Contacts of the strand formed by residues 1239 - 1243 (chain A) in PDB entry 5UAK
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 ARG1239 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1238A GLN* 1.3 70.4 - - - +
1240A VAL* 1.3 61.0 + - - +
1385A ARG* 3.9 25.5 - - - +
1389A LYS* 3.4 41.9 + - - +
1392A PHE 5.4 3.6 + - - -
1393A ALA* 6.1 1.0 - - - +
1397A VAL* 3.7 28.2 - - + +
1399A LEU* 5.6 1.1 - - + -
1409A GLU* 3.5 20.8 + - - +
1410A CYS* 3.4 27.1 - - - +
1411A GLN* 2.8 45.9 + - - +
1412A GLN 3.1 7.7 + - - -
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Residues in contact with VAL1240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1234A ILE* 3.6 25.8 - - + -
1238A GLN 3.5 12.3 - - - +
1239A ARG* 1.3 74.5 - - - +
1241A GLY* 1.3 63.3 + - - +
1242A LEU 4.0 0.7 - - - +
1396A THR* 4.8 1.1 - - + -
1397A VAL 2.8 20.5 + - - +
1398A ILE* 4.1 16.2 - - + -
1399A LEU 2.9 28.1 + - - +
1410A CYS* 3.7 7.8 - - - -
1412A GLN* 3.5 22.9 - - + +
1414A LEU* 3.5 39.0 - - + -
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Residues in contact with GLY1241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1240A VAL* 1.3 74.2 - - - +
1242A LEU* 1.3 59.1 + - - -
1243A LEU* 3.6 2.6 + - - +
1399A LEU 3.6 2.5 - - - -
1407A MET* 3.6 24.9 - - - -
1410A CYS* 3.9 7.8 - - - +
1412A GLN 2.8 16.7 + - - -
1413A PHE* 3.5 4.7 - - - +
1414A LEU* 2.8 31.4 + - - -
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Residues in contact with LEU1242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1232A PHE* 6.4 1.3 - - + -
1240A VAL 3.9 0.8 + - - -
1241A GLY* 1.3 69.4 - - - +
1243A LEU* 1.3 62.2 + - - +
1250A LYS* 5.1 9.2 - - + +
1253A LEU* 5.2 16.6 - - + -
1254A LEU* 5.2 13.9 - - + -
1257A PHE* 5.8 5.2 - - + -
1398A ILE* 4.3 20.0 - - + -
1399A LEU 2.8 18.8 + - - +
1400A CYS* 3.6 38.1 - - + -
1401A GLU 4.1 2.1 + - - +
1407A MET* 3.6 13.2 - - - +
1414A LEU* 4.1 25.6 - - + -
1416A ILE* 3.7 28.3 - - + -
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Residues in contact with LEU1243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1241A GLY 4.3 1.6 - - - +
1242A LEU* 1.3 82.0 - - - +
1244A GLY* 1.3 58.7 + - - +
1400A CYS* 5.7 0.2 - - - -
1401A GLU 3.8 15.9 - - - +
1402A HIS 5.4 2.7 - - - +
1404A ILE* 3.3 35.9 - - + -
1407A MET* 3.6 25.4 - - + -
1413A PHE* 4.0 9.2 - - + -
1414A LEU 2.8 17.4 + - - +
1415A VAL* 4.2 4.5 - - + -
1416A ILE* 2.8 32.5 + - - +
1430A LEU* 3.4 26.0 - - + -
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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