Contacts of the strand formed by residues 1297 - 1302 (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 LYS1297 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1196B ASP 5.1 0.8 + - - -
1197B ALA* 2.8 27.5 + - - +
1199B GLU 5.5 2.4 + - - -
1201B LEU* 4.2 17.3 - - + +
1262B ASP 3.1 11.9 + - - +
1263B ALA* 3.2 6.6 - - + -
1264B VAL 3.0 24.3 + - - -
1289B LEU* 3.5 12.3 - - - +
1296B GLY* 1.3 75.7 - - - +
1298B LEU* 1.3 64.0 + - - +
1299B MET* 4.0 21.3 - - + -
1365B GLU* 2.7 34.7 + - + +
1366B VAL 3.5 13.5 - - - +
1367B TYR* 4.2 23.5 - - + -
1368B PRO* 4.4 0.2 - - - -
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Residues in contact with LEU1298 (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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1264B VAL* 3.6 15.5 - - + +
1266B PHE* 3.4 38.4 - - + -
1282B LEU* 3.6 27.1 - - + -
1285B CYS* 4.7 5.2 - - + -
1289B LEU* 3.8 7.0 - - + +
1297B LYS* 1.3 73.3 - - - +
1299B MET* 1.3 63.2 + - - +
1300B ILE* 4.1 13.7 - - + -
1344B PHE* 5.1 1.3 - - + -
1349B PHE* 3.7 29.4 - - + -
1365B GLU* 3.3 5.0 - - - -
1366B VAL* 2.9 54.2 + - + +
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Residues in contact with MET1299 (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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1197B ALA* 4.0 14.1 - - + +
1198B PHE* 3.7 31.4 - - + -
1201B LEU* 4.2 6.5 - - - -
1204B LEU* 4.3 9.6 - - - -
1263B ALA* 3.7 24.7 - - + -
1264B VAL 2.7 13.9 + - - +
1265B LEU* 3.2 15.6 - - + +
1266B PHE* 2.8 27.7 + - - +
1297B LYS* 4.0 21.8 - - + -
1298B LEU* 1.3 77.5 - - - +
1300B ILE* 1.3 62.1 + - - +
1301B ALA 4.0 0.2 - - - -
1363B LEU* 3.9 32.5 - - + -
1364B ILE 3.4 4.0 - - - -
1365B GLU* 4.7 2.9 - - + -
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Residues in contact with ILE1300 (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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1266B PHE* 3.6 7.6 - - + +
1270B LEU* 3.7 29.2 - - + -
1282B LEU* 5.0 0.4 - - + -
1298B LEU* 4.3 17.9 - - + -
1299B MET* 1.3 76.3 - - - +
1301B ALA* 1.3 62.0 + - - +
1302B ASP* 3.7 22.4 + - + +
1340B TRP* 4.0 16.4 - - + -
1344B PHE* 3.6 35.9 - - + -
1362B VAL 3.5 1.9 - - - +
1363B LEU* 3.4 3.2 - - - +
1364B ILE* 2.7 54.0 + - + +
1366B VAL* 4.2 8.7 - - + -
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Residues in contact with ALA1301 (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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1186B PHE* 3.6 33.8 - - + -
1190B LEU* 5.0 4.9 - - + -
1265B LEU* 4.4 11.0 - - + -
1266B PHE 2.9 8.1 + - - +
1267B LYS* 3.5 16.5 - - + +
1268B TRP* 3.0 27.0 + - - +
1299B MET 4.0 1.0 + - - -
1300B ILE* 1.3 71.1 - - - +
1302B ASP* 1.3 59.7 + - - +
1361B ARG* 5.1 1.7 - - - -
1362B VAL 3.3 7.0 - - - +
1363B LEU* 4.5 7.0 - - + +
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Residues in contact with ASP1302 (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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1266B PHE 5.1 0.7 - - - +
1268B TRP* 3.7 11.3 + - - -
1269B VAL 3.8 3.1 + - - -
1270B LEU* 3.9 5.0 + - - +
1271B CYS* 3.3 43.2 + - - +
1300B ILE* 3.7 20.1 + - + +
1301B ALA* 1.3 75.6 - - - +
1303B HIS* 1.3 93.5 + - - +
1304B VAL* 5.5 0.4 - - - -
1340B TRP* 4.3 11.8 - - + -
1361B ARG* 3.7 14.9 - - - +
1362B VAL* 2.9 34.3 + - - +
1364B ILE* 5.9 1.3 - - + +
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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