Contacts of the strand formed by residues 222 - 227 (chain I) in PDB entry 5TJ4
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 222 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118I ASN* 4.4 7.3 + - - +
121I LEU* 5.4 2.0 - - - -
144I LYS* 5.1 1.3 - - - -
145I SER* 2.9 27.2 + - - +
147I LEU 3.6 7.4 + - - -
148I MET* 3.8 17.4 + - + +
213I ALA 4.8 0.2 - - - +
216I ALA* 3.4 9.2 + - + -
217I PHE* 3.6 44.6 - - + +
220I GLY 3.3 5.1 - - - +
221I GLU* 1.3 80.4 - - - +
223I ALA* 1.3 70.3 + - - +
224I MET 3.6 21.3 + - - +
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Residues in contact with ALA 223 (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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117I TYR* 4.0 0.5 - - - +
118I ASN* 2.9 30.1 + - - +
121I LEU* 4.2 25.1 - - + +
122I LEU* 4.8 14.7 - - + +
135I LEU* 5.6 3.1 - - + -
139I LEU* 5.4 6.7 - - + -
144I LYS* 5.6 1.7 - - + +
145I SER 2.8 14.1 + - - +
146I ALA* 3.5 14.6 - - - +
217I PHE* 3.6 1.3 - - - -
222I THR* 1.3 73.9 + - - +
224I MET* 1.3 67.5 + - + +
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Residues in contact with MET 224 (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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115I LEU* 3.9 22.9 - - + -
116I ILE 3.4 8.3 - - - +
117I TYR* 3.9 13.7 - - + -
122I LEU* 4.3 9.9 - - + -
126I PRO* 3.6 31.0 - - + -
132I ILE* 3.6 32.8 - - + -
135I LEU* 5.0 4.3 - - + -
146I ALA* 3.0 25.1 + - + +
147I LEU* 3.2 22.6 - - + +
148I MET 3.2 12.8 + - - +
217I PHE* 3.7 6.1 - - - -
222I THR* 3.5 8.0 + - - +
223I ALA* 1.3 88.8 - - + +
225I THR* 1.3 63.5 - - - +
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Residues in contact with THR 225 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115I LEU* 3.5 4.3 - - - +
116I ILE* 2.9 49.4 + - + +
147I LEU* 3.6 4.0 - - - -
148I MET 2.6 23.8 + - - -
149I PHE* 3.9 4.0 - - - -
213I ALA* 4.2 9.0 + - - +
214I GLU* 5.1 2.4 + - - -
217I PHE* 3.8 31.4 - - + -
224I MET* 1.3 72.1 - - - +
226I ILE* 1.3 75.8 + - - +
227I ASN* 4.7 13.0 + - + +
235I ILE* 5.6 3.1 - - + -
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Residues in contact with ILE 226 (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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113I LEU* 4.1 24.9 - - + -
114I SER 3.7 4.9 - - - +
115I LEU* 4.6 8.7 - - + -
129I TRP* 3.7 35.2 - - + -
147I LEU* 4.6 4.9 - - + -
149I PHE* 3.7 38.6 - - + +
150I ASN 5.2 0.3 + - - -
156I PHE* 3.7 23.5 - - + +
159I PRO* 5.7 1.8 - - + -
225I THR* 1.3 82.8 + - - +
227I ASN* 1.3 71.4 + - - +
247I LEU* 3.9 29.6 - - + -
248I PRO* 5.7 0.7 - - + -
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Residues in contact with ASN 227 (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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113I LEU* 3.5 13.2 - - - -
114I SER* 3.3 29.0 + - - +
116I ILE* 3.9 18.5 - - + +
156I PHE* 4.0 3.8 - - - -
210I TYR* 3.6 26.7 + - - -
214I GLU* 5.2 10.5 - - - +
225I THR* 4.2 12.8 + - + +
226I ILE* 1.3 80.2 + - - +
228I GLY* 1.3 70.5 + - - +
230I TRP* 3.0 22.2 + - - -
231I ALA* 3.5 25.6 - - + +
232I TRP* 5.0 0.5 + - - -
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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