Contacts of the strand formed by residues 228 - 235 (chain A) in PDB entry 4TZM
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 GLN 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A GLY 3.6 9.8 + - - +
227A ILE* 1.3 79.8 - - - +
229A SER* 1.3 65.2 + - - +
246A CYS 3.8 0.7 - - - +
247A TRP* 3.3 23.9 - - - -
248A SER 3.3 9.2 + - - +
251A MET* 3.6 45.3 - - + +
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Residues in contact with SER 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ILE 4.0 2.0 + - - -
228A GLN* 1.3 80.4 + - - +
230A VAL* 1.3 61.1 + - - +
231A THR* 5.7 0.3 + - - -
245A GLN* 4.3 16.3 + - - +
246A CYS 3.5 4.9 + - - -
247A TRP* 3.3 33.0 + - - -
251A MET* 4.6 2.4 - - - +
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Residues in contact with VAL 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A LEU* 4.1 23.8 - - + -
229A SER* 1.3 76.1 + - - +
231A THR* 1.3 72.5 + - - +
232A ILE* 3.7 2.5 - - + +
245A GLN* 3.7 4.7 - - - +
246A CYS* 2.9 52.9 + - + +
251A MET* 3.8 23.3 - - + +
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Residues in contact with THR 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A SER* 5.6 0.7 - - - -
229A SER* 5.7 0.2 + - - -
230A VAL* 1.3 83.4 - - - +
232A ILE* 1.3 64.2 + - - +
233A GLY* 3.7 14.6 - - - +
243A HIS* 3.5 35.0 + - + +
244A MET 3.9 4.5 - - - +
245A GLN* 4.2 7.9 + - - +
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Residues in contact with ILE 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A PHE* 4.6 4.7 - - + -
173A THR* 4.4 5.2 - - - +
174A ILE* 3.6 41.8 - - + +
177A SER* 3.7 25.8 + - - -
178A VAL* 3.8 18.6 - - + +
181A LEU* 4.1 17.3 - - + -
230A VAL* 3.7 3.4 - - + +
231A THR* 1.3 74.8 - - - +
233A GLY* 1.3 58.4 + - - +
244A MET* 3.1 22.6 + - + -
245A GLN* 3.4 34.5 - - - +
246A CYS* 3.5 18.4 - - + +
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Residues in contact with GLY 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A THR* 5.4 5.2 - - - -
174A ILE* 4.0 13.7 - - - -
231A THR* 3.5 9.7 - - - +
232A ILE* 1.3 81.2 - - - +
234A HIS* 1.3 65.5 + - - +
243A HIS* 3.9 5.9 - - - -
244A MET* 2.9 29.0 + - - +
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Residues in contact with HIS 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A LEU* 3.9 16.4 - - + -
159A LEU* 3.4 33.7 - - + +
170A GLN* 3.4 46.9 + - + +
174A ILE* 3.7 6.6 - - - +
233A GLY* 1.3 76.1 - - - +
235A LEU* 1.3 71.8 + - - +
242A ALA 3.2 14.1 - - - +
243A HIS* 4.7 8.5 - - + -
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Residues in contact with LEU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A PHE* 4.0 13.9 - - + -
42A MET* 4.3 8.3 - - + -
45A ALA* 3.6 30.5 - - + -
49A VAL* 5.5 2.2 - - + -
127A MET* 5.3 5.6 - - + -
156A LEU* 4.9 0.3 - - - +
167A VAL* 4.4 2.2 - - + +
170A GLN* 3.6 7.4 - - + +
171A MET* 3.8 38.4 - - + +
174A ILE* 3.6 17.9 - - + -
234A HIS* 1.3 84.8 - - - +
236A ARG* 1.3 62.3 + - - +
237A PRO* 3.6 9.6 - - + -
241A ALA* 3.2 7.8 - - - +
242A ALA* 3.0 42.3 + - + +
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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