Contacts of the helix formed by residues 1442 - 1454 (chain N) in PDB entry 5D4D
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 ASN1442 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1429N LEU* 4.2 17.7 - - + +
1441N GLN* 1.3 100.8 + - - +
1443N THR* 1.3 63.5 + - - +
1444N THR* 3.3 3.6 - - - -
1445N HIS* 3.1 21.6 + - + +
1446N VAL* 3.0 20.7 + - + +
11R G 3.5 35.3 - - - +
12R T 2.8 18.8 + - - -
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Residues in contact with THR1443 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103N TRP* 5.9 1.1 - - + -
607N LEU* 5.0 4.3 - - + -
608N SER* 3.8 31.5 - - - -
609N GLY 4.8 2.1 + - - -
614N PHE* 3.8 18.4 - - + -
1438N ALA* 2.9 33.0 + - - +
1439N SER 5.4 0.2 - - - -
1440N PHE 5.3 0.3 - - - -
1441N GLN* 4.0 8.3 - - - -
1442N ASN* 1.3 73.3 - - - +
1444N THR* 1.3 57.5 + - - +
1446N VAL* 3.9 0.5 - - - +
1447N LEU* 2.9 55.6 + - + +
12R T 4.5 1.9 + - - -
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Residues in contact with THR1444 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103N TRP* 3.4 55.7 + - + -
107N ASP* 4.6 12.1 - - + -
583N ASP* 4.4 3.5 + - - +
586N ARG* 6.3 1.3 - - - +
604N THR* 3.7 16.6 - - - +
608N SER* 5.4 1.9 + - - -
1442N ASN 3.3 0.8 - - - -
1443N THR* 1.3 76.4 - - - +
1445N HIS* 1.3 66.6 + - - +
1447N LEU* 3.8 0.7 - - - +
1448N THR* 2.9 34.8 + - + +
11R G 6.0 2.0 - - - -
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Residues in contact with HIS1445 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107N ASP* 3.1 28.8 + - - +
108N VAL 4.0 17.2 + - - -
109N PRO* 5.2 4.7 - - + -
111N LYS* 6.2 0.4 - - - -
1442N ASN* 3.1 28.9 + - + +
1444N THR* 1.3 78.4 - - - +
1446N VAL* 1.3 68.9 + - + +
1448N THR* 2.5 23.6 + - - -
1449N GLU* 3.0 40.8 + - + +
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Residues in contact with VAL1446 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1429N LEU* 4.0 29.8 - - + +
1434N TRP* 3.8 13.7 - - + +
1437N ALA* 3.7 22.0 - - + +
1438N ALA* 3.4 31.4 - - + +
1441N GLN 4.0 0.9 - - - +
1442N ASN* 3.0 16.3 + - + +
1443N THR 3.9 0.2 - - - +
1445N HIS* 1.3 82.0 - - + +
1447N LEU* 1.3 58.4 + - - +
1449N GLU* 3.5 4.0 + - - +
1450N ALA* 2.9 30.2 + - + +
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Residues in contact with LEU1447 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092M LEU* 3.7 25.1 - - + -
1097M LEU* 4.5 5.1 - - + +
10N ILE* 3.8 13.0 - - + +
103N TRP* 3.8 25.8 - - + -
607N LEU* 4.2 6.1 - - + -
614N PHE* 4.7 4.7 - - + -
1434N TRP* 3.6 38.1 - - + -
1438N ALA* 3.8 15.0 - - + -
1443N THR* 2.9 37.3 + - + +
1446N VAL* 1.3 77.5 - - - +
1448N THR* 1.3 57.3 + - - +
1450N ALA* 3.8 2.5 - - - +
1451N ALA* 2.9 31.7 + - - +
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Residues in contact with THR1448 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103N TRP* 3.5 50.9 - - + +
104N PHE* 4.2 17.7 - - + -
107N ASP* 3.5 11.6 + - - +
111N LYS* 4.8 5.8 - - - -
1444N THR* 2.9 19.7 + - + +
1445N HIS* 2.5 25.6 + - - -
1447N LEU* 1.3 72.2 - - - +
1449N GLU* 1.3 67.8 + - - +
1451N ALA* 3.1 3.8 + - - +
1452N ILE* 2.9 30.0 + - - +
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Residues in contact with GLU1449 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109N PRO* 5.9 1.9 - - - +
111N LYS* 3.0 37.1 + - - +
1445N HIS* 3.0 45.0 + - + +
1446N VAL* 3.9 5.4 - - - +
1448N THR* 1.3 84.2 + - - +
1450N ALA* 1.3 57.5 + - - +
1452N ILE* 3.4 4.4 + - - +
1453N ALA* 3.0 30.9 + - - +
1455N LYS* 4.7 6.8 + - - +
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Residues in contact with ALA1450 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10N ILE* 3.4 13.5 - - + +
1434N TRP* 3.7 30.3 - - + -
1446N VAL* 2.9 19.7 + - + +
1447N LEU* 4.0 3.6 - - - +
1449N GLU* 1.3 77.5 - - - +
1451N ALA* 1.3 58.3 + - - +
1453N ALA* 3.3 0.4 + - - -
1454N GLY 3.0 22.5 + - - -
1455N LYS* 3.0 33.2 + - + +
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Residues in contact with ALA1451 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097M LEU* 3.8 29.4 - - + -
10N ILE* 3.9 17.0 - - + +
11N ALA* 3.2 19.4 - - - +
12N LEU* 3.3 4.3 + - - +
104N PHE* 4.8 4.7 - - + -
507N ASN* 3.0 17.0 + - - -
1447N LEU 2.9 20.6 + - - +
1448N THR* 3.6 5.6 - - - +
1450N ALA* 1.3 74.0 - - - +
1452N ILE* 1.3 65.5 + - - +
1454N GLY 3.4 1.4 + - - -
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Residues in contact with ILE1452 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N LEU* 3.9 9.6 - - + -
104N PHE* 3.9 16.8 - - + -
111N LYS* 3.4 53.2 - - + +
498N VAL* 4.6 3.1 - - + +
501N ALA* 3.6 24.1 - - + +
502N PHE* 3.8 34.5 - - + -
505N SER* 3.0 12.0 + - - -
507N ASN* 2.9 20.1 + - - +
1448N THR 2.9 12.9 + - - +
1449N GLU* 3.5 8.5 - - - +
1451N ALA* 1.3 76.7 - - - +
1453N ALA* 1.3 59.0 + - - +
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Residues in contact with ALA1453 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501N ALA* 4.3 18.1 - - + +
504N ASP* 5.6 1.2 - - - +
505N SER* 3.3 16.4 + - - -
1449N GLU 3.0 18.2 + - - +
1450N ALA* 3.9 4.3 - - - +
1451N ALA 3.3 0.2 - - - -
1452N ILE* 1.3 78.4 - - - +
1454N GLY* 1.3 63.2 + - - +
1455N LYS* 3.3 20.5 + - + +
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Residues in contact with GLY1454 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9N ARG* 3.7 16.3 - - - +
10N ILE 3.2 16.2 - - - -
11N ALA* 4.1 9.0 - - - -
505N SER* 4.0 11.2 - - - -
1450N ALA 3.0 4.0 + - - -
1451N ALA 3.4 4.0 + - - -
1452N ILE 3.1 5.3 - - - -
1453N ALA* 1.3 78.6 - - - +
1455N LYS* 1.3 66.2 + - - +
1456N LYS* 3.4 5.5 + - - +
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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