* 1.3 66.8 - - - +
99F VAL 4.0 0.4 - - - -
119F LEU* 4.1 26.9 - - + -
127F ILE* 4.3 11.7 - - + -
128F VAL 3.1 7.1 + - - +
129F ILE* 4.6 4.0 - - - -
130F ALA* 2.8 28.1 + - - +
178F ILE* 4.6 0.7 - - - +
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Residues in contact with ILE 98 (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* 4.0 10.1 - - + -
25F VAL 2.8 11.7 + - - +
26F LEU* 3.3 14.3 - - + -
27F LEU 3.0 23.3 + - - +
37F LEU* 5.3 4.3 - - + -
97F ALA* 1.3 76.8 - - - +
99F VAL* 1.3 62.1 + - - +
100F VAL* 3.6 20.5 + - + +
130F ALA* 4.1 6.7 - - + +
132F ALA* 4.4 14.8 - - + -
174F ILE* 4.7 17.0 - - + -
175F PHE* 3.6 39.3 - - + -
178F ILE* 3.7 25.4 - - + -
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Residues in contact with VAL 99 (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* 3.2 15.9 - - + +
28F GLY* 4.9 0.2 - - - -
97F ALA* 5.3 0.2 - - + -
98F ILE* 1.3 71.5 - - - +
100F VAL* 1.3 63.1 + - - +
112F ALA* 3.6 40.4 - - + +
115F TRP* 4.1 14.4 - - + -
116F VAL* 4.2 13.2 - - + -
119F LEU* 3.7 30.3 - - + -
129F ILE* 4.3 7.0 - - + -
130F ALA 3.3 10.2 + - - +
131F LEU* 3.3 12.3 - - + +
132F ALA* 3.0 24.1 + - - +
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Residues in contact with VAL 100 (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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26F LEU* 4.7 4.7 - - + -
27F LEU 2.7 13.3 + - - +
28F GLY* 3.7 18.0 - - - -
29F GLU 4.3 1.0 + - - -
32F VAL* 3.6 44.9 - - + +
33F GLY 4.2 4.9 - - - +
34F LYS* 4.3 12.3 - - + -
37F LEU* 4.1 14.1 - - + -
98F ILE* 3.9 24.0 - - + +
99F VAL* 1.3 78.3 - - - +
101F TYR* 1.3 63.5 + - - +
108F THR 4.8 2.3 - - - +
112F ALA* 5.1 0.5 - - - +
132F ALA* 3.6 9.6 - - + +
134F ASN* 3.9 17.0 - - + -
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Residues in contact with TYR 101 (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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32F VAL* 4.5 0.9 - - - -
99F VAL 4.0 0.2 + - - -
100F VAL* 1.3 76.9 - - - +
102F ASP* 1.3 82.9 + - - +
103F ILE* 4.1 9.6 - - + +
108F THR* 3.5 24.2 - - - +
109F PHE* 3.6 37.0 - + + -
112F ALA* 4.0 5.8 - - + -
131F LEU* 3.8 15.5 - - + -
132F ALA 2.8 32.5 + - - +
133F GLY* 3.4 27.1 - - - -
134F ASN* 3.0 15.8 + - - -
142F ARG* 5.7 0.3 + - - -
144F VAL* 3.7 28.8 + - + +
145F GLU 4.9 0.9 + - - -
146F PHE* 5.7 0.2 - - - -
149F ALA* 3.6 16.4 - - + +
160F PHE* 3.8 19.4 - + - -
162F GLU* 4.9 4.9 + - - +
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Residues in contact with ASP 102 (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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31F ALA 5.0 1.6 - - - +
32F VAL* 4.0 22.4 - - + +
101F TYR* 1.3 83.2 - - - +
103F ILE* 1.3 73.8 + - - +
104F THR* 2.2 36.7 + - - -
105F ASN* 2.9 26.4 + - + +
108F THR* 2.9 19.2 + - + +
134F ASN* 4.3 3.8 - - - +
135F LYS* 3.2 39.5 + - + +
144F VAL* 4.5 0.7 - - - +
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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