Contacts of the helix formed by residues 1408 - 1417 (chain A) in PDB entry 3F2B
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 SER1408 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1406A PHE* 3.5 1.0 - - - +
1407A LEU* 1.3 83.2 + - - +
1409A LYS* 1.3 65.8 + - - +
1410A GLU* 3.4 8.1 + - - +
1411A ASP* 3.0 17.2 + - - +
1412A LEU* 3.1 21.5 + - - +
1435A LEU* 4.1 9.5 - - - +
1436A PRO* 3.3 18.6 - - - -
1438A HIS* 3.5 18.1 - - - -
1439A ASN* 2.9 22.7 + - - -
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Residues in contact with LYS1409 (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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1408A SER* 1.3 75.7 - - - +
1410A GLU* 1.3 62.3 + - - +
1412A LEU* 3.6 7.9 + - - +
1413A GLN* 3.1 21.8 + - - +
1423A LEU* 3.8 15.9 - - + +
1427A GLU* 3.0 35.0 + - + -
1432A LEU* 3.3 51.7 + - + -
1433A ASP* 5.2 3.2 + - - +
1435A LEU* 3.4 21.2 + - + -
1436A PRO 3.1 9.5 + - - +
1437A ASP* 3.3 34.8 + - - +
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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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1408A SER* 3.0 6.2 - - - +
1409A LYS* 1.3 79.0 - - - +
1411A ASP* 1.3 62.2 + - - +
1413A GLN* 3.1 11.3 + - - +
1414A GLN* 3.0 53.3 + - + +
1437A ASP 3.1 13.2 + - - +
1438A HIS* 3.2 25.7 - - + +
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Residues in contact with ASP1411 (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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1405A GLU 3.7 1.6 - - - +
1406A PHE* 3.4 1.0 - - - -
1407A LEU* 3.1 29.1 + - - +
1408A SER* 3.0 28.0 + - - +
1410A GLU* 1.3 77.3 - - - +
1412A LEU* 1.3 55.7 + - - +
1414A GLN* 4.0 4.7 - - - +
1415A ARG* 2.9 76.7 + - - +
1439A ASN* 4.4 4.0 - - - +
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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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1364A LEU* 4.0 21.3 - - + -
1397A ILE* 4.5 9.2 - - + -
1406A PHE* 3.4 47.0 - - + -
1408A SER 3.1 14.4 + - - +
1409A LYS* 3.8 3.8 - - - +
1411A ASP* 1.3 74.8 - - - +
1413A GLN* 1.3 61.2 + - - +
1416A GLY* 2.9 31.8 + - - -
1418A LEU* 3.8 23.9 - - + +
1423A LEU* 4.2 7.2 - - + -
1426A LEU* 4.6 2.7 - - + -
1432A LEU* 3.8 33.4 - - + -
1435A LEU* 5.0 1.8 - - + -
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Residues in contact with GLN1413 (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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1409A LYS 3.1 15.6 + - - +
1410A GLU* 3.1 14.7 + - - +
1412A LEU* 1.3 76.4 - - - +
1414A GLN* 1.3 66.5 + - - +
1417A LYS* 2.9 24.1 + - - -
1418A LEU* 3.0 43.0 + - + +
1419A SER* 4.1 1.0 - - - +
1420A LYS* 4.0 21.5 - - - +
1423A LEU* 4.3 19.0 - - + +
18T C 5.0 4.0 + - - -
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Residues in contact with GLN1414 (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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1410A GLU* 3.0 43.6 + - + +
1411A ASP* 4.0 5.8 - - - +
1413A GLN* 1.3 83.2 + - - +
1415A ARG* 1.3 67.0 + - + +
1417A LYS* 3.2 32.6 + - - +
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Residues in contact with ARG1415 (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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1396A ALA* 4.3 5.4 - - - +
1400A ALA* 3.0 53.8 + - + +
1403A GLU* 4.4 10.1 + - - +
1404A GLY* 2.6 26.3 + - - -
1405A GLU 2.7 19.2 + - - -
1406A PHE* 3.5 12.0 - - + -
1407A LEU* 5.9 0.2 - - - +
1411A ASP* 2.9 40.5 + - - +
1414A GLN* 1.3 84.0 - - + +
1416A GLY* 1.3 60.0 + - - +
1417A LYS* 3.3 6.0 - - - +
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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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1393A VAL* 3.8 7.3 - - - +
1396A ALA* 4.2 5.1 - - - +
1397A ILE* 3.8 35.7 - - - +
1400A ALA* 4.7 2.0 - - - -
1406A PHE* 4.8 0.4 - - - -
1412A LEU* 2.9 23.4 + - - +
1415A ARG* 1.3 78.8 - - - +
1417A LYS* 1.3 73.8 + - - +
1418A LEU* 3.4 4.0 - - - +
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Residues in contact with LYS1417 (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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1393A VAL* 3.8 23.4 - - + +
1396A ALA* 4.7 13.0 - - + -
1413A GLN 2.9 7.8 + - - -
1414A GLN* 3.2 25.0 + - - +
1415A ARG* 3.3 7.6 - - - +
1416A GLY* 1.3 83.3 - - - +
1418A LEU* 1.3 60.5 + - - +
1419A SER 4.0 1.2 + - - -
1422A LEU* 5.4 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