Contacts of the strand formed by residues 1412 - 1417 (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 GLN1412 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1233A SER 4.0 2.8 - - - +
1234A ILE* 3.3 31.9 - - - +
1235A SER* 3.6 25.1 + - - +
1238A GLN* 4.1 17.8 - - + +
1239A ARG 3.1 8.2 + - - +
1240A VAL* 3.5 17.1 - - + +
1241A GLY* 2.8 27.7 + - - -
1410A CYS 4.1 1.9 - - - -
1411A GLN* 1.3 80.8 - - - +
1413A PHE* 1.3 64.6 + - - +
1414A LEU* 5.2 1.3 - - - -
1423A GLN* 3.2 45.2 + - + +
1424A TYR 4.1 2.0 - - - -
1425A ASP* 4.4 2.7 - - - +
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Residues in contact with PHE1413 (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* 3.5 4.0 - - - +
1243A LEU* 4.0 19.7 - - + -
1404A ILE* 5.4 0.2 - - + -
1407A MET* 3.6 33.9 - - + -
1408A LEU 5.0 1.6 - - - -
1410A CYS* 3.2 19.7 - - + -
1411A GLN 3.2 21.3 - - - -
1412A GLN* 1.3 75.6 - - - +
1414A LEU* 1.3 65.0 + - - +
1423A GLN* 3.5 6.8 - - - +
1424A TYR* 2.8 48.7 + - + +
1426A SER* 3.8 30.1 - - - -
1427A ILE* 3.4 34.5 - - + -
1430A LEU* 4.4 13.0 - - + -
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Residues in contact with LEU1414 (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* 4.1 35.2 - - + -
1233A SER 4.5 3.6 - - - +
1234A ILE* 4.2 13.0 - - + -
1240A VAL* 3.5 28.0 - - + -
1241A GLY 2.8 12.9 + - - +
1242A LEU* 4.1 22.9 - - + -
1243A LEU* 2.8 36.3 + - - +
1398A ILE* 5.5 2.2 - - + -
1412A GLN* 5.1 1.6 - - + -
1413A PHE* 1.3 81.5 - - - +
1415A VAL* 1.3 62.4 + - - +
1416A ILE* 5.0 1.8 - - + -
1421A VAL* 5.4 5.2 - - + -
1422A ARG 3.6 4.0 - - - +
1423A GLN* 3.9 26.9 - - + +
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Residues in contact with VAL1415 (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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1243A LEU* 3.4 6.5 - - + -
1244A GLY* 5.0 3.8 - - - -
1414A LEU* 1.3 73.9 - - - +
1416A ILE* 1.3 69.7 + - - +
1417A GLU* 4.0 21.7 - - - +
1420A LYS 4.3 0.3 - - - +
1421A VAL* 3.4 8.7 - - - +
1422A ARG* 2.8 35.7 + - + +
1424A TYR* 3.3 37.7 - - + +
1430A LEU* 3.4 32.5 - - + -
1434A ARG* 6.2 4.5 - - + -
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Residues in contact with ILE1416 (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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1227A LEU* 5.2 7.4 - - + -
1230A ILE* 5.3 1.1 - - + -
1242A LEU* 3.7 29.6 - - + -
1243A LEU 2.8 22.7 + - - +
1244A GLY* 3.1 20.5 - - - -
1245A ARG* 3.5 15.3 + - - +
1250A LYS* 6.5 0.9 - - - -
1253A LEU* 3.6 34.3 - - + -
1414A LEU* 4.7 2.9 - - + +
1415A VAL* 1.3 79.3 - - - +
1417A GLU* 1.3 70.6 + - - +
1420A LYS 4.1 2.2 - - - -
1421A VAL* 4.3 20.2 - - + -
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Residues in contact with GLU1417 (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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1230A ILE* 5.8 2.3 - - - +
1245A ARG* 3.8 23.3 + - + +
1415A VAL* 4.0 19.0 - - + +
1416A ILE* 1.3 83.3 - - - +
1418A GLU* 1.3 68.7 + - - +
1419A ASN 3.0 3.5 + - - -
1420A LYS* 2.9 52.0 + - + +
1421A VAL* 5.0 1.4 - - - +
1422A ARG* 5.6 4.5 + - - +
1424A TYR* 5.4 2.4 + - - -
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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