Contacts of the strand formed by residues 150 - 155 (chain J) in PDB entry 3LUE
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 GLY 150 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44H MET* 1.3 90.3 - - - +
149J THR* 1.3 62.5 - - - +
151J ILE* 1.3 56.8 + - - -
165J ILE 2.9 16.3 + - - -
292J ASP 4.5 0.2 - - - -
293J LEU* 3.0 22.3 - - - +
296J ASN* 3.4 11.7 - - - -
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Residues in contact with ILE 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H MET* 2.9 1.1 - - - +
150J GLY* 1.3 74.4 - - - +
152J VAL* 1.3 73.6 + - - +
162J THR* 4.3 7.9 - - + -
163J VAL 3.2 20.6 - - - +
164J PRO* 4.0 14.8 - - + -
278J THR* 4.0 20.4 - - + +
281J SER* 3.7 30.1 - - - -
282J ILE* 4.3 12.3 - - + -
293J LEU* 3.4 32.3 - - + +
296J ASN 2.9 6.6 + - - +
297J THR* 3.4 12.4 - - + +
298J VAL* 2.9 25.1 + - - +
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Residues in contact with VAL 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H VAL* 3.0 15.7 - - + +
138J ALA* 3.5 22.9 - - + +
142J LEU* 2.1 51.8 - - + -
151J ILE* 1.3 77.9 - - - +
153J MET* 1.3 64.5 + - - +
154J ASP* 3.9 0.7 - - - -
161J HIS 3.7 1.1 - - - +
162J THR* 3.4 4.9 - - - -
163J VAL* 3.2 31.0 + - + +
165J ILE* 4.7 1.3 - - + -
298J VAL* 3.2 11.2 - - + +
300J SER* 3.5 26.9 - - - +
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Residues in contact with MET 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151J ILE* 5.9 0.7 - - + -
152J VAL* 1.3 75.6 - - - +
154J ASP* 1.3 61.0 + - - +
155J SER* 3.9 4.7 + - - -
160J THR* 3.5 29.2 - - + -
161J HIS 3.5 2.5 - - - -
162J THR* 3.6 9.0 - - + -
261J LEU* 6.5 0.4 - - + -
274J ILE* 3.5 25.1 - - + -
278J THR* 3.5 25.6 - - + +
297J THR* 5.5 3.8 - - + -
298J VAL 2.8 13.4 + - - +
299J LEU* 3.5 17.0 - - + -
300J SER 2.9 23.5 + - - +
304J THR* 4.0 17.8 - - + +
309J ILE* 5.3 6.1 - - + -
313J MET* 3.8 20.0 - - + -
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Residues in contact with ASP 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109J PRO* 3.7 11.0 - - + +
137J GLN* 2.9 18.5 - - - +
138J ALA* 1.5 71.4 + - + +
141J SER* 3.4 1.6 + - - -
153J MET* 1.3 73.0 - - - +
155J SER* 1.3 61.6 + - - +
156J GLY 4.5 2.1 + - - -
159J VAL 3.6 1.0 - - - +
160J THR* 3.1 24.9 - - - +
161J HIS 2.9 11.1 + - - +
300J SER* 2.6 19.8 + - - +
301J GLY* 4.9 2.4 - - - -
339J VAL* 4.4 0.3 - - - +
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Residues in contact with SER 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153J MET* 3.9 6.7 + - - -
154J ASP* 1.3 72.4 + - - +
156J GLY* 1.3 61.4 + - - +
159J VAL 3.7 2.7 - - - -
160J THR* 2.9 24.4 + - - +
181J ALA* 4.2 3.8 - - - -
261J LEU* 4.4 5.9 - - - +
300J SER 3.0 10.7 + - - -
301J GLY* 3.3 12.2 - - - -
303J THR* 3.0 49.8 + - - +
304J THR* 4.2 13.5 - - - -
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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