Contacts of the helix formed by residues 1392 - 1399 (chain B) in PDB entry 5IRC
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 THR1392 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1383B SER* 4.4 2.2 - - - -
1386B ASN* 4.0 24.9 - - + +
1390B LEU 3.4 7.6 + - - +
1391B MET* 1.3 76.2 - - - +
1393B SER* 1.3 65.9 + - - +
1394B GLU* 3.6 10.8 + - - +
1395B ASN* 3.1 27.7 + - - +
1396B LEU* 2.9 23.1 + - - +
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Residues in contact with SER1393 (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 SER* 3.8 13.1 + - - -
1392B THR* 1.3 74.0 - - - +
1394B GLU* 1.3 57.1 + - - +
1396B LEU* 3.8 3.5 - - - +
1397B SER* 2.9 30.1 + - - -
1426B GLU* 4.0 12.6 - - - +
1429B ILE* 3.5 32.9 - - - +
1430B GLN* 2.7 42.4 + - - -
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Residues in contact with GLU1394 (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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1392B THR* 3.1 9.5 + - - +
1393B SER* 1.3 79.3 - - - +
1395B ASN* 1.3 68.1 + - - +
1397B SER* 3.3 3.1 + - - -
1398B ILE* 3.0 38.7 + - + +
1422B GLN* 4.2 13.9 + - + +
1426B GLU* 3.7 34.5 + - - +
35D VAL* 5.9 5.7 - - - +
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Residues in contact with ASN1395 (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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1390B LEU 3.0 22.6 + - - -
1391B MET* 3.7 18.2 - - + -
1392B THR* 3.1 21.9 + - - +
1394B GLU* 1.3 85.8 - - - +
1396B LEU* 1.3 58.7 + - - +
1398B ILE* 3.3 10.2 + - - +
1399B CYS* 3.0 33.3 + - - -
34D TYR* 3.0 30.7 + - - +
35D VAL* 4.2 4.7 - - - +
36D PRO* 3.2 24.9 - - + +
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Residues in contact with LEU1396 (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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1282B ILE 4.1 0.2 - - - +
1283B TYR* 3.9 29.3 - - + +
1379B LEU* 3.3 38.6 - - + +
1382B VAL* 3.9 8.1 - - + -
1383B SER* 3.8 12.8 - - - +
1391B MET* 3.5 47.1 - - + +
1392B THR 2.9 14.6 + - - +
1393B SER* 3.8 5.6 - - - +
1395B ASN* 1.3 72.7 - - - +
1397B SER* 1.3 66.9 + - - +
1399B CYS* 3.2 2.2 + - - -
1400B PHE* 3.0 29.1 + - - +
1429B ILE* 4.0 13.2 - - + -
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Residues in contact with SER1397 (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 SER 2.9 18.1 + - - -
1394B GLU 3.3 4.5 + - - -
1396B LEU* 1.3 76.8 - - - +
1398B ILE* 1.3 63.8 + - - +
1401B TRP* 2.8 30.8 + - - +
1422B GLN* 2.7 38.3 + - - -
1425B ILE* 3.5 23.1 - - - +
1426B GLU* 3.7 15.3 - - - -
1429B ILE* 3.9 1.2 - - - +
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Residues in contact with ILE1398 (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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1394B GLU* 3.0 31.7 + - + +
1395B ASN* 3.6 12.8 - - - +
1397B SER* 1.3 76.7 - - - +
1399B CYS* 1.3 58.1 + - - +
1400B PHE 3.6 0.5 + - - -
1401B TRP* 4.2 3.4 - - - -
1402B PRO* 4.1 2.9 - - - +
1422B GLN* 3.4 33.7 - - - +
35D VAL* 5.1 5.4 - - + -
36D PRO* 3.7 42.4 - - + +
37D THR 4.9 0.9 - - - +
38D VAL* 3.9 16.4 - - + -
63D GLN* 5.6 0.4 - - - +
66D TYR* 2.6 45.9 + - + +
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Residues in contact with CYS1399 (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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1283B TYR* 3.4 20.4 - - + +
1284B ARG* 3.7 32.1 - - - -
1322B LYS* 2.8 29.2 + - - +
1391B MET* 4.2 5.4 - - + -
1395B ASN 3.0 20.0 + - - +
1396B LEU 3.4 2.2 - - - +
1397B SER 3.1 0.4 - - - -
1398B ILE* 1.3 79.0 - - - +
1400B PHE* 1.3 61.1 + - - +
36D PRO* 3.8 21.8 - - - -
63D GLN* 4.1 14.6 - - + -
65D ASP* 3.8 7.0 - - - -
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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