Contacts of the strand formed by residues 16 - 22 (chain B) in PDB entry 2I6A
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 16 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B ASN* 3.1 9.5 + - + +
15B PRO* 1.3 73.7 - - - +
17B LEU* 1.3 56.0 + - - +
63B GLY 2.8 35.1 + - - +
64B GLY* 4.2 6.7 - - - +
99B LEU* 3.5 10.0 - - - +
121B GLY* 3.4 31.0 - - - +
122B THR* 3.8 6.3 - - - +
123B CYS* 4.2 10.3 - - + +
136B ALA* 4.2 9.2 - - + -
137B ASN 4.4 0.2 - - - +
138B LEU* 3.6 29.6 - - + -
141B ALA* 3.8 13.0 - - + -
500B 5I5 3.7 45.5 - - + +
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Residues in contact with LEU 17 (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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16B LEU* 1.3 72.4 - - - +
18B ASP* 1.3 66.9 + - - +
19B ILE* 3.6 3.9 + - + +
60B TYR* 3.6 33.9 - - + -
61B HIS 3.7 25.4 - - - +
62B ALA 3.8 4.0 - - - +
95B PHE* 3.7 41.3 - - + +
98B ILE* 4.0 20.9 - - + -
99B LEU* 4.0 17.7 - - + +
121B GLY 3.1 11.1 + - - +
122B THR* 3.5 12.3 - - + +
123B CYS 3.4 16.2 + - - -
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Residues in contact with ASP 18 (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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16B LEU* 4.7 0.7 - - - +
17B LEU* 1.3 72.3 - - - +
19B ILE* 1.3 62.3 - - - +
20B SER 4.0 0.6 + - - +
59B GLU 3.3 6.8 - - - +
60B TYR* 3.4 3.1 - - - -
61B HIS* 2.8 31.3 + - - +
63B GLY* 3.3 7.3 - - - -
123B CYS* 3.4 14.9 - - - +
125B ALA* 5.6 4.3 - - + -
134B LEU* 6.2 2.7 - - - -
332B ARG* 2.8 41.7 + - - +
500B 5I5 2.6 47.8 + - - -
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Residues in contact with ILE 19 (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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17B LEU* 3.7 10.1 - - + +
18B ASP* 1.3 77.4 - - - +
20B SER* 1.3 59.1 + - - +
49B PHE* 5.4 7.9 - - + -
52B LEU* 3.7 19.1 - - + +
53B VAL* 4.6 10.8 - - + -
58B VAL* 3.0 34.3 - - + -
59B GLU 3.5 0.9 - - - -
60B TYR* 3.6 33.7 - - + -
95B PHE* 4.5 7.9 - - + -
122B THR* 3.8 26.5 - - + -
123B CYS 2.8 11.5 + - - +
124B ALA* 3.3 6.3 - - + -
125B ALA* 2.9 21.7 + - - +
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Residues in contact with SER 20 (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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18B ASP 4.0 0.4 - - - -
19B ILE* 1.3 73.5 - - - +
21B ALA* 1.3 62.7 + - - +
57B LYS 4.1 0.5 - - - +
58B VAL* 2.9 4.6 - - - +
59B GLU* 2.8 45.6 + - - +
61B HIS* 4.8 6.6 - - - -
125B ALA* 3.4 25.1 - - - -
127B ILE* 4.5 9.2 - - - -
132B ARG* 5.0 4.0 - - - -
332B ARG* 5.2 8.7 - - - -
334B THR* 4.4 11.4 + - - -
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Residues in contact with ALA 21 (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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20B SER* 1.3 77.0 - - - +
22B VAL* 1.3 64.4 + - - +
23B VAL* 3.8 0.5 + - - +
52B LEU* 3.6 25.2 - - + +
56B PHE* 3.8 21.1 - - + -
57B LYS 4.0 7.4 - - - +
58B VAL* 3.9 12.6 - - - -
125B ALA 3.4 4.0 + - - +
126B CYS* 4.0 1.7 - - - -
127B ILE* 2.9 30.6 + - - +
334B THR* 5.8 1.8 - - - -
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Residues in contact with VAL 22 (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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21B ALA* 1.3 73.8 - - - +
23B VAL* 1.3 70.3 + - - +
56B PHE* 3.1 21.7 - - - +
57B LYS 4.8 3.1 + - - +
127B ILE* 3.2 27.4 - - + +
128B THR* 5.1 3.4 - - - -
129B GLY 5.4 2.7 - - - +
334B THR* 4.9 17.7 - - + +
289C GLN* 6.1 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