Contacts of the strand formed by residues 1401 - 1405 (chain B) in PDB entry 1G50
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 LYS1401 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1395B SER* 3.4 13.5 - - - -
1398B HIS* 3.1 27.2 - - + +
1399B PRO* 3.0 13.8 + - + +
1400B GLY* 1.3 85.7 + - - +
1402B LEU* 1.3 58.8 + - - +
1403B LEU 3.6 1.3 + - - -
1409B LEU* 3.3 32.4 - - + +
1410B LEU 3.1 12.8 - - - +
1411B ASP* 4.0 21.7 + - + +
1429B LEU* 3.5 9.1 - - - +
1432B SER* 4.6 0.2 + - - -
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Residues in contact with LEU1402 (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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1391B LEU* 4.1 7.6 - - + -
1392B VAL* 5.4 1.8 - - + -
1395B SER* 3.2 13.7 - - - +
1401B LYS* 1.3 70.9 - - - +
1403B LEU* 1.3 61.3 + - - +
1404B PHE* 2.9 33.2 + - + -
1409B LEU* 4.3 0.4 - - - -
1410B LEU 2.9 26.5 + - - +
1411B ASP* 6.2 0.4 - - - -
1425B PHE* 3.6 49.1 - - + +
1428B LEU* 3.6 42.2 - - + +
1429B LEU* 3.3 26.2 - - + -
1432B SER* 4.6 0.7 - - - -
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Residues in contact with LEU1403 (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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1391B LEU* 3.7 4.4 - - - +
1394B ARG* 3.1 50.4 + - + +
1395B SER* 2.8 10.5 + - - -
1398B HIS* 3.5 35.2 - - + +
1401B LYS 3.6 2.8 + - - +
1402B LEU* 1.3 68.5 - - - +
1404B PHE* 1.3 67.2 + - - +
1405B ALA* 2.9 37.0 - - - +
1406B PRO* 3.5 14.1 - - + -
1408B LEU 4.4 0.4 - - - -
1409B LEU* 3.4 21.3 - - + -
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Residues in contact with PHE1404 (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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1327B LEU 5.5 0.7 - - - +
1346B LEU* 3.1 37.5 - - + -
1349B LEU* 3.8 19.4 - - + +
1391B LEU* 3.6 26.9 - - + -
1394B ARG* 3.1 20.1 + - - +
1402B LEU* 2.9 43.5 + - + -
1403B LEU* 1.3 75.2 - - - +
1405B ALA* 1.3 60.6 + - - +
1408B LEU* 3.3 16.1 + - + +
1410B LEU* 3.9 22.4 - - + -
1425B PHE* 4.5 12.3 - + - -
1428B LEU* 5.0 1.8 - - + -
1600B EST 3.6 40.8 - + + -
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Residues in contact with ALA1405 (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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1327B LEU 4.5 3.1 - - - +
1328B TYR* 4.2 2.5 - - - -
1329B SER* 3.5 20.6 - - - +
1349B LEU* 4.3 4.3 - - + -
1403B LEU* 2.9 14.6 - - - +
1404B PHE* 1.3 75.6 - - - +
1406B PRO* 1.3 77.5 - - + +
1407B ASN* 3.1 20.9 - - - +
1408B LEU* 2.8 28.7 + - + +
1409B LEU 3.8 0.3 + - - -
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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