Contacts of the helix formed by residues 1406 - 1417 (chain C) in PDB entry 3DQV
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 GLU1406 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1404C CYS* 2.9 15.9 + - - -
1405C PRO* 1.3 80.1 - - - +
1407C GLU* 1.3 57.9 + - - +
1408C LEU 2.8 4.7 - - - -
1409C ALA* 2.6 27.9 + - - +
1410C ASN* 2.8 20.9 + - + +
1449C VAL* 4.6 4.7 - - + +
1453C TYR* 3.2 56.0 + - + -
1698C ARG* 4.0 5.4 + - - -
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Residues in contact with GLU1407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1402C SER* 5.3 15.3 + - - +
1403C LYS* 5.4 2.4 + - - +
1404C CYS* 3.3 34.5 + - + +
1406C GLU* 1.3 79.1 - - + +
1408C LEU* 1.3 59.8 + - - +
1410C ASN* 3.2 10.4 + - - +
1411C TYR* 3.1 22.2 + - - +
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Residues in contact with LEU1408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1402C SER* 3.9 32.3 - - - +
1403C LYS 4.1 6.3 - - - +
1404C CYS 3.1 22.1 + - - +
1405C PRO* 3.9 9.0 - - + +
1407C GLU* 1.3 77.7 - - - +
1409C ALA* 1.3 62.6 + - - +
1411C TYR* 3.2 15.9 + - + +
1412C CYS* 3.5 17.7 + - - -
1437C VAL* 3.8 23.8 - - + +
1440C LYS* 4.6 18.8 - - + +
1441C LEU* 3.9 12.8 - - + -
1444C VAL* 3.6 30.5 - - + -
1450C PHE* 3.7 9.6 - - + -
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Residues in contact with ALA1409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1405C PRO 4.0 4.3 - - - +
1406C GLU 2.6 16.4 + - - +
1408C LEU* 1.3 76.5 - - - +
1410C ASN* 1.3 58.4 + - - +
1411C TYR 3.3 0.5 + - - -
1412C CYS* 3.4 5.6 + - - +
1413C ASP 3.4 14.9 + - - -
1450C PHE* 3.2 33.7 - - + +
1453C TYR* 3.6 32.5 - - + -
1454C HIS* 4.2 3.8 + - - +
1457C HIS* 3.6 10.8 - - - -
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Residues in contact with ASN1410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1406C GLU* 2.8 19.7 + - + +
1407C GLU* 3.5 15.5 - - - +
1408C LEU 3.2 0.4 - - - -
1409C ALA* 1.3 77.9 - - - +
1411C TYR* 1.3 59.1 + - - +
1413C ASP* 3.8 7.8 + - - +
1414C MSE 3.3 29.5 + - - +
1417C ARG* 5.4 1.0 + - - -
1453C TYR* 6.2 1.4 - - - -
1457C HIS* 3.9 24.2 + - - +
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Residues in contact with TYR1411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1402C SER* 6.1 1.3 - - - -
1407C GLU 3.1 12.1 + - - +
1408C LEU* 3.5 12.6 - - + +
1409C ALA 3.1 0.6 - - - -
1410C ASN* 1.3 75.8 - - - +
1412C CYS* 1.3 60.4 + - - +
1413C ASP 3.1 1.3 - - - -
1414C MSE 3.0 8.7 + - + +
1415C LEU* 2.9 62.9 + - + +
1421C LEU* 4.1 28.6 - - + +
1433C LYS* 3.5 26.3 - - + +
1436C GLU* 4.4 16.6 + - - -
1437C VAL* 4.4 14.8 - - + -
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Residues in contact with CYS1412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1408C LEU 3.5 14.4 - - - -
1409C ALA 3.4 6.7 + - - +
1411C TYR* 1.3 75.5 - - - +
1413C ASP* 1.3 58.5 + - - +
1415C LEU* 3.2 9.9 + - - +
1416C LEU* 2.8 37.8 + - + +
1434C LEU* 4.3 18.6 - - + -
1437C VAL* 4.3 18.8 - - - -
1438C LEU* 5.6 3.4 - - - -
1450C PHE* 3.8 22.9 - - - -
1454C HIS* 4.3 19.1 - - + +
1476C MSE 5.4 4.5 - - - -
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Residues in contact with ASP1413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1409C ALA 3.4 2.6 + - - +
1410C ASN* 3.9 11.1 - - - +
1411C TYR 3.1 0.4 - - - -
1412C CYS* 1.3 76.9 - - - +
1414C MSE 1.3 66.5 + - - +
1417C ARG* 2.8 73.2 + - - +
1454C HIS* 5.6 0.8 + - - -
1457C HIS* 3.5 48.6 + - + +
1460C ARG* 5.8 1.2 - - - +
1461C ARG* 3.1 27.6 + - - +
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Residues in contact with MSE1414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1410C ASN* 3.3 22.1 + - - +
1411C TYR* 3.0 19.5 + - + +
1413C ASP* 1.3 81.6 + - - +
1415C LEU* 1.3 57.7 + - - +
1417C ARG* 3.5 21.9 - - - +
1419C THR* 2.9 51.0 - - + +
1421C LEU* 3.6 25.9 - - + +
1422C SER* 3.8 2.9 + - - -
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Residues in contact with LEU1415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1411C TYR* 2.9 39.8 + - + +
1412C CYS* 3.6 6.1 - - - +
1413C ASP 3.1 0.2 - - - -
1414C MSE 1.3 78.7 - - - +
1416C LEU* 1.3 60.0 + - - +
1421C LEU* 3.6 28.9 - - + +
1422C SER* 3.3 22.9 - - - -
1425C LEU* 5.2 6.7 - - + -
1430C ILE* 4.1 23.7 - - + +
1433C LYS* 3.7 38.4 - - + +
1434C LEU* 3.8 31.2 - - + -
1437C VAL* 5.1 1.3 - - + -
1468C ALA* 4.8 2.1 - - - +
1469C ASP* 6.1 1.0 - - - +
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Residues in contact with LEU1416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1412C CYS* 2.8 23.8 + - + +
1415C LEU* 1.3 75.8 - - - +
1417C ARG* 1.3 56.7 + - - +
1434C LEU* 4.3 10.8 - - + -
1454C HIS* 4.3 9.6 - - + -
1461C ARG* 3.6 25.3 - - - +
1467C SER* 3.6 8.7 + - - -
1468C ALA* 2.9 24.8 + - - +
1469C ASP* 4.0 7.0 + - + +
1472C ILE* 3.6 35.0 - - + -
1473C GLU* 3.2 32.8 - - + +
1476C MSE 3.6 24.9 - - + -
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Residues in contact with ARG1417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1410C ASN* 5.4 2.0 + - - -
1413C ASP* 2.8 43.1 + - - +
1414C MSE 3.5 33.6 - - - +
1416C LEU* 1.3 78.5 - - - +
1418C LYS* 1.3 63.9 + - - +
1419C THR* 2.8 18.4 + - - +
1422C SER* 2.5 28.9 + - - -
1460C ARG* 6.6 0.9 - - - -
1461C ARG* 3.6 19.1 - - + +
1466C ILE* 4.0 31.0 - - + +
1468C ALA* 3.8 2.7 - - - -
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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