Contacts of the strand formed by residues 186 - 191 (chain B) in PDB entry 1L4W
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 HIS 186 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ALA* 2.0 24.4 + - - +
8A THR 3.7 0.3 - - - +
184B TRP* 3.0 37.4 - + + -
185B LYS* 1.3 69.7 - - - +
187B TRP* 1.3 72.2 + - - +
188B VAL* 4.1 6.1 - - + -
200B ASP* 2.2 66.0 + - + +
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Residues in contact with TRP 187 (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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6A THR* 2.9 33.8 + - - +
7A ALA* 2.9 24.0 - - - +
8A THR 2.5 30.3 + - - -
9A SER 2.6 21.5 + - - -
10A PRO* 2.7 18.4 + - + -
40A VAL 5.5 0.2 - - - +
186B HIS* 1.3 77.4 + - - +
188B VAL* 1.3 76.0 + - - +
189B TYR* 2.9 59.0 - + - -
197B PRO* 3.5 18.6 - - + -
198B TYR 2.8 35.9 - - - -
199B LEU* 3.6 14.8 - - + -
200B ASP 4.3 0.4 - - - +
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Residues in contact with VAL 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TRP* 6.1 0.4 - - + -
30A ASP* 5.8 0.7 - - - +
39A VAL* 4.0 20.2 - - + -
40A VAL 4.6 2.7 - - - -
186B HIS* 4.1 7.9 - - + -
187B TRP* 1.3 85.8 - - - +
189B TYR* 1.3 58.2 + - - +
190B TYR* 3.0 40.3 - - + +
198B TYR* 2.9 43.0 + - + +
200B ASP* 3.5 21.1 - - - +
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Residues in contact with TYR 189 (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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6A THR* 3.4 24.5 - - + -
10A PRO* 4.1 1.6 - - - +
11A ILE* 3.1 45.1 + - + +
40A VAL* 2.5 55.2 + - - +
68A HIS* 3.0 28.9 - + + +
71A GLN* 2.9 36.5 + - - -
187B TRP* 2.9 58.6 - + - +
188B VAL* 1.3 71.9 - - - +
190B TYR* 1.3 54.5 + - - +
197B PRO* 3.7 9.6 - - + +
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Residues in contact with TYR 190 (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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30A ASP* 3.5 40.1 + - + -
36A ARG* 4.1 9.0 + - - -
37A GLY* 3.7 15.7 - - - -
38A LYS 2.6 12.6 - - - +
39A VAL* 4.6 2.9 - - + -
40A VAL* 3.9 1.1 - - - -
68A HIS* 5.0 4.3 + - - -
70A LYS* 5.1 0.9 - - - +
71A GLN* 5.4 1.4 + - - +
188B VAL* 3.0 34.2 - - + +
189B TYR* 1.3 74.3 - - - +
191B THR* 1.3 63.7 + - - +
192B CYS 3.3 2.9 + - - -
193B CYS* 3.5 22.9 + - - +
196B THR* 5.4 0.2 - - - +
197B PRO* 5.8 0.4 - - - +
198B TYR* 2.9 76.1 - + + +
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Residues in contact with THR 191 (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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27A MET* 3.9 21.3 - - + -
32A PHE* 4.4 5.2 - - - -
38A LYS* 2.5 51.2 + - + +
39A VAL 4.3 0.9 - - - +
40A VAL* 2.9 26.6 - - + +
68A HIS* 5.4 2.2 - - - -
69A PRO* 4.5 14.4 - - + -
70A LYS* 4.6 7.2 - - - -
190B TYR* 1.3 69.3 - - - +
192B CYS* 1.3 69.9 + - - +
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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