Contacts of the strand formed by residues 1241 - 1247 (chain B) in PDB entry 4Z4Q
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 LYS1241 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1217B ALA* 4.5 7.7 - - - +
1218B ILE* 4.4 16.2 - - + -
1239B ARG 3.7 2.4 + - - -
1240B SER* 1.3 67.7 - - - +
1242B THR* 1.3 67.7 + - - +
1256B ILE* 3.7 1.2 - - - +
1257B THR* 2.9 40.9 + - - +
1258B GLU* 3.1 54.1 + - + +
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Residues in contact with THR1242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1218B ILE* 5.5 0.8 - - - +
1240B SER* 3.4 18.5 + - - +
1241B LYS* 1.3 85.3 - - - +
1243B GLU* 1.3 65.5 + - - +
1244B ILE* 6.1 1.1 - - - +
1254B ILE* 4.6 4.0 - - + -
1255B VAL 3.3 7.2 - - - -
1256B ILE* 4.0 23.3 - - + -
1257B THR* 5.6 1.6 - - - -
1312B LEU* 4.3 33.1 - - + +
1316B PHE* 4.6 7.7 - - + -
1321B LEU* 4.8 1.8 - - + -
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Residues in contact with GLU1243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1242B THR* 1.3 79.8 - - - +
1244B ILE* 1.3 68.8 + - - +
1245B GLU* 5.8 3.1 - - + -
1254B ILE* 3.7 3.3 - - - +
1255B VAL* 2.8 40.2 + - + +
1257B THR* 5.8 3.8 - - + -
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Residues in contact with ILE1244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1242B THR* 6.1 1.1 - - - +
1243B GLU* 1.3 81.1 - - - +
1245B GLU* 1.3 74.3 + - - +
1246B LYS* 4.2 4.4 + - + +
1252B GLU* 3.6 30.1 - - + +
1253B GLN 3.6 7.9 - - - +
1254B ILE* 4.0 25.1 - - + -
1308B THR* 4.1 12.6 - - - +
1312B LEU* 5.1 11.0 - - + -
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Residues in contact with GLU1245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1243B GLU* 4.1 2.9 + - + -
1244B ILE* 1.3 77.4 - - - +
1246B LYS* 1.3 68.0 + - - +
1247B LEU* 4.9 2.7 - - + +
1252B GLU* 3.6 1.0 - - - -
1253B GLN* 2.9 60.8 + - - +
1255B VAL* 3.9 13.1 - - + +
1297B ARG* 2.8 33.3 + - - -
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Residues in contact with LYS1246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1244B ILE* 4.2 4.2 + - + +
1245B GLU* 1.3 77.6 - - - +
1247B LEU* 1.3 69.3 + - - +
1251B LYS 4.3 2.9 - - - -
1252B GLU* 4.4 20.6 - - + +
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Residues in contact with LEU1247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1245B GLU* 4.6 4.7 - - + +
1246B LYS* 1.3 84.9 - - - +
1248B LYS* 1.3 70.8 + - - +
1250B GLY* 3.5 10.9 + - - -
1251B LYS* 3.0 29.0 + - + +
1252B GLU 3.9 4.9 - - - +
1253B GLN* 3.6 52.7 - - + +
1301B GLU* 4.1 19.1 - - + +
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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