Contacts of the strand formed by residues 96 - 102 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D PHE* 5.8 1.8 - - + -
23D LYS 3.1 16.3 + - - +
24D LEU* 4.3 13.5 - - + -
25D VAL* 3.4 18.0 + - - +
72D PHE* 5.9 1.1 - - + -
94D ALA* 3.2 4.9 - - - +
95D GLN* 1.3 81.8 - - + +
97D ALA* 1.3 65.5 + - - +
127D ILE* 4.4 2.9 - - - +
128D VAL* 3.3 9.4 - - + +
178D ILE* 3.6 31.6 - - + -
182D LEU* 4.7 6.5 - - + -
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Residues in contact with ALA 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D VAL* 3.3 22.2 - - + +
27D LEU* 5.9 0.7 - - + -
96D ALA* 1.3 77.7 - - - +
98D ILE* 1.3 70.4 + - - +
99D VAL 4.1 0.2 - - - -
119D LEU* 4.0 26.7 - - + -
127D ILE* 4.3 10.1 - - + -
128D VAL 2.8 11.4 + - - +
129D ILE* 4.5 5.6 - - + -
130D ALA* 3.1 24.5 + - - +
178D ILE* 4.2 1.9 - - - +
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Residues in contact with ILE 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D LEU* 3.7 15.5 - - + -
25D VAL 2.8 12.0 + - - +
26D LEU* 3.5 12.2 - - + -
27D LEU* 3.0 27.0 + - - +
37D LEU* 5.4 2.5 - - + -
97D ALA* 1.3 81.3 - - - +
99D VAL* 1.3 61.8 + - - +
100D VAL* 3.4 21.0 + - + +
130D ALA* 3.7 6.5 - - + +
132D ALA* 3.9 20.4 - - + -
174D ILE* 4.7 11.9 - - + -
175D PHE* 3.6 39.3 - - + -
178D ILE* 3.8 18.4 - - + -
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Residues in contact with VAL 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D LEU* 3.5 9.4 - - + +
97D ALA 4.1 0.2 - - - -
98D ILE* 1.3 69.2 - - - +
100D VAL* 1.3 63.2 + - - +
112D ALA* 3.4 42.0 - - + +
115D TRP* 4.0 16.6 - - + -
116D VAL* 3.7 23.1 - - + -
119D LEU* 3.9 25.6 - - + -
129D ILE* 4.0 7.4 - - + -
130D ALA 2.9 13.3 + - - +
131D LEU* 3.7 8.2 - - + +
132D ALA 3.0 23.4 + - - +
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Residues in contact with VAL 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D LEU* 4.6 6.1 - - + -
27D LEU 2.8 13.9 + - - +
28D GLY* 3.6 18.2 - - - -
29D GLU 4.3 4.2 + - - -
32D VAL* 3.7 18.2 - - + +
34D LYS* 3.8 22.0 - - + +
37D LEU* 4.0 25.8 - - + -
98D ILE* 3.5 29.4 - - + +
99D VAL* 1.3 77.4 - - - +
101D TYR* 1.3 65.9 + - - +
108D THR* 5.0 2.4 - - - +
112D ALA* 5.0 1.2 - - - +
132D ALA* 3.4 10.5 - - + +
134D ASN* 4.1 14.6 - - + -
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Residues in contact with TYR 101 (chain D).
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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32D VAL* 4.1 8.3 - - - -
100D VAL* 1.3 76.2 - - - +
102D ASP* 1.3 72.8 + - - +
103D ILE* 4.3 13.3 - - + +
108D THR* 3.5 29.2 - - - +
109D PHE* 4.3 20.4 - + + -
112D ALA* 4.3 5.2 - - + -
131D LEU* 3.7 36.1 - - + -
132D ALA 2.8 28.9 + - - -
133D GLY* 3.3 17.5 - - - -
134D ASN* 2.8 26.5 + - - +
142D ARG* 5.9 0.5 + - - -
144D VAL* 4.2 22.3 + - + +
145D GLU 5.0 0.7 + - - -
149D ALA* 3.5 10.6 - - - +
160D PHE* 3.1 24.1 - + - -
162D GLU* 5.4 0.9 + - - -
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Residues in contact with ASP 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ALA 3.8 2.8 - - - +
32D VAL* 3.8 13.9 - - + +
101D TYR* 1.3 78.8 - - - +
103D ILE* 1.3 68.7 + - - +
104D THR* 2.9 30.2 + - - +
105D ASN* 2.9 17.1 - - + +
108D THR* 2.8 37.0 + - + -
134D ASN 4.1 3.1 - - - -
135D LYS* 3.2 48.5 + - - +
144D VAL* 5.2 0.2 - - - +
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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