Contacts of the helix formed by residues 1489 - 1502 (chain N) in PDB entry 5D4E
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 GLN1489 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1487N VAL 4.0 0.4 + - - -
1488N ASP* 1.3 73.0 - - - +
1490N LYS* 1.3 57.5 + - + +
1492N LEU* 3.5 11.9 - - - +
1493N LYS* 2.9 62.7 + - + +
39O VAL* 5.4 0.2 - - - +
72O ARG* 3.7 22.9 + - + +
74O VAL* 3.4 24.8 - - + +
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Residues in contact with LYS1490 (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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1488N ASP* 3.2 9.5 - - + +
1489N GLN* 1.3 78.4 - - + +
1491N THR* 1.3 58.3 + - - +
1493N LYS* 3.5 3.0 + - - +
1494N ALA* 2.9 28.8 + - - +
92O LEU* 4.3 5.7 - - + +
93O TYR* 3.8 21.4 + - + +
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Residues in contact with THR1491 (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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1487N VAL* 3.8 7.0 - - - -
1488N ASP* 2.8 26.2 + - - -
1490N LYS* 1.3 71.9 - - - +
1492N LEU* 1.3 60.2 + - - +
1494N ALA* 3.2 5.5 + - - +
1495N ILE* 2.9 43.4 + - + +
85O LEU* 3.8 17.3 - - + -
88O GLU* 4.2 11.2 - - + -
89O MET* 3.6 30.8 - - + +
92O LEU* 3.8 4.6 - - + +
93O TYR* 3.8 19.2 - - - -
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Residues in contact with LEU1492 (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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1487N VAL* 3.8 24.4 - - + +
1488N ASP 2.8 18.6 + - - +
1489N GLN* 3.5 36.1 - - - +
1490N LYS 3.2 0.2 - - - -
1491N THR* 1.3 78.2 - - - +
1493N LYS* 1.3 71.9 + - - +
1495N ILE* 3.3 7.5 + - + +
1496N GLU* 2.9 26.3 + - + +
74O VAL* 3.8 20.6 - - + -
79O LEU* 5.3 15.3 - - + +
80O VAL* 5.8 3.6 - - + -
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Residues in contact with LYS1493 (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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1489N GLN* 2.9 39.4 + - + +
1490N LYS* 4.1 3.1 - - - +
1492N LEU* 1.3 89.5 - - - +
1494N ALA* 1.3 60.2 + - - +
1496N GLU* 3.5 28.3 + - + +
1497N GLU* 2.9 45.1 + - + +
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Residues in contact with ALA1494 (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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1490N LYS 2.9 19.5 + - - +
1491N THR* 3.2 12.3 + - + +
1493N LYS* 1.3 78.7 - - - +
1495N ILE* 1.3 59.6 + - + +
1497N GLU* 3.9 6.2 + - - +
1498N ALA* 3.6 16.3 + - - +
88O GLU* 4.1 17.3 - - - +
92O LEU* 3.9 20.6 - - + -
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Residues in contact with ILE1495 (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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1487N VAL* 4.9 1.1 - - + -
1491N THR* 2.9 25.5 + - + +
1492N LEU* 3.7 7.6 - - + +
1494N ALA* 1.3 74.0 - - - +
1496N GLU* 1.3 61.2 + - - +
1497N GLU 3.2 0.2 - - - -
1498N ALA* 3.0 7.1 + - - +
1499N ARG* 2.9 41.9 + - + +
80O VAL* 3.6 41.1 - - + -
84O ARG* 4.1 16.8 - - + +
85O LEU* 3.8 32.3 - - + -
88O GLU* 3.6 20.6 - - + -
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Residues in contact with GLU1496 (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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1492N LEU 2.9 17.7 + - - +
1493N LYS* 3.5 32.9 + - + +
1495N ILE* 1.3 77.6 - - - +
1497N GLU* 1.3 62.5 + - - +
1499N ARG* 3.4 23.5 + - - +
1500N LYS* 2.9 34.6 + - + +
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Residues in contact with GLU1497 (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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1493N LYS* 2.9 29.6 + - + +
1494N ALA* 4.2 6.7 - - - +
1496N GLU* 1.3 80.4 - - - +
1498N ALA* 1.3 60.4 + - - +
1500N LYS* 3.6 26.5 + - - +
1501N GLU* 2.9 31.5 + - - +
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Residues in contact with ALA1498 (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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1494N ALA 3.6 11.2 + - - +
1495N ILE* 3.0 11.5 + - + +
1497N GLU* 1.3 80.9 - - - +
1499N ARG* 1.3 59.6 + - - +
1501N GLU* 3.3 24.4 - - - +
1502N ALA* 3.7 8.1 + - - +
84O ARG* 3.6 31.9 + - - +
88O GLU* 4.1 13.9 - - - +
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Residues in contact with ARG1499 (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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1495N ILE* 2.9 27.5 + - + +
1496N GLU* 3.7 28.1 + - - +
1498N ALA* 1.3 77.0 - - - +
1500N LYS* 1.3 61.9 + - - +
1501N GLU 3.6 0.2 + - - -
1502N ALA* 3.7 18.4 + - - +
78O ASN 5.3 1.4 + - - -
79O LEU 3.5 24.5 + - - -
80O VAL* 3.5 4.2 - - - +
81O PRO* 3.3 31.9 - - - +
84O ARG* 5.7 3.6 - - + +
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Residues in contact with LYS1500 (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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1496N GLU* 2.9 26.1 + - + +
1497N GLU* 3.2 29.1 + - - +
1499N ARG* 1.3 78.9 - - - +
1501N GLU* 1.3 61.8 + - - +
1502N ALA 3.3 4.9 + - - +
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Residues in contact with GLU1501 (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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1497N GLU 2.9 15.9 + - - +
1498N ALA* 3.3 18.3 - - - +
1500N LYS* 1.3 75.0 - - - +
1502N ALA* 1.3 83.9 + - - +
84O ARG* 5.8 0.7 + - - -
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Residues in contact with ALA1502 (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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1498N ALA 3.7 6.7 + - - +
1499N ARG* 3.7 17.8 + - - +
1500N LYS 3.3 5.5 - - - +
1501N GLU* 1.3 98.1 - - - +
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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