Contacts of the helix formed by residues 1384 - 1397 (chain B) in PDB entry 4QY4
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 THR1384 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1383B LEU* 1.3 78.1 - - - +
1385B LYS* 1.3 57.4 + - - +
1387B MET* 3.2 6.1 + - - +
1388B ASN* 2.9 48.3 + - - +
1438B ILE* 4.0 26.0 + - + +
1439B ARG* 4.9 4.7 - - - +
1441B HIS* 3.2 33.5 + - + -
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Residues in contact with LYS1385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1383B LEU* 3.2 14.2 - - + +
1384B THR* 1.3 76.2 - - - +
1386B GLN* 1.3 65.9 + - + +
1388B ASN* 3.6 6.5 + - + +
1389B ALA* 3.2 23.0 + - - +
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Residues in contact with GLN1386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1383B LEU* 3.5 28.3 + - + +
1384B THR 3.4 0.2 - - - -
1385B LYS* 1.3 76.6 - - + +
1387B MET* 1.3 63.7 + - - +
1389B ALA* 3.1 6.4 + - - +
1390B ILE* 3.0 33.4 + - + +
1446B LEU* 4.8 11.8 - - + +
1488B ILE* 3.5 30.5 - - + +
1489B ALA* 4.0 23.6 + - - +
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Residues in contact with MET1387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1383B LEU 3.3 20.5 + - - +
1384B THR* 3.2 9.9 + - - +
1386B GLN* 1.3 78.3 - - - +
1388B ASN* 1.3 56.3 + - - +
1390B ILE* 3.4 4.5 + - - +
1391B ILE* 3.0 33.4 + - - +
1438B ILE* 3.9 22.9 - - + -
1443B TYR* 3.7 40.6 - - + +
1444B ARG 4.9 0.2 - - - -
1445B SER* 3.3 37.9 - - - +
1446B LEU* 3.6 23.1 - - + +
1449B LEU* 4.0 14.1 - - + +
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Residues in contact with ASN1388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1384B THR* 2.9 34.1 + - - +
1385B LYS* 4.1 6.5 - - + +
1387B MET* 1.3 75.7 - - - +
1389B ALA* 1.3 56.9 + - - +
1391B ILE* 4.4 1.5 - - - +
1392B ASP* 2.8 43.2 + - - +
1435B LYS* 3.7 24.9 + - - +
1438B ILE* 3.4 24.5 - - - +
1439B ARG* 5.2 2.2 + - - +
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Residues in contact with ALA1389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1385B LYS 3.2 16.5 + - - +
1386B GLN* 3.1 5.9 + - - +
1388B ASN* 1.3 77.0 - - - +
1390B ILE* 1.3 58.1 + - - +
1392B ASP* 3.9 4.4 - - - +
1393B THR* 2.7 34.0 + - - -
1488B ILE* 3.6 23.7 - - + +
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Residues in contact with ILE1390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1386B GLN* 3.0 21.6 + - + +
1387B MET* 3.7 5.6 - - - +
1389B ALA* 1.3 78.2 - - - +
1391B ILE* 1.3 60.8 + - - +
1393B THR* 3.5 4.7 + - - -
1394B VAL* 3.4 20.6 + - - +
1446B LEU* 4.2 23.6 - - + -
1449B LEU* 4.6 3.4 - - + -
1481B PHE* 3.5 35.4 - - + -
1484B ALA* 3.9 19.6 - - + +
1485B ARG* 3.8 33.9 - - + +
1488B ILE* 3.7 15.5 - - + -
1489B ALA* 4.6 8.1 - - + -
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Residues in contact with ILE1391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1387B MET 3.0 20.8 + - - +
1388B ASN 4.4 1.6 - - - +
1390B ILE* 1.3 73.6 - - - +
1392B ASP* 1.3 61.5 + - - +
1394B VAL* 3.2 6.7 + - + +
1395B ILE* 2.9 48.0 + - + +
1431B PHE* 4.2 17.0 - - + -
1434B ILE* 4.0 9.2 - - + -
1435B LYS* 4.1 17.0 - - + -
1438B ILE* 3.7 20.0 - - + -
1449B LEU* 4.0 13.9 - - + -
1453B VAL* 3.8 29.2 - - + -
1481B PHE* 4.2 11.2 - - + -
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Residues in contact with ASP1392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1388B ASN* 2.8 33.0 + - - +
1389B ALA* 4.0 4.8 - - - +
1391B ILE* 1.3 77.0 - - - +
1393B THR* 1.3 55.3 + - - +
1395B ILE* 3.8 7.7 - - - +
1396B ASN* 2.8 50.2 + - - +
1435B LYS* 2.5 36.0 + - - +
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Residues in contact with THR1393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1389B ALA 2.7 21.5 + - - -
1390B ILE 3.5 8.7 - - - -
1391B ILE 3.3 0.2 - - - -
1392B ASP* 1.3 72.2 - - - +
1394B VAL* 1.3 62.9 + - - -
1396B ASN* 3.9 4.4 - - - +
1397B TYR* 3.0 25.8 + - + +
1480B VAL* 4.4 7.2 - - + -
1484B ALA* 3.9 21.1 - - + -
1488B ILE* 3.6 13.2 - - + +
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Residues in contact with VAL1394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1390B ILE 3.4 14.4 - - - +
1391B ILE* 3.2 11.3 + - + +
1393B THR* 1.3 74.4 - - - +
1395B ILE* 1.3 64.5 + - - +
1397B TYR* 3.3 15.6 + - - +
1406B SER* 4.0 2.1 - - - -
1431B PHE* 3.7 32.1 - - + -
1453B VAL* 5.6 1.3 - - + -
1477B LEU* 3.8 32.3 - - + +
1480B VAL* 3.9 10.5 - - + +
1481B PHE* 3.6 43.3 - - + +
1484B ALA* 4.9 0.4 - - + -
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Residues in contact with ILE1395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1391B ILE* 2.9 38.0 + - + +
1392B ASP* 3.9 8.1 - - - +
1394B VAL* 1.3 76.4 - - - +
1396B ASN* 1.3 66.5 + - - +
1397B TYR 3.5 0.2 + - - -
1404B GLN* 3.1 21.6 - - - +
1406B SER* 2.5 29.8 + - - +
1410B ILE* 3.9 17.3 - - + -
1431B PHE* 4.0 31.0 - - + -
1435B LYS* 4.3 19.1 - - + -
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Residues in contact with ASN1396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1392B ASP* 2.8 36.3 + - - +
1393B THR* 4.2 3.8 - - - +
1395B ILE* 1.3 83.0 - - - +
1397B TYR* 1.3 66.1 + - - +
1398B LYS* 3.3 14.6 + - - +
1404B GLN* 4.3 10.5 - - - +
1469C GLN* 5.7 4.9 - - - +
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Residues in contact with TYR1397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1393B THR* 3.0 19.4 + - + +
1394B VAL 3.5 11.1 - - - +
1395B ILE 3.3 2.5 - - - +
1396B ASN* 1.3 78.9 - - - +
1398B LYS* 1.3 81.4 + - - +
1399B ASP* 3.9 10.3 - - - +
1404B GLN* 3.3 20.1 - - - +
1405B LEU* 3.4 38.8 + - + -
1476B VAL* 4.0 11.8 - - + +
1477B LEU* 4.8 2.5 - - + -
1480B VAL* 3.8 35.4 - - + -
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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