Contacts of the helix formed by residues 1382 - 1397 (chain r) in PDB entry 6FF7
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 MET1382 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1380r THR* 3.2 6.3 - - - +
1381r PRO* 1.3 79.4 - - - +
1383r GLU* 1.3 60.8 + - - +
1384r ALA* 4.4 2.0 - - + +
1385r LEU* 3.4 21.9 - - + +
1386r ALA* 2.8 27.4 + - - +
1652r TRP* 4.8 14.1 - - + -
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Residues in contact with GLU1383 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1381r PRO 4.0 2.4 + - - -
1382r MET* 1.3 69.1 - - - +
1384r ALA* 1.3 65.9 + - - +
1386r ALA* 3.2 9.7 + - - +
1387r GLU* 3.0 23.9 + - - +
1428r THR* 4.8 12.8 - - - -
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Residues in contact with ALA1384 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1382r MET* 3.2 1.8 - - + -
1383r GLU* 1.3 76.2 - - - +
1385r LEU* 1.3 66.2 + - - +
1386r ALA 3.2 0.2 + - - -
1387r GLU* 3.2 7.7 + - - +
1388r GLN* 3.0 22.7 + - - +
1652r TRP* 4.3 9.6 - - + -
1653r GLY* 3.6 31.6 - - - +
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Residues in contact with LEU1385 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1380r THR* 4.6 11.7 - - - -
1382r MET* 3.1 24.2 + - + +
1384r ALA* 1.3 78.7 - - - +
1386r ALA* 1.3 58.6 + - - +
1388r GLN* 3.2 10.4 + - - +
1389r VAL* 2.9 28.5 + - - +
1652r TRP* 4.7 11.8 + - + +
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Residues in contact with ALA1386 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1380r THR* 4.5 15.2 - - - +
1382r MET 2.8 12.7 + - - +
1383r GLU* 3.3 14.8 - - - +
1384r ALA 3.1 0.2 - - - -
1385r LEU* 1.3 74.7 - - - +
1387r GLU* 1.3 60.7 + - - +
1389r VAL* 3.0 7.9 + - - +
1390r TYR* 2.9 28.9 + - - +
1426r ILE* 5.0 7.8 - - + +
1427r SER* 5.1 16.8 - - - +
1428r THR* 5.2 2.7 - - - -
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Residues in contact with GLU1387 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1383r GLU 3.0 12.8 + - - +
1384r ALA* 3.7 7.9 - - - +
1386r ALA* 1.3 75.6 - - - +
1388r GLN* 1.3 55.8 + - - +
1390r TYR* 3.2 9.3 + - - +
1391r MET* 3.0 31.4 + - - +
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Residues in contact with GLN1388 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1384r ALA 3.0 15.0 + - - +
1385r LEU* 3.2 16.6 - - - +
1387r GLU* 1.3 78.1 - - - +
1389r VAL* 1.3 59.4 + - - +
1391r MET* 3.9 5.4 + - - +
1392r ASP* 3.8 15.1 + - - +
1652r TRP 5.5 1.8 - - - +
1653r GLY* 5.4 10.3 - - - +
1654r MET 6.4 0.4 - - - -
1655r ASN* 5.9 7.2 - - + -
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Residues in contact with VAL1389 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1385r LEU 2.9 12.5 + - - +
1386r ALA* 3.0 10.3 + - - +
1388r GLN* 1.3 74.5 - - - +
1390r TYR* 1.3 62.6 + - - +
1392r ASP* 3.1 7.8 + - - +
1393r TRP* 2.9 31.4 + - + +
1426r ILE* 5.6 5.6 - - + -
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Residues in contact with TYR1390 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1386r ALA 2.9 15.7 + - - +
1387r GLU* 3.2 9.4 + - - +
1389r VAL* 1.3 77.1 - - - +
1391r MET* 1.3 57.1 + - - +
1393r TRP* 4.5 4.3 - - - +
1394r TYR* 2.9 35.3 + - - +
1406r VAL 5.6 0.9 - - - +
1407r LEU* 4.3 24.0 - - + -
1426r ILE* 4.9 10.9 - - + +
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Residues in contact with MET1391 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1387r GLU 3.0 15.8 + - - +
1388r GLN* 4.2 6.7 - - - +
1389r VAL 3.3 0.4 - - - -
1390r TYR* 1.3 77.3 - - - +
1392r ASP* 1.3 63.8 + - - +
1394r TYR* 4.2 4.3 - - - +
1395r GLU* 3.8 14.0 + - - +
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Residues in contact with ASP1392 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1388r GLN 3.8 9.6 + - - +
1389r VAL* 3.1 10.4 + - - +
1391r MET* 1.3 79.9 - - - +
1393r TRP* 1.3 60.0 + - - +
1395r GLU* 3.1 7.8 + - - +
1396r LYS* 2.9 28.2 + - + +
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Residues in contact with TRP1393 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1389r VAL* 2.9 21.9 + - + +
1390r TYR* 4.3 3.6 - - - +
1392r ASP* 1.3 73.2 - - + +
1394r TYR* 1.3 56.6 + - - +
1396r LYS* 3.8 10.1 - - - -
1397r PHE* 2.9 34.6 + - + +
1398r GLN 3.9 0.2 + - - -
1405r VAL* 4.4 8.2 - - + +
1424r ILE* 6.1 4.7 - - + -
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Residues in contact with TYR1394 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1390r TYR 2.9 19.3 + - - +
1391r MET* 4.2 6.1 - - - +
1393r TRP* 1.3 78.3 - - - +
1395r GLU* 1.3 57.0 + - - +
1398r GLN* 3.1 13.3 + - + +
1399r ASP* 3.0 22.9 + - - +
1405r VAL* 4.3 18.3 - - + +
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Residues in contact with GLU1395 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1391r MET 3.8 7.9 + - - +
1392r ASP* 3.1 7.3 + - - +
1394r TYR* 1.3 79.0 - - - +
1396r LYS* 1.3 65.2 + - - +
1397r PHE 3.2 1.3 + - - -
1399r ASP* 3.3 28.0 - - + +
1400r ARG* 3.4 9.0 + - - +
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Residues in contact with LYS1396 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1320r LEU* 4.6 18.9 - - + +
1392r ASP* 2.9 17.3 + - + +
1393r TRP* 4.0 9.0 - - + -
1395r GLU* 1.3 78.7 - - - +
1397r PHE* 1.3 57.3 + - + +
1400r ARG* 4.0 13.0 - - - +
1401r LEU* 4.4 4.3 + - - +
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Residues in contact with PHE1397 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1393r TRP* 2.9 18.3 + - + +
1395r GLU 3.2 0.2 - - - -
1396r LYS* 1.3 79.5 - - + +
1398r GLN* 1.3 61.1 + - - +
1399r ASP 3.3 0.7 - - - -
1401r LEU* 2.7 36.4 + - + +
1402r ASN 3.0 6.2 + - - -
1403r LYS* 3.7 16.4 - - + +
1405r VAL* 5.1 4.9 - - + -
1424r ILE* 6.0 4.9 - - + -
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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