Contacts of the helix formed by residues 1447 - 1454 (chain A) in PDB entry 6CNC
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 LEU1447 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1445A ARG* 3.1 43.7 - - + +
1446A CYS* 1.3 81.9 - - - +
1448A PHE* 1.3 65.8 + - - +
1449A GLU* 3.1 3.8 - - + +
1450A SER* 3.1 34.8 + - - +
1451A LEU* 3.3 18.8 - - + +
103D PHE* 4.1 0.4 - - - -
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Residues in contact with PHE1448 (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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1445A ARG* 4.9 7.4 - - + +
1446A CYS* 3.3 26.6 - - - -
1447A LEU* 1.3 74.1 - - - +
1449A GLU* 1.3 63.5 - - + +
1451A LEU* 3.8 2.6 + - - +
1452A SER* 3.7 21.0 + - - -
10D PHE 4.4 13.9 - - - +
11D LEU* 3.4 18.6 - - + -
12D SER* 3.2 28.3 - - - +
14D TYR* 3.7 25.1 - - + -
15D GLU* 3.8 13.7 - - - -
16D VAL* 3.5 32.5 - - + -
19D PHE* 4.4 8.1 - + - -
103D PHE* 3.5 27.6 - + - -
121D LEU* 4.9 6.4 - - + +
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Residues in contact with GLU1449 (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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1445A ARG* 5.3 10.7 - - - +
1447A LEU* 3.1 3.5 - - + +
1448A PHE* 1.3 78.0 - - - +
1450A SER* 1.3 62.9 + - - +
1451A LEU 3.2 0.7 + - - -
1453A ASN* 3.0 9.2 + - - +
8D ASN 5.3 0.9 - - - -
9D ALA* 4.3 16.4 - - + -
10D PHE* 2.5 56.5 + - - +
117D LYS* 2.6 41.9 + - - +
121D LEU* 6.2 0.4 - - - -
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Residues in contact with SER1450 (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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1447A LEU* 3.1 38.3 + - - +
1449A GLU* 1.3 78.5 - - - +
1451A LEU* 1.3 68.3 + - - +
1453A ASN* 3.4 20.6 - - - +
1454A GLU* 4.3 8.7 + - - +
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Residues in contact with LEU1451 (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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1446A CYS 4.3 3.4 - - - +
1447A LEU* 3.3 17.4 + - + +
1448A PHE 4.3 5.6 - - - +
1449A GLU 3.3 0.8 - - - -
1450A SER* 1.3 84.0 - - - +
1452A SER* 1.3 60.6 + - - +
1453A ASN 3.1 1.1 + - - -
1454A GLU 3.6 0.9 + - - -
103D PHE* 3.1 61.9 - - + +
104D ALA* 4.6 1.3 - - - -
106D LEU* 4.8 4.3 - - + -
107D MET* 3.6 42.4 - - + +
111D ASN* 2.5 31.9 + - - +
120D LYS* 3.6 1.5 + - - -
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Residues in contact with SER1452 (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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1448A PHE 3.7 6.6 + - - -
1449A GLU 3.3 2.0 + - - -
1451A LEU* 1.3 75.7 - - - +
1453A ASN* 1.3 64.0 + - - +
1454A GLU 3.3 0.7 - - - -
1455A ALA* 3.4 13.9 + - - +
1456A ALA 4.2 0.2 + - - -
116D PHE 3.8 1.0 - - - +
117D LYS* 3.1 28.4 - - - +
120D LYS* 3.2 37.6 + - - +
121D LEU* 3.3 26.1 - - - +
124D VAL* 5.8 1.2 - - - +
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Residues in contact with ASN1453 (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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1449A GLU 3.0 11.1 + - - +
1450A SER* 3.4 18.5 - - - +
1451A LEU 3.1 0.6 - - - -
1452A SER* 1.3 77.5 - - - +
1454A GLU* 1.3 59.0 + - + +
1456A ALA* 3.0 24.8 + - - +
1457A LEU* 3.6 27.6 + - - +
117D LYS* 3.6 10.8 - - - +
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Residues in contact with GLU1454 (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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1450A SER 4.5 10.8 - - - +
1451A LEU 3.6 1.4 + - - -
1452A SER 3.3 1.4 - - - -
1453A ASN* 1.3 76.5 - - + +
1455A ALA* 1.3 59.8 + - - +
1456A ALA 3.3 0.6 + - - -
1457A LEU* 3.6 35.7 + - + +
1458A LYS* 4.6 5.0 + - - -
107D MET* 4.5 9.0 - - - +
111D ASN* 3.0 59.3 - - + +
113D PHE 4.5 0.7 - - - +
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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