Contacts of the strand formed by residues 22 - 27 (chain B) in PDB entry 1LI5
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 GLU 22 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PRO* 3.1 25.6 - - - +
19B HIS* 2.9 30.6 + - + +
20B ALA 3.6 10.0 - - - +
21B GLY* 1.3 85.7 - - - +
23B VAL* 1.3 65.5 + - - +
59B TYR* 4.0 0.6 - - - -
60B LYS* 3.2 37.1 + - + +
222B ASP* 3.9 3.1 - - - +
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Residues in contact with VAL 23 (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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15B PHE* 3.8 25.1 - - + -
22B GLU* 1.3 82.8 - - - +
24B GLY* 1.3 69.5 + - - +
25B MET* 4.5 1.6 - - + +
54B LEU* 4.1 16.6 - - + -
59B TYR* 3.5 33.0 - - + -
60B LYS 2.9 8.4 + - - +
61B LEU* 3.5 23.0 - - + +
62B LYS* 3.0 28.8 + - - +
222B ASP* 3.3 9.2 - - + +
223B ILE* 4.4 6.3 - - + -
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Residues in contact with GLY 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B VAL* 1.3 74.4 - - - +
25B MET* 1.3 59.9 + - - +
62B LYS* 3.7 6.3 - - - -
217B LEU* 4.2 17.9 - - - -
221B PHE* 3.9 7.9 - - - -
222B ASP* 2.8 22.7 + - - +
223B ILE 3.1 23.4 + - - +
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Residues in contact with MET 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B VAL* 4.1 2.2 - - + -
24B GLY* 1.3 75.5 - - - +
26B TYR* 1.3 64.3 + - - +
27B VAL* 4.2 6.7 - - + -
47B PHE* 3.9 20.0 - - - +
50B VAL* 3.7 19.5 - - + -
51B ALA* 3.8 31.2 - - + +
54B LEU* 4.8 3.1 - - + -
61B LEU* 4.0 15.7 - - + -
62B LYS 3.0 7.9 + - - +
63B TYR* 3.7 28.0 - - + -
64B VAL 2.8 26.6 + - - -
217B LEU* 3.5 9.6 - - - +
223B ILE* 3.2 35.9 - - + -
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Residues in contact with TYR 26 (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 MET* 1.3 76.4 - - - +
27B VAL* 1.3 72.7 + - - +
28B CYS 4.2 0.9 - - - -
64B VAL* 3.0 38.8 - - + -
66B ASN* 3.1 39.3 - - + +
112B PRO* 5.0 2.7 - - + -
209B CYS* 3.1 30.3 - - - -
212B MET* 4.5 2.3 - - + +
213B ASN* 3.3 43.3 - - + -
217B LEU* 3.7 4.5 - - + -
221B PHE* 3.6 20.6 - - + -
223B ILE 3.0 6.9 + - - -
224B HIS* 3.1 28.1 - + - -
225B GLY 2.9 22.2 + - - -
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Residues in contact with VAL 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B MET* 4.2 6.5 - - + -
26B TYR* 1.3 85.0 - - - +
28B CYS* 1.3 74.8 + - - +
29B GLY 3.4 0.9 + - - -
43B THR* 4.9 0.2 - - + -
44B PHE* 4.0 15.0 - - + -
47B PHE* 3.7 44.6 - - + -
63B TYR* 3.6 29.2 - - + +
64B VAL 3.0 6.3 + - - -
65B ARG* 3.2 23.1 - - + +
66B ASN* 3.6 2.9 + - - +
225B GLY 3.7 15.0 - - - +
226B GLY* 4.1 4.0 - - - +
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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