Contacts of the helix formed by residues 1435 - 1446 (chain A) in PDB entry 5IYB
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 THR1435 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343A LEU* 3.9 35.2 - - + +
344A LYS* 3.2 19.3 + - - +
350A VAL* 4.0 16.1 - - + +
351A ARG* 6.2 0.2 - - - +
1430A CYS* 3.1 32.7 + - - +
1431A SER 5.4 0.3 - - - -
1433A GLU* 3.2 10.6 + - - -
1434A GLU* 1.3 75.1 - - - +
1436A VAL* 1.3 71.5 + - + +
1438A VAL* 3.1 15.1 + - - +
1439A LEU* 3.1 20.8 + - + +
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Residues in contact with VAL1436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A VAL* 6.4 0.7 - - + -
340A LYS* 3.5 45.1 - - + +
343A LEU* 3.9 34.5 - - + -
344A LYS* 4.8 2.9 - - - +
1434A GLU 2.8 5.6 + - - +
1435A THR* 1.3 87.7 - - + +
1437A ASP* 1.3 56.8 + - - +
1439A LEU* 3.4 7.7 + - + +
1440A MET* 2.9 51.8 + - + +
1162B LEU* 6.2 2.7 - - + -
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Residues in contact with ASP1437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLY 5.6 1.9 - - - +
102A LYS* 5.1 6.1 + - - -
340A LYS* 5.8 0.2 - - - +
1434A GLU* 3.2 31.0 + - + +
1436A VAL* 1.3 79.6 - - - +
1438A VAL* 1.3 52.7 + - - +
1440A MET* 3.3 8.0 + - - +
1441A GLU* 2.7 41.4 + - - +
48Y C 5.7 6.0 - - - +
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Residues in contact with VAL1438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1420A ASN* 3.4 23.8 - - - +
1426A PRO* 4.3 11.4 - - + +
1429A LYS* 3.9 37.9 - - + +
1430A CYS* 4.5 4.9 - - - +
1434A GLU* 3.5 27.6 - - + +
1435A THR 3.1 10.0 + - - +
1437A ASP* 1.3 73.9 - - - +
1439A LEU* 1.3 55.4 + - - +
1441A GLU* 3.6 13.3 - - + +
1442A ALA* 2.7 33.0 + - + +
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Residues in contact with LEU1439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 3.9 33.8 - - + -
343A LEU* 4.8 6.5 - - + -
350A VAL* 5.1 0.7 - - + -
1426A PRO* 4.5 8.5 - - + +
1427A LEU* 4.9 3.1 - - + -
1430A CYS* 3.5 40.6 - - + -
1435A THR* 3.1 21.0 + - + +
1436A VAL* 3.8 7.9 - - - +
1438A VAL* 1.3 72.1 - - - +
1440A MET* 1.3 61.1 + - + +
1442A ALA* 3.9 3.7 - - - +
1443A ALA* 3.0 28.4 + - - +
1158B LEU* 5.1 2.7 - - + -
1162B LEU* 3.7 38.8 - - + -
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Residues in contact with MET1440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A HIS* 4.2 28.3 - - + -
98A GLY* 4.6 22.0 - - - +
99A PHE* 3.8 19.3 - - + -
102A LYS* 6.5 0.2 - - - -
318A VAL* 4.7 12.8 - - + -
1436A VAL* 2.9 43.0 + - + +
1437A ASP* 3.5 9.4 - - - +
1439A LEU* 1.3 76.6 - - + +
1441A GLU* 1.3 58.3 + - - +
1443A ALA* 3.3 6.3 + - - +
1444A ALA* 3.0 30.0 + - - +
1162B LEU* 5.6 9.9 - - + -
1165B MET* 4.5 17.0 - - + -
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Residues in contact with GLU1441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LYS* 3.2 34.0 + - - +
138A LYS* 2.4 41.8 + - + +
1421A ARG* 5.9 1.2 + - - -
1434A GLU* 5.5 1.9 - - - +
1437A ASP* 2.7 27.2 + - - +
1438A VAL* 3.7 15.3 - - + +
1440A MET* 1.3 74.4 - - - +
1442A ALA* 1.3 62.0 + - - +
1444A ALA* 4.2 1.9 - - - +
1445A HIS* 3.2 32.7 + - + +
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Residues in contact with ALA1442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 3.8 13.0 - - + +
1426A PRO* 3.6 30.1 - - + -
1438A VAL* 2.7 23.6 + - + +
1439A LEU* 3.9 5.8 - - - +
1440A MET 3.3 0.2 - - - -
1441A GLU* 1.3 73.1 - - - +
1443A ALA* 1.3 58.3 + - - +
1445A HIS* 4.7 0.2 - - - -
1446A GLY* 3.2 4.0 + - - -
1447A GLU* 2.9 44.8 + - + +
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Residues in contact with ALA1443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 4.2 5.5 - - + +
24A GLY* 3.4 23.5 - - - +
25A VAL* 3.7 12.5 + - + -
99A PHE* 4.7 3.8 - - + -
243A ALA* 3.3 13.9 - - - +
1439A LEU 3.0 18.2 + - - +
1440A MET* 3.5 8.5 - - - +
1441A GLU 3.3 0.2 - - - -
1442A ALA* 1.3 75.4 - - - +
1444A ALA* 1.3 63.4 + - - +
1446A GLY 3.2 8.3 + - - -
1165B MET* 4.3 19.7 - - + +
1166B SER 4.9 1.6 - - - +
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Residues in contact with ALA1444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A VAL* 4.5 1.8 - - - -
99A PHE* 3.7 19.0 - - + -
102A LYS* 4.9 14.1 - - + +
238A MET* 3.9 11.3 - - + +
243A ALA* 3.3 15.2 - - - +
248A MET* 3.6 31.9 - - + +
1440A MET 3.0 17.0 + - - +
1441A GLU* 4.2 4.9 - - - +
1443A ALA* 1.3 77.1 - - - +
1445A HIS* 1.3 60.8 + - - +
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Residues in contact with HIS1445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A GLN* 4.1 3.1 - - - -
137A PRO* 3.0 31.9 - - + +
138A LYS* 2.9 53.8 - - + +
141A LEU* 5.9 6.3 - - + +
237A GLY* 3.7 16.4 - - - +
238A MET* 4.2 8.8 - - - -
239A GLU* 4.6 1.4 + - - +
243A ALA* 4.5 0.7 - - - -
1441A GLU* 3.2 22.6 + - + +
1442A ALA* 4.3 3.4 - - - +
1444A ALA* 1.3 78.0 - - - +
1446A GLY* 1.3 58.6 + - - +
1447A GLU* 3.5 28.3 + - + +
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Residues in contact with GLY1446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLN* 3.8 9.5 + - - -
23A PHE 4.1 11.2 - - - -
24A GLY* 4.7 0.2 - - - -
239A GLU* 4.6 14.2 - - - +
242A TYR* 4.7 5.3 - - - -
243A ALA* 4.2 12.3 - - - -
1442A ALA 3.2 7.6 + - - -
1443A ALA 3.2 11.1 + - - -
1444A ALA 3.3 0.4 - - - -
1445A HIS* 1.3 82.4 - - - +
1447A GLU* 1.3 66.5 + - - +
1448A SER* 4.0 0.5 + - - -
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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