Contacts of the helix formed by residues 1474 - 1478 (chain N) in PDB entry 5X22
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 ALA1474 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041M GLU 4.9 2.9 - - - +
1044M GLY* 4.0 5.6 - - - +
1046M ALA* 4.0 6.9 - - - +
1106N VAL* 3.9 10.8 - - + -
1218N GLY 3.2 11.2 - - - +
1220N ALA* 4.0 16.2 - - + +
1462N LEU* 4.0 18.4 - - + -
1472N ILE* 2.7 22.7 + - + +
1473N PRO* 1.3 76.5 - - - +
1475N GLY* 1.3 66.6 + - - +
1476N THR 3.3 1.2 + - - -
1477N GLY 3.2 9.2 + - - -
1478N SER* 3.9 5.5 - - - +
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Residues in contact with GLY1475 (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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1044M GLY* 3.3 15.0 - - - -
1218N GLY* 2.3 25.5 + - - -
1474N ALA* 1.3 61.4 - - - +
1476N THR* 1.3 58.9 + - - -
1477N GLY 3.0 4.0 - - - -
1478N SER* 3.0 17.0 + - - -
1481N VAL* 3.2 15.2 - - - +
17O TYR* 3.4 28.2 - - - +
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Residues in contact with THR1476 (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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1044M GLY 3.2 3.8 + - - +
1046M ALA* 3.1 15.1 + - - +
1047M HIS* 3.5 18.0 + - - -
754N PHE* 4.6 1.3 - - + -
758N GLU* 2.3 32.2 + - + +
762N GLN* 3.2 26.7 - - - +
1471N LEU* 4.4 0.2 - - - +
1474N ALA 3.3 0.6 + - - -
1475N GLY* 1.3 70.3 - - - -
1477N GLY* 1.3 55.4 + - - +
1478N SER 3.4 0.4 - - - -
1481N VAL* 4.3 0.9 - - - -
1482N ARG* 3.6 17.4 - - - +
17O TYR* 3.9 11.0 - - + +
20O THR* 3.7 22.9 - - + -
21O VAL* 4.0 16.6 - - + +
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Residues in contact with GLY1477 (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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1046M ALA* 3.6 3.0 - - - +
1471N LEU* 3.7 22.8 - - - +
1472N ILE 3.4 25.7 - - - +
1473N PRO* 3.8 6.2 - - - +
1474N ALA 3.2 4.4 + - - -
1475N GLY 3.0 1.0 - - - -
1476N THR* 1.3 79.7 + - - +
1478N SER* 1.3 64.1 + - - +
1479N ASP* 3.6 2.1 + - - +
1482N ARG* 3.3 14.7 + - - -
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Residues in contact with SER1478 (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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1106N VAL* 5.6 0.5 - - - +
1107N VAL 4.9 2.4 + - - -
1108N ARG* 5.7 4.3 - - - +
1217N ILE* 5.0 0.7 - - - +
1218N GLY* 3.7 25.3 - - - -
1473N PRO* 4.2 6.3 + - - -
1474N ALA* 3.9 10.1 + - - +
1475N GLY 3.0 20.5 + - - -
1476N THR 3.4 0.2 - - - -
1477N GLY* 1.3 77.6 - - - +
1479N ASP* 1.3 66.9 + - - +
1480N PHE* 3.0 15.0 + - - +
1481N VAL* 3.2 5.9 + - - -
1482N ARG* 3.0 23.1 + - - +
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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