Contacts of the strand formed by residues 1251 - 1258 (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 LYS1251 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1246B LYS* 5.1 0.2 - - - -
1247B LEU* 3.0 39.4 + - + +
1248B LYS 4.6 5.4 - - - +
1249B GLY 3.3 7.8 - - - +
1250B GLY* 1.3 77.6 - - - +
1252B GLU* 1.3 62.1 + - - +
1301B GLU* 6.1 0.9 - - + -
1302B LEU 4.3 9.9 - - - +
1303B LYS 4.1 20.0 - - - +
1304B LYS* 4.5 3.8 - - - -
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Residues in contact with GLU1252 (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* 3.6 21.2 - - + +
1245B GLU 3.6 4.3 - - - -
1246B LYS* 4.4 19.2 - - + +
1247B LEU* 3.9 4.5 - - - +
1250B GLY 4.4 1.5 + - - +
1251B LYS* 1.3 77.4 - - - +
1253B GLN* 1.3 65.6 + - - +
1302B LEU* 3.3 36.0 + - + +
1303B LYS 4.7 4.2 + - - -
1308B THR* 2.9 37.5 + - + +
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Residues in contact with GLN1253 (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* 3.6 4.4 - - - +
1245B GLU* 2.9 66.3 + - - +
1247B LEU* 3.6 25.5 - - + +
1252B GLU* 1.3 80.8 - - - +
1254B ILE* 1.3 69.9 + - - +
1255B VAL* 3.6 11.2 + - + +
1288B ARG* 3.0 30.0 + - - -
1297B ARG* 4.6 8.4 + - - +
1299B ALA* 4.9 5.2 - - - -
1300B ILE 3.6 15.9 - - - +
1301B GLU* 3.6 13.0 - - - +
1302B LEU* 4.5 1.5 - - - +
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Residues in contact with ILE1254 (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* 4.6 4.3 - - + -
1243B GLU 3.8 6.1 - - - +
1244B ILE* 4.0 16.2 - - + -
1253B GLN* 1.3 71.6 - - - +
1255B VAL* 1.3 70.3 + - - +
1256B ILE* 4.4 12.8 - - + -
1298B ILE 3.7 0.7 - - - +
1299B ALA* 3.5 2.3 - - - -
1300B ILE* 2.6 55.8 + - + +
1302B LEU* 4.1 16.5 - - + +
1308B THR* 4.3 6.7 - - - +
1311B VAL* 4.4 11.4 - - + -
1312B LEU* 3.3 56.1 - - + +
1315B LEU* 5.1 4.0 - - + -
1321B LEU* 5.9 0.2 - - + -
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Residues in contact with VAL1255 (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* 3.3 4.7 - - - -
1243B GLU* 2.8 42.1 + - + +
1245B GLU* 3.7 31.2 - - + +
1253B GLN* 3.8 21.1 - - + +
1254B ILE* 1.3 81.7 - - - +
1256B ILE* 1.3 64.4 + - - +
1257B THR* 3.9 20.0 + - + +
1297B ARG* 4.0 33.0 - - + +
1298B ILE 3.5 2.5 - - - +
1299B ALA* 4.7 3.1 - - - -
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Residues in contact with ILE1256 (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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1240B SER* 4.0 8.5 - - - -
1241B LYS 3.7 6.7 - - - +
1242B THR* 4.0 13.9 - - + -
1254B ILE* 4.4 6.7 - - + -
1255B VAL* 1.3 76.2 - - - +
1257B THR* 1.3 64.3 + - - +
1258B GLU 3.6 19.5 - - - +
1259B ILE* 3.8 17.5 - - + -
1272B ILE* 4.3 4.0 - - + -
1296B LEU* 3.3 6.6 - - - +
1297B ARG* 3.4 4.2 - - - -
1298B ILE* 2.8 55.4 + - + +
1300B ILE* 4.0 19.1 - - + -
1321B LEU* 3.4 31.2 - - + -
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Residues in contact with THR1257 (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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1241B LYS* 2.9 37.5 + - - +
1242B THR* 5.4 0.9 - - - -
1243B GLU* 5.8 4.9 - - + +
1255B VAL* 4.1 20.9 - - + +
1256B ILE* 1.3 78.9 - - - +
1258B GLU* 1.3 68.9 + - - +
1296B LEU* 3.7 35.5 + - - +
1297B ARG* 5.1 1.8 - - + +
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Residues in contact with GLU1258 (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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1215B THR 3.7 8.7 - - - +
1216B GLY* 3.5 8.1 - - - -
1217B ALA* 2.8 36.8 + - - +
1240B SER* 3.2 9.6 - - - -
1241B LYS* 3.1 68.0 + - + +
1256B ILE* 3.6 1.6 - - - +
1257B THR* 1.3 88.5 + - - +
1259B ILE* 1.3 64.4 + - - +
1296B LEU* 4.8 3.6 - - - -
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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