Contacts of the strand formed by residues 241 - 246 (chain A) in PDB entry 1CEZ
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 SER 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A THR* 4.4 14.4 - - - -
231A ARG* 3.3 9.2 - - - -
232A GLN* 2.7 62.0 + - - +
239A GLN 3.8 5.3 + - - -
240A ASP* 1.3 80.5 + - - +
242A GLU* 1.3 59.1 + - - +
243A THR* 3.8 10.9 - - - +
5T G 5.0 1.1 - - - -
6T T 4.1 8.3 - - - -
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Residues in contact with GLU 242 (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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133A THR* 3.3 8.1 - - - +
134A VAL* 2.7 38.8 + - + +
135A GLN* 5.6 0.8 + - - -
229A LEU* 3.6 31.0 - - + +
230A HIS* 3.6 1.4 + - - -
231A ARG* 3.6 31.3 + - - +
241A SER* 1.3 75.2 - - - +
243A THR* 1.3 59.3 + - - +
755A PHE* 4.4 6.4 - - - -
757A LEU* 3.4 21.3 - - + -
6T T 3.0 21.1 + - - +
7T G 2.4 27.8 + - - +
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Residues in contact with THR 243 (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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132A THR* 3.5 20.4 - - - +
133A THR* 4.4 8.7 - - + -
134A VAL 4.3 0.4 - - - +
229A LEU* 3.4 7.5 - - - -
230A HIS* 2.8 48.5 + - - +
232A GLN* 3.8 14.4 - - + +
241A SER* 3.8 20.2 - - - +
242A GLU* 1.3 79.2 - - - +
244A ILE* 1.3 63.4 + - - +
245A GLU* 2.7 25.6 + - - -
389A LYS* 4.7 7.6 + - - +
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Residues in contact with ILE 244 (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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122A THR* 4.6 7.9 - - + -
126A LEU* 3.7 18.9 - - + +
132A THR* 3.0 25.3 + - - +
134A VAL* 4.5 7.4 - - + -
137A VAL* 3.9 29.8 - - + -
217A ILE* 3.8 30.1 - - + -
221A ILE* 5.4 0.2 - - + -
227A VAL* 3.4 36.3 - - + -
228A SER 3.5 4.5 - - - +
229A LEU* 3.5 26.9 - - + -
243A THR* 1.3 71.9 - - - +
245A GLU* 1.3 68.6 + - - +
389A LYS* 5.0 0.2 - - - -
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Residues in contact with GLU 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 4.7 0.8 - - - +
227A VAL* 3.3 4.8 - - - -
228A SER* 3.0 33.0 + - - +
230A HIS* 3.4 34.2 - - + +
232A GLN* 4.6 4.1 + - - -
243A THR* 2.7 28.1 + - - -
244A ILE* 1.3 77.3 - - - +
246A LEU* 1.3 69.4 + - - +
247A ALA 3.4 0.2 + - - -
389A LYS* 3.3 41.7 + - + +
392A LYS* 4.2 14.7 - - - +
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Residues in contact with LEU 246 (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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123A LEU* 4.5 8.5 - - + -
126A LEU* 3.9 31.8 - - + +
226A MET* 3.1 30.7 - - + +
227A VAL* 4.2 3.8 - - + -
245A GLU* 1.3 75.0 - - - +
247A ALA* 1.3 66.6 + - - +
248A PRO* 3.6 1.7 - - - +
250A TYR* 4.0 11.0 - - + -
251A ALA* 3.6 33.7 - - + +
254A ILE* 3.9 16.4 - - + -
392A LYS* 2.9 37.2 + - + +
396A ILE* 3.9 16.4 - - + -
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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