Contacts of the strand formed by residues 160 - 166 (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 THR 160 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109I PRO* 3.2 7.5 - - - +
110I LEU* 3.4 0.2 - - - +
153I MET* 3.5 19.5 - - - -
154I ASP 3.1 12.6 - - - +
155I SER* 2.9 19.3 + - - +
159I VAL* 1.3 73.9 - - - +
161I HIS* 1.3 65.0 + - - +
162I THR* 5.3 1.1 - - + -
177I ARG* 3.3 3.8 - - - -
178I LEU* 2.7 43.9 + - + -
180I LEU 2.8 22.6 + - - -
261I LEU* 5.0 0.5 - - - +
274I ILE* 3.4 27.5 - - + +
277I THR* 6.2 0.4 - - + -
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Residues in contact with HIS 161 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109I PRO* 1.6 40.6 - - + +
110I LEU* 2.1 39.4 + - - -
136I ILE* 4.2 21.7 - - + +
138I ALA* 4.7 0.5 - - - +
152I VAL 3.7 1.2 - - - +
153I MET* 3.5 3.1 - - - -
154I ASP* 2.9 34.8 + - + +
160I THR* 1.3 74.6 - - - +
162I THR* 1.3 65.3 + - - +
163I VAL* 3.9 15.0 + - + -
175I ILE* 3.3 22.3 - - + +
176I LEU 3.0 17.7 - - - -
177I ARG* 3.3 14.0 - - + +
277I THR* 6.0 0.7 - - - -
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Residues in contact with THR 162 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151I ILE* 4.3 4.0 - - + -
152I VAL 3.4 5.4 - - - +
153I MET* 3.6 19.5 - - + -
160I THR* 5.3 1.6 - - + -
161I HIS* 1.3 75.7 - - - +
163I VAL* 1.3 60.3 + - - +
175I ILE* 3.3 6.2 - - - -
176I LEU* 3.0 28.8 + - - +
274I ILE* 4.9 1.6 - - + +
277I THR* 3.4 25.2 + - + +
278I THR* 3.4 38.8 - - - +
281I SER* 3.0 25.6 + - - -
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Residues in contact with VAL 163 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136I ILE* 5.4 2.0 - - + -
138I ALA* 5.0 6.5 - - + -
139I VAL* 3.6 33.9 - - + -
151I ILE* 3.2 22.7 - - - +
152I VAL* 3.2 16.3 + - + +
161I HIS* 3.9 20.6 - - + +
162I THR* 1.3 77.6 - - - +
164I PRO* 1.3 60.1 - - - +
165I ILE* 3.8 15.6 + - + +
170I ALA* 3.8 23.3 - - + -
175I ILE* 4.0 18.4 - - + -
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Residues in contact with PRO 164 (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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150I GLY 3.8 5.2 - - - +
151I ILE* 4.0 7.4 - - + -
162I THR 4.1 0.2 - - - +
163I VAL* 1.3 82.2 - - - +
165I ILE* 1.3 55.2 + - - +
170I ALA* 3.5 2.3 - - - -
171I LEU* 2.7 43.2 + - + +
174I ALA* 3.5 30.5 - - + +
175I ILE* 4.1 2.7 - - + +
281I SER* 3.8 15.0 - - - -
285I CYS* 3.2 36.8 - - - -
293I LEU* 3.8 13.2 - - + -
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Residues in contact with ILE 165 (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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43G VAL* 2.1 21.8 - - - +
44G MET* 1.3 111.7 - - + +
61G LYS* 3.1 5.5 - - - -
139I VAL* 5.3 4.0 - - + -
142I LEU* 1.5 58.1 - - + -
148I THR 3.4 0.9 - - - +
149I THR* 3.5 0.3 - - - +
150I GLY 2.9 16.2 + - - +
152I VAL* 4.1 5.4 - - + -
163I VAL* 3.9 20.2 - - + +
164I PRO* 1.3 77.2 - - - +
166I TYR* 1.3 56.1 + - - +
169I TYR 3.2 7.0 - - - +
170I ALA* 3.8 13.2 - - + -
171I LEU* 4.7 0.9 - - - -
293I LEU* 4.1 2.5 - - - +
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Residues in contact with TYR 166 (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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53G TYR* 3.0 2.9 - - - -
57G GLU 2.1 28.3 - - - -
58G ALA* 1.5 49.7 - - - +
61G LYS* 0.8 352.6 - - + +
64G ILE* 3.0 20.2 - - + +
65G LEU* 2.3 41.7 - - + +
165I ILE* 1.3 63.3 - - - +
167I GLU* 1.3 69.8 + - + +
168I GLY 3.4 0.4 - - - -
169I TYR* 2.9 27.4 + - - +
289I ILE* 3.8 2.5 - - + -
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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