Contacts of the strand formed by residues 150 - 155 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C MET* 1.3 91.4 - - - +
149E THR* 1.3 62.3 - - - +
151E ILE* 1.3 56.3 + - - -
165E ILE 2.9 16.1 + - - -
293E LEU* 3.0 22.2 - - - +
296E ASN* 3.4 11.7 - - - -
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Residues in contact with ILE 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C MET* 2.9 1.3 - - - +
150E GLY* 1.3 74.4 - - - +
152E VAL* 1.3 73.1 + - - +
162E THR* 4.3 6.3 - - + -
163E VAL 3.2 20.6 - - - +
164E PRO* 4.0 15.5 - - + -
278E THR* 4.0 20.2 - - + +
281E SER* 3.7 29.8 - - - -
282E ILE* 4.3 11.9 - - + -
293E LEU* 3.4 32.1 - - + +
296E ASN 2.9 5.6 + - - +
297E THR* 3.4 13.2 - - + +
298E VAL* 2.9 24.6 + - - +
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Residues in contact with VAL 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C VAL* 3.0 15.7 - - + +
138E ALA* 3.5 22.7 - - + +
142E LEU* 2.1 51.4 - - + -
151E ILE* 1.3 79.0 - - - +
153E MET* 1.3 63.2 + - - +
154E ASP* 3.9 0.4 - - - -
161E HIS 3.7 1.1 - - - +
162E THR* 3.4 4.9 - - - -
163E VAL* 3.2 30.5 + - + +
165E ILE* 4.7 1.3 - - + -
298E VAL* 3.2 10.8 - - + +
300E SER* 3.5 27.4 - - - +
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Residues in contact with MET 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E ILE* 5.9 0.2 - - + -
152E VAL* 1.3 75.6 - - - +
154E ASP* 1.3 60.0 + - - +
155E SER* 3.9 4.7 + - - -
160E THR* 3.5 28.9 - - + -
161E HIS 3.5 2.7 - - - -
162E THR* 3.6 9.0 - - + -
261E LEU* 6.6 0.2 - - + -
274E ILE* 3.5 26.0 - - + -
278E THR* 3.5 25.6 - - + +
297E THR* 5.5 3.8 - - + -
298E VAL 2.8 14.0 + - - +
299E LEU* 3.5 16.3 - - + -
300E SER 2.9 23.0 + - - +
304E THR* 4.0 18.0 - - + +
309E ILE* 5.3 6.5 - - + -
313E MET* 3.8 20.2 - - + -
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Residues in contact with ASP 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E PRO* 3.7 11.1 - - + +
137E GLN* 2.9 18.5 - - - +
138E ALA* 1.5 71.3 + - + +
141E SER* 3.4 1.4 + - - -
153E MET* 1.3 72.3 - - - +
155E SER* 1.3 62.1 + - - +
156E GLY 4.5 2.4 + - - -
159E VAL 3.6 1.2 - - - +
160E THR* 3.1 25.0 - - - +
161E HIS 2.9 12.1 + - - +
300E SER* 2.6 19.9 + - - +
301E GLY* 4.9 2.9 - - - -
339E VAL* 4.4 0.3 - - - +
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Residues in contact with SER 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E MET* 3.9 6.5 + - - -
154E ASP* 1.3 71.8 + - - +
156E GLY* 1.3 60.8 + - - +
159E VAL 3.7 2.7 - - - -
160E THR* 2.9 24.0 + - - +
181E ALA* 4.2 3.6 - - - -
261E LEU* 4.4 5.8 - - - +
274E ILE* 5.7 0.2 - - - +
300E SER 3.0 10.5 + - - -
301E GLY* 3.3 13.0 - - - -
303E THR* 3.0 49.9 + - - +
304E 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