Contacts of the helix formed by residues 1430 - 1440 (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 ASP1430 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1409B PHE 3.4 10.1 - - - +
1410B ILE 3.4 15.5 - - - +
1411B GLN* 3.4 7.7 - - - +
1412B LEU* 3.0 39.7 + - + +
1429B VAL* 1.3 75.6 - - - +
1431B PHE* 1.3 64.5 + - - +
1432B LYS* 3.4 4.6 + - - +
1433B LYS* 2.8 44.1 + - - +
1434B ILE* 3.2 14.0 + - - +
1456B LEU* 3.6 8.7 - - - -
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Residues in contact with PHE1431 (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* 4.2 24.7 - - + -
1394B VAL* 3.7 26.5 - - + -
1395B ILE* 4.0 21.3 - - + -
1406B SER* 4.1 14.4 - - - -
1409B PHE* 2.9 48.8 + - + +
1410B ILE* 4.1 16.8 - - + -
1430B ASP* 1.3 71.5 - - - +
1432B LYS* 1.3 57.1 + - - +
1434B ILE* 3.7 15.3 - - + +
1435B LYS* 2.9 32.8 + - - +
1453B VAL* 4.7 12.3 - - + -
1456B LEU* 3.6 24.1 - - + +
1457B CYS* 5.9 0.2 - - - -
1477B LEU* 4.4 10.5 - - + -
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Residues in contact with LYS1432 (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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1487A LYS 5.2 8.1 + - - -
1490A LYS* 6.0 0.2 - - - -
1410B ILE* 3.0 34.3 + - - +
1411B GLN* 2.9 40.8 - - + +
1430B ASP* 3.6 7.9 - - - +
1431B PHE* 1.3 76.5 - - - +
1433B LYS* 1.3 57.6 + - - +
1435B LYS* 3.4 7.1 + - - +
1436B GLU* 2.9 27.6 + - - +
1439B ARG* 5.3 0.7 + - - -
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Residues in contact with LYS1433 (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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1428B PRO 5.8 0.7 - - - +
1429B VAL* 4.2 7.9 - - + -
1430B ASP* 2.8 27.8 + - - +
1432B LYS* 1.3 74.3 - - - +
1434B ILE* 1.3 58.9 + - - +
1436B GLU* 2.7 39.3 + - - +
1437B ARG* 2.8 71.1 + - + +
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Residues in contact with ILE1434 (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* 4.0 16.2 - - + -
1429B VAL* 4.0 11.7 - - + -
1430B ASP 3.2 15.1 + - - +
1431B PHE* 3.7 17.0 - - + +
1433B LYS* 1.3 76.0 - - - +
1435B LYS* 1.3 57.3 + - - +
1437B ARG 3.3 0.9 + - - -
1438B ILE* 2.9 28.1 + - + +
1443B TYR* 3.6 19.1 - - - +
1449B LEU* 3.4 31.0 - - + -
1452B ASP* 3.9 24.0 - - + +
1453B VAL* 4.1 8.7 - - + +
1456B LEU* 3.9 21.3 - - + -
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Residues in contact with LYS1435 (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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1388B ASN* 3.7 23.7 + - - +
1391B ILE* 4.1 19.3 - - + -
1392B ASP* 2.5 37.6 + - - +
1395B ILE* 4.3 14.1 - - + -
1431B PHE 2.9 22.7 + - - +
1432B LYS* 3.6 7.4 - - - +
1434B ILE* 1.3 74.8 - - - +
1436B GLU* 1.3 57.9 + - - +
1438B ILE* 3.3 6.7 + - + +
1439B ARG* 2.9 39.7 + - - +
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Residues in contact with GLU1436 (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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1432B LYS 2.9 13.9 + - - +
1433B LYS* 2.7 45.7 + - + +
1435B LYS* 1.3 77.6 - - - +
1437B ARG* 1.3 62.6 + - + +
1439B ARG* 3.3 31.0 + - - +
1440B ASN* 3.0 39.1 + - + +
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Residues in contact with ARG1437 (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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1428B PRO 5.6 2.8 + - - -
1429B VAL* 3.9 9.5 - - - +
1433B LYS* 2.8 55.5 + - + +
1434B ILE 3.3 0.4 + - - -
1436B GLU* 1.3 74.3 - - + +
1438B ILE* 1.3 59.9 + - - +
1440B ASN* 3.6 0.4 + - - -
1441B HIS 3.2 2.6 + - - -
1442B LYS* 2.8 50.8 + - + +
1443B TYR* 3.4 28.5 + - + +
1452B ASP* 2.8 42.7 + - - -
1455B LEU* 6.0 0.6 - - - +
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Residues in contact with ILE1438 (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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1384B THR* 4.0 25.6 + - + +
1387B MET* 3.8 29.6 - - + +
1388B ASN* 3.4 34.1 - - - +
1391B ILE* 3.7 31.9 - - + -
1434B ILE* 2.9 19.9 + - + +
1435B LYS* 3.5 8.5 - - - +
1437B ARG* 1.3 76.1 - - - +
1439B ARG* 1.3 59.8 + - - +
1441B HIS* 2.9 23.0 + - - -
1443B TYR* 3.7 19.7 - - + +
1449B LEU* 4.2 5.2 - - + -
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Residues in contact with ARG1439 (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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1384B THR* 4.9 5.2 - - - +
1388B ASN* 5.6 2.5 - - - +
1432B LYS 5.3 0.8 + - - -
1435B LYS* 2.9 28.2 + - - +
1436B GLU* 3.6 40.1 - - - +
1438B ILE* 1.3 74.9 - - - +
1440B ASN* 1.3 72.6 + - - +
1441B HIS* 3.5 20.8 + - - -
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Residues in contact with ASN1440 (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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1436B GLU* 3.0 36.6 + - + +
1439B ARG* 1.3 96.0 + - - +
1441B HIS* 1.3 76.3 + - - +
1442B LYS* 3.4 33.3 + - + +
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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