Contacts of the strand formed by residues 1351 - 1358 (chain B) in PDB entry 4E70
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 ASP1351 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1344B PHE* 6.5 0.2 - - - -
1349B PHE 3.8 0.6 - - - -
1350B LYS* 1.3 84.0 - - + +
1352B TYR* 1.3 83.0 + - - +
1366B VAL* 3.6 4.9 - - - +
1367B TYR* 2.9 49.8 + - + +
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Residues in contact with TYR1352 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1337B GLU* 2.6 39.1 + - + +
1340B TRP* 6.4 0.4 - - + -
1341B ALA* 3.8 27.8 - - + +
1344B PHE* 3.9 20.9 - + + -
1351B ASP* 1.3 89.9 + - - +
1353B LYS* 1.3 64.9 + - - +
1354B ILE* 4.0 17.5 - - + -
1364B ILE* 4.1 19.7 - - + -
1365B GLU 3.0 14.1 - - - +
1366B VAL* 4.2 7.9 - - + -
1367B TYR* 3.9 5.4 - - - -
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Residues in contact with LYS1353 (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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1196B ASP* 5.6 8.7 + - - +
1352B TYR* 1.3 77.5 - - - +
1354B ILE* 1.3 71.7 + - - +
1355B THR* 4.0 13.8 + - - +
1363B LEU 3.6 1.4 - - - +
1364B ILE* 3.5 2.0 - - - -
1365B GLU* 2.9 51.4 + - - +
1367B TYR* 3.8 20.2 - - + +
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Residues in contact with ILE1354 (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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1304B VAL* 4.3 13.9 - - + -
1307B HIS* 3.5 35.1 + - + +
1337B GLU* 3.7 37.5 - - + +
1352B TYR* 4.0 17.7 - - + -
1353B LYS* 1.3 81.1 - - - +
1355B THR* 1.3 65.0 + - - +
1356B PRO* 4.2 3.9 - - - +
1362B VAL* 3.7 28.7 - - + -
1363B LEU 3.3 2.5 - - - -
1364B ILE* 4.2 13.7 - - + -
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Residues in contact with THR1355 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1193B LYS 3.9 12.6 - - - +
1194B CYS* 3.7 27.6 - - + -
1353B LYS* 4.0 18.4 + - - +
1354B ILE* 1.3 75.2 + - - +
1356B PRO* 1.3 75.7 - - + +
1357B VAL* 3.8 0.9 - - - +
1362B VAL* 4.2 2.5 - - - -
1363B LEU* 2.8 43.1 + - - +
1365B GLU* 4.4 8.7 + - - -
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Residues in contact with PRO1356 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1193B LYS* 3.8 16.0 - - - +
1307B HIS* 3.8 22.0 - - + -
1309B SER* 3.7 25.1 - - - +
1354B ILE 4.2 5.4 - - - +
1355B THR* 1.3 98.5 - - + +
1357B VAL* 1.3 61.1 + - - +
1358B GLY 5.4 0.2 - - - +
1362B VAL* 3.9 10.7 - - + -
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Residues in contact with VAL1357 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A VAL* 4.3 8.3 - - - +
10A LEU* 4.1 2.0 - - + +
1186B PHE* 3.8 24.7 - - + -
1189B ALA* 3.8 28.2 - - + +
1190B LEU* 3.8 22.9 - - + +
1193B LYS* 3.7 24.7 - - - +
1194B CYS* 3.7 25.1 - - - -
1355B THR 3.6 0.2 + - - -
1356B PRO* 1.3 77.9 - - - +
1358B GLY* 1.3 59.2 + - - +
1361B ARG 3.2 10.5 + - - +
1362B VAL 4.0 1.8 - - - -
1363B LEU 3.8 17.5 - - - +
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Residues in contact with GLY1358 (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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10A LEU* 3.5 15.7 - - - +
11A ASP* 3.2 15.3 - - - -
1186B PHE* 4.0 2.9 - - - -
1356B PRO* 5.4 0.2 - - - +
1357B VAL* 1.3 80.1 - - - +
1359B GLY* 1.3 67.5 + - - +
1360B LEU 3.2 2.5 - - - -
1361B ARG* 3.0 20.9 + - - +
1401B GOL 3.8 9.9 - - - -
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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