Contacts of the helix formed by residues 1622 - 1628 (chain A) in PDB entry 5JCY
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 MET1622 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1618A ILE* 3.6 21.8 - - + +
1619A LEU* 2.8 15.7 + - + +
1621A PRO* 1.3 79.2 - - + +
1623A ILE* 1.3 60.1 + - - +
1624A VAL 3.5 1.1 - - - -
1625A SER* 3.6 2.9 + - - -
1626A GLY* 2.8 30.0 + - - -
1657A TYR* 3.7 47.0 - - + +
1661A SER* 3.9 26.5 - - - +
1662A ILE* 3.8 16.5 - - + +
1665A GLN* 3.6 32.3 - - + +
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Residues in contact with ILE1623 (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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1619A LEU* 3.4 34.5 - - + +
1620A GLN* 3.5 6.6 + - - +
1622A MET* 1.3 79.8 - - + +
1624A VAL* 1.3 59.6 + - - +
1627A MET* 2.8 39.8 + - + +
1662A ILE* 4.1 11.4 - - + -
1693A ILE* 4.2 6.7 - - + -
1694A ILE* 3.7 35.0 - - + +
1697A ILE* 3.7 45.8 - - + -
1698A THR* 3.4 22.4 - - - +
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Residues in contact with VAL1624 (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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1620A GLN 4.8 3.2 + - - +
1621A PRO 5.2 1.0 + - - -
1623A ILE* 1.3 75.9 - - + +
1625A SER* 1.3 58.3 + - - +
1627A MET* 5.0 0.9 - - - -
1628A LEU* 2.8 37.1 + - + +
1629A GLU* 3.1 24.8 + - + -
1697A ILE* 4.0 14.4 - - + +
1698A THR* 5.3 2.2 - - - +
1701A ASN* 3.3 48.0 - - + +
1705A ARG* 4.8 10.3 - - - +
1708A MET* 5.8 0.2 - - + -
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Residues in contact with SER1625 (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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1621A PRO 4.8 5.5 + - - -
1622A MET 3.6 7.5 + - - -
1623A ILE 3.3 0.2 - - - -
1624A VAL* 1.3 80.9 - - - +
1626A GLY* 1.3 60.4 + - - +
1629A GLU* 3.5 21.2 + - - +
1630A HIS* 2.9 30.0 + - - +
1656A THR* 3.2 19.1 - - - +
1657A TYR* 2.3 36.7 + - - -
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Residues in contact with GLY1626 (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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1622A MET 2.8 18.1 + - - -
1623A ILE 3.9 0.2 - - - -
1625A SER* 1.3 80.2 + - - +
1627A MET* 1.3 59.6 + - - +
1630A HIS* 4.7 6.4 + - - +
1657A TYR 3.7 0.4 + - - -
1658A THR* 3.6 29.2 - - - -
1659A LEU* 3.7 15.7 + - - +
1662A ILE* 4.0 5.8 - - - -
1720A ASN* 3.5 11.1 + - - +
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Residues in contact with MET1627 (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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1623A ILE* 2.8 25.2 + - + +
1624A VAL 4.6 0.2 - - - +
1626A GLY* 1.3 75.9 - - - +
1628A LEU* 1.3 63.7 + - + +
1630A HIS 5.4 0.2 - - - -
1659A LEU* 4.1 13.2 - - - -
1662A ILE* 4.1 9.9 - - + -
1694A ILE* 4.2 13.7 - - + -
1698A THR* 3.4 27.4 - - + +
1716A GLN* 4.4 5.8 - - - +
1717A ILE* 4.5 9.5 - - + +
1720A ASN* 2.9 42.4 + - + +
1721A VAL* 4.6 6.1 - - + -
1724A LEU* 3.9 30.3 - - + -
1742A LEU* 6.1 0.2 - - + -
1745A LEU* 4.0 26.2 - - + -
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Residues in contact with LEU1628 (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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1624A VAL* 2.8 21.4 + - + +
1626A GLY 3.6 0.2 - - - -
1627A MET* 1.3 84.4 - - + +
1629A GLU* 1.3 55.0 + - - +
1630A HIS 3.7 2.2 - - - -
1698A THR* 3.6 39.5 - - + +
1701A ASN* 4.3 10.8 - - + -
1702A LEU* 3.9 22.9 - - + +
1705A ARG* 5.6 0.4 - - - -
1708A MET* 4.0 27.1 - - + +
1713A LYS* 2.5 45.2 + - + +
1716A GLN* 4.8 1.4 - - - +
1717A ILE* 3.9 29.2 - - + -
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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