Contacts of the strand formed by residues 1406 - 1412 (chain B) in PDB entry 1OFD
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 THR1406 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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950B PHE* 5.5 0.4 - - + -
993B ARG 3.1 24.0 + - - +
994B SER* 4.0 19.8 - - - -
995B LYS* 3.6 15.8 - - - +
1000B LEU* 4.9 8.7 - - + -
1386B ARG* 3.0 26.7 + - - +
1387B ASN 2.9 5.1 + - - -
1388B SER* 3.3 5.7 + - - -
1404B TYR 3.7 4.7 - - - +
1405B MET* 1.3 74.4 - - - +
1407B GLY* 1.3 57.3 + - - +
1423B GLY 5.7 0.2 - - - +
1425B THR* 3.7 20.6 - - + -
1426B GLY* 3.2 23.9 - - - -
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Residues in contact with GLY1407 (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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995B LYS* 5.3 1.1 - - - -
1387B ASN* 3.2 19.5 + - - -
1388B SER 3.0 20.7 + - - +
1405B MET* 3.3 9.0 - - - +
1406B THR* 1.3 79.6 - - - +
1408B GLY* 1.3 64.0 + - - -
1426B GLY 3.5 2.4 + - - -
1427B GLY* 3.6 12.8 - - - -
1499B GLU* 5.0 0.9 - - - -
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Residues in contact with GLY1408 (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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1388B SER 3.6 2.8 + - - -
1389B VAL* 3.9 17.6 - - - +
1390B GLY 3.3 13.9 - - - -
1391B LYS* 5.1 4.5 - - - -
1405B MET* 4.0 2.9 - - - -
1407B GLY* 1.3 73.3 - - - -
1409B VAL* 1.3 71.1 + - - +
1427B GLY* 3.3 3.4 - - - -
1428B LEU 3.1 23.0 + - - -
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Residues in contact with VAL1409 (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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1390B GLY 3.2 6.1 + - - -
1391B LYS* 3.0 28.7 - - + +
1392B ALA 3.0 23.1 + - - +
1405B MET* 4.2 0.8 - - - +
1408B GLY* 1.3 82.4 - - - +
1410B ILE* 1.3 64.4 + - - +
1411B VAL* 4.8 0.4 - - + -
1428B LEU* 3.2 13.9 - - + +
1430B TYR* 3.9 24.9 - - + -
1460B GLN* 3.5 27.6 - - + +
1464B LEU* 3.8 25.2 - - + +
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Residues in contact with ILE1410 (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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1365B LEU* 4.2 4.5 - - + -
1383B PHE* 3.9 19.3 - - + -
1384B ALA* 3.6 22.7 - - + -
1387B ASN* 3.8 10.8 - - - +
1390B GLY 4.3 0.7 - - - +
1392B ALA* 3.6 23.8 - - + +
1401B CYS* 4.8 0.2 - - - -
1402B CYS* 3.9 21.1 - - - -
1405B MET* 3.7 26.0 - - + -
1409B VAL* 1.3 82.7 - - - +
1411B VAL* 1.3 61.4 + - - +
1412B VAL* 4.0 17.3 - - + -
1428B LEU 3.1 5.5 + - - -
1429B ALA* 3.1 5.5 - - + -
1430B TYR* 2.8 33.1 + - - +
1431B PHE* 5.5 0.2 - - + -
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Residues in contact with VAL1411 (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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1392B ALA 2.8 14.2 + - - +
1393B VAL* 3.3 14.1 - - + -
1394B ILE* 2.9 27.4 + - - +
1409B VAL* 4.8 0.2 - - + -
1410B ILE* 1.3 78.3 - - - +
1412B VAL* 1.3 67.3 + - - +
1413B LEU* 3.5 28.0 - - + -
1430B TYR* 3.5 13.7 - - + +
1461B LEU* 3.8 27.6 - - + -
1464B LEU* 4.0 37.2 - - + -
1465B ILE* 4.2 4.0 - - + -
1491B PHE* 4.9 0.4 - - + -
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Residues in contact with VAL1412 (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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1394B ILE* 3.5 15.7 - - + -
1396B GLY* 3.7 22.0 - - - +
1401B CYS* 4.1 9.6 - - - -
1410B ILE* 4.0 15.3 - - + -
1411B VAL* 1.3 76.8 - - - +
1413B LEU* 1.3 62.4 + - - +
1414B GLY 3.2 22.2 + - - +
1416B VAL* 3.6 15.5 - - + -
1430B TYR 2.8 9.9 + - - +
1431B PHE* 3.6 30.8 - - + -
1432B LEU* 3.0 26.3 + - - +
1491B PHE* 4.6 0.2 - - - -
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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