Contacts of the strand formed by residues 96 - 102 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B PHE* 6.3 0.7 - - + -
23B LYS 3.4 4.5 + - - +
24B LEU* 3.7 19.7 - - + -
25B VAL* 3.4 27.2 + - - +
72B PHE* 5.5 0.2 - - + -
94B ALA* 3.3 5.3 - - - +
95B GLN* 1.3 83.3 - - + +
97B ALA* 1.3 61.4 + - - +
127B ILE* 3.6 5.1 - - - +
128B VAL 3.6 6.3 - - - +
178B ILE* 3.6 30.7 - - + -
182B LEU* 4.8 6.5 - - + -
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Residues in contact with ALA 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B VAL* 3.3 19.3 - - + +
27B LEU* 4.9 3.6 - - + -
96B ALA* 1.3 78.0 - - - +
98B ILE* 1.3 58.8 + - - +
99B VAL 3.8 0.4 + - - -
119B LEU* 3.7 25.8 - - + -
127B ILE* 3.7 19.2 - - + +
128B VAL 3.4 6.2 + - - -
129B ILE* 3.5 3.6 - - - +
130B ALA* 2.7 35.3 + - - +
178B ILE* 5.5 0.2 - - - -
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Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LEU* 3.8 19.1 - - + -
25B VAL 3.0 7.7 + - - -
26B LEU* 3.4 14.3 - - + -
27B LEU* 2.8 28.2 + - - +
37B LEU* 5.4 2.5 - - + -
97B ALA* 1.3 72.2 - - - +
99B VAL* 1.3 61.8 + - - +
100B VAL* 3.6 21.8 + - + +
130B ALA* 3.8 4.9 - - + +
132B ALA* 4.3 6.3 - - + -
174B ILE* 4.2 24.0 - - + -
175B PHE* 3.6 44.4 - - + -
178B ILE* 4.0 20.2 - - + -
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LEU* 3.7 9.4 - - + +
28B GLY* 4.9 0.9 - - - -
97B ALA 4.6 0.7 - - - +
98B ILE* 1.3 72.5 - - - +
100B VAL* 1.3 60.2 + - - +
112B ALA* 3.6 40.4 - - + +
115B TRP* 3.9 18.6 - - + -
116B VAL* 3.9 17.3 - - + -
119B LEU* 3.9 28.5 - - + -
129B ILE* 4.3 2.5 - - + -
130B ALA 3.0 16.5 + - - +
131B LEU* 3.4 10.2 - - + +
132B ALA 3.0 23.6 + - - -
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Residues in contact with VAL 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LEU* 4.4 4.3 - - + -
27B LEU 2.9 10.1 + - - +
28B GLY* 3.5 18.9 - - - -
29B GLU 4.2 1.0 + - - -
32B VAL* 3.6 26.0 - - + +
34B LYS* 3.9 18.8 - - + +
37B LEU* 4.0 21.1 - - + -
98B ILE* 3.7 29.6 - - + +
99B VAL* 1.3 74.2 - - - +
101B TYR* 1.3 64.2 + - - +
108B THR 5.1 0.3 - - - +
112B ALA* 5.1 1.4 - - - +
132B ALA* 3.6 7.9 - - + +
134B ASN* 3.8 27.6 - - + -
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Residues in contact with TYR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B VAL* 4.1 10.2 - - - +
100B VAL* 1.3 75.1 - - - +
102B ASP* 1.3 84.9 + - - +
103B ILE* 4.0 7.4 - - + +
108B THR* 3.5 23.8 - - - +
109B PHE* 3.5 41.7 - + + -
112B ALA* 4.1 4.7 - - + -
131B LEU* 3.7 23.1 - - + -
132B ALA 3.0 30.6 + - - -
133B GLY* 3.5 16.5 - - - -
134B ASN* 3.0 30.1 + - - +
144B VAL* 4.0 14.4 - - + +
145B GLU 5.9 0.2 - - - -
146B PHE* 5.8 0.7 - - - -
149B ALA* 3.2 22.9 - - - +
160B PHE* 3.6 11.5 - + - -
162B GLU* 5.5 0.9 + - - -
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Residues in contact with ASP 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ALA 4.3 3.2 - - - +
32B VAL* 4.2 10.1 - - + +
101B TYR* 1.3 84.2 - - - +
103B ILE* 1.3 69.0 + - - +
104B THR* 2.7 32.3 + - - -
105B ASN* 2.8 33.7 - - + +
108B THR* 2.9 23.8 + - + +
134B ASN 3.9 2.2 - - - -
135B LYS* 3.2 42.5 + - + +
144B VAL* 3.5 1.6 - - - +
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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