Contacts of the helix formed by residues 1407 - 1417 (chain A) in PDB entry 6A5T
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 GLU1407 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331A LYS* 6.4 0.4 - - - -
1389A ARG* 2.3 43.2 + - - -
1393A ASN* 4.3 11.5 + - - -
1406A GLU* 1.3 77.7 - - - +
1408A THR* 1.3 66.0 + - - +
1409A VAL* 3.3 2.9 - - - +
1410A GLU* 4.2 21.4 - - + +
1411A ILE* 3.3 26.6 + - + +
31T T 3.8 25.1 - - - +
32T A 3.7 22.1 + - - +
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Residues in contact with THR1408 (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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330A LEU* 4.4 25.4 + - + +
331A LYS* 5.1 7.0 - - - +
337A LEU* 4.0 19.3 - - + +
338A ARG* 6.0 2.6 - - - +
1403A CYS* 2.6 32.3 + - + +
1404A SER* 4.5 5.2 - - - -
1405A PHE 5.2 0.2 - - - -
1406A GLU* 3.4 5.1 + - - -
1407A GLU* 1.3 74.7 - - - +
1409A VAL* 1.3 71.2 + - - +
1411A ILE* 3.9 1.8 - - - +
1412A LEU* 3.0 39.9 + - + +
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Residues in contact with VAL1409 (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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327A ARG* 3.2 59.9 - - + +
330A LEU* 5.2 7.6 - - + -
331A LYS* 4.2 20.6 - - + +
1407A GLU* 3.3 0.8 - - - -
1408A THR* 1.3 74.8 - - - +
1410A GLU* 1.3 72.4 + - - +
1412A LEU* 2.9 23.1 + - - +
1413A PHE* 3.0 37.9 + - + +
1210B MET* 6.1 1.1 - - - -
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Residues in contact with GLU1410 (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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327A ARG* 2.8 31.5 + - - -
1407A GLU* 3.9 23.1 + - + +
1408A THR 3.5 0.2 - - - -
1409A VAL* 1.3 86.1 + - + +
1411A ILE* 1.3 66.9 + - + +
1413A PHE* 4.1 6.4 - - + +
1414A GLU* 2.9 32.1 + - + +
31T T 3.2 18.0 + - - +
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Residues in contact with ILE1411 (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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132A LYS* 6.3 2.0 - - - -
1393A ASN* 4.3 26.0 - - + +
1399A ALA 4.2 19.1 - - - +
1402A ARG* 3.8 34.3 - - + +
1403A CYS* 4.4 11.0 - - + +
1406A GLU 4.7 1.6 - - - +
1407A GLU* 3.3 24.4 + - + +
1408A THR* 3.9 4.7 - - - +
1409A VAL 3.2 0.6 - - - -
1410A GLU* 1.3 79.9 - - + +
1412A LEU* 1.3 67.5 + - + +
1414A GLU* 3.4 7.1 + - + +
1415A ALA* 2.9 25.7 + - + +
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Residues in contact with LEU1412 (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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19A PHE* 4.6 26.4 - - + -
330A LEU* 4.9 11.4 - - + -
337A LEU* 5.2 3.6 - - + -
1399A ALA* 5.5 2.2 - - + -
1400A LEU* 5.1 3.6 - - + -
1403A CYS* 4.3 21.1 - - + -
1408A THR* 3.0 32.8 + - + +
1409A VAL* 2.9 10.3 + - - +
1411A ILE* 1.3 77.9 - - + +
1413A PHE* 1.3 66.9 + - + +
1415A ALA* 3.3 5.4 + - + +
1416A GLY* 2.9 25.5 + - - -
1203B LEU* 6.1 4.3 - - + -
1207B LEU* 4.7 26.2 - - + -
1210B MET* 6.2 0.7 - - + -
1212B ILE* 4.2 8.3 - - + +
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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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92A HIS* 4.1 11.7 - + - -
93A ILE* 5.0 2.5 - - + -
94A GLY* 3.7 35.7 - - - +
95A PHE* 3.4 28.7 - + + -
305A MET* 5.0 9.6 - - + -
327A ARG* 6.0 0.7 - - + -
1409A VAL* 3.0 36.8 + - + +
1410A GLU* 4.1 6.1 - - + +
1411A ILE 3.2 0.2 - - - -
1412A LEU* 1.3 78.5 - - + +
1414A GLU* 1.3 67.4 + - - +
1416A GLY 3.4 1.3 + - - +
1417A ALA 3.2 12.6 + - - -
1207B LEU* 5.4 0.2 - - + -
1210B MET* 3.3 44.2 - - + -
1212B ILE* 3.9 28.9 - - + -
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Residues in contact with GLU1414 (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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95A PHE* 5.4 0.2 - - - -
97A PRO* 6.2 0.2 - - - +
98A LYS* 3.2 38.9 + - - +
132A LYS* 5.3 17.9 - - - +
1410A GLU* 2.9 24.0 + - + +
1411A ILE* 3.8 8.3 - - + +
1413A PHE* 1.3 76.2 - - - +
1415A ALA* 1.3 53.9 + - - +
1417A ALA* 2.6 27.1 + - - +
1418A ALA* 3.2 14.0 + - - +
1420A GLU* 4.4 3.1 - - - +
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Residues in contact with ALA1415 (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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19A PHE* 3.7 21.2 - - + +
1399A ALA* 4.2 12.6 - - + -
1402A ARG* 5.7 0.2 - - - +
1411A ILE* 2.9 20.5 + - + +
1412A LEU* 3.7 7.4 - - + +
1414A GLU* 1.3 76.4 - - - +
1416A GLY* 1.3 62.3 + - - +
1417A ALA 3.3 0.5 + - - -
1419A ALA 3.3 18.4 + - - -
1420A GLU* 3.1 40.1 + - + +
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Residues in contact with GLY1416 (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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19A PHE* 4.3 11.6 - - - +
20A GLY* 4.0 5.4 - - - -
21A LEU* 3.1 32.2 + - - +
230A ALA* 4.3 2.3 - - - +
1412A LEU 2.9 12.1 + - - -
1413A PHE 3.4 1.3 + - - -
1414A GLU 3.1 0.4 - - - -
1415A ALA* 1.3 77.5 - - - +
1417A ALA* 1.3 58.9 + - - +
1418A ALA 3.6 0.7 + - - -
1419A ALA 4.2 1.4 + - - -
1212B ILE* 3.5 26.5 - - - -
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Residues in contact with ALA1417 (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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21A LEU* 4.6 7.2 - - + -
95A PHE* 3.6 26.9 - - + -
98A LYS* 3.6 29.6 + - + +
224A GLY 5.2 0.2 - - - +
225A PHE* 3.6 29.5 - - + -
230A ALA* 4.4 5.1 - - - +
235A MET* 4.9 2.0 - - - -
1413A PHE 3.2 2.7 + - - +
1414A GLU 2.6 17.2 + - - +
1416A GLY* 1.3 72.1 - - - +
1418A ALA* 1.3 58.0 + - - +
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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