Contacts of the strand formed by residues 150 - 155 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44G MET* 1.3 91.9 - - - +
149I THR* 1.3 62.1 - - - +
151I ILE* 1.3 57.0 + - - -
165I ILE 2.9 16.3 + - - -
293I LEU* 3.0 22.0 - - - +
296I ASN* 3.4 11.0 - - - -
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Residues in contact with ILE 151 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G MET* 2.9 1.5 - - - +
150I GLY* 1.3 74.4 - - - +
152I VAL* 1.3 73.8 + - - +
162I THR* 4.3 7.2 - - + -
163I VAL 3.2 19.7 - - - +
164I PRO* 4.0 15.3 - - + -
278I THR* 4.0 20.4 - - + +
281I SER* 3.7 29.6 - - - -
282I ILE* 4.3 11.9 - - + -
293I LEU* 3.4 32.1 - - + +
296I ASN 2.9 5.8 + - - +
297I THR* 3.4 12.8 - - + +
298I VAL* 2.9 24.6 + - - +
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Residues in contact with VAL 152 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G VAL* 3.0 15.9 - - + +
138I ALA* 3.5 22.4 - - + +
142I LEU* 2.1 51.8 - - + -
151I ILE* 1.3 78.9 - - - +
153I MET* 1.3 63.5 + - - +
154I ASP* 3.9 0.4 - - - -
161I HIS 3.7 0.9 - - - +
162I THR* 3.4 4.5 - - - -
163I VAL* 3.2 30.7 + - + +
165I ILE* 4.7 1.3 - - + -
298I VAL* 3.2 10.8 - - + +
300I SER* 3.5 27.4 - - - +
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Residues in contact with MET 153 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151I ILE* 5.9 0.2 - - + -
152I VAL* 1.3 75.4 - - - +
154I ASP* 1.3 59.1 + - - +
155I SER* 3.9 5.1 + - - -
160I THR* 3.5 28.7 - - + -
161I HIS 3.5 2.7 - - - -
162I THR* 3.6 8.7 - - + -
261I LEU* 6.5 0.4 - - + -
274I ILE* 3.5 25.8 - - + -
278I THR* 3.5 25.6 - - + +
297I THR* 5.5 3.8 - - + -
298I VAL 2.8 14.4 + - - +
299I LEU* 3.5 16.3 - - + -
300I SER 2.9 23.3 + - - +
304I THR* 4.0 18.3 - - + +
309I ILE* 5.3 6.3 - - + -
313I MET* 3.8 20.4 - - + -
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Residues in contact with ASP 154 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109I PRO* 3.7 10.6 - - + +
137I GLN* 2.9 18.8 - - - +
138I ALA* 1.5 71.3 + - + +
141I SER* 3.4 1.2 + - - -
153I MET* 1.3 72.5 - - - +
155I SER* 1.3 62.1 + - - +
156I GLY 4.5 2.4 + - - -
159I VAL 3.6 1.2 - - - +
160I THR* 3.1 25.5 - - - +
161I HIS 2.9 12.7 + - - +
300I SER* 2.6 20.4 + - - +
301I GLY* 4.9 2.8 - - - -
339I VAL* 4.4 0.5 - - - +
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Residues in contact with SER 155 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153I MET* 3.9 6.7 + - - -
154I ASP* 1.3 72.4 + - - +
156I GLY* 1.3 61.7 + - - +
159I VAL 3.7 2.9 - - - -
160I THR* 2.9 23.8 + - - +
181I ALA* 4.2 3.6 - - - -
261I LEU* 4.4 5.8 - - - +
274I ILE* 5.7 0.2 - - - +
300I SER 3.0 10.5 + - - -
301I GLY* 3.3 12.6 - - - -
303I THR* 3.0 49.1 + - - +
304I THR* 4.1 13.7 - - - -
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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