Contacts of the strand formed by residues 1649 - 1654 (chain A) in PDB entry 3H6N
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 SER1649 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1559A ASN* 3.4 13.9 - - - +
1610A TRP* 3.6 8.8 - - - +
1611A PHE* 3.5 42.5 + - - +
1647A GLY 3.5 4.4 + - - -
1648A ALA* 1.3 71.2 - - - +
1650A LEU* 1.3 60.4 + - - +
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Residues in contact with LEU1650 (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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1558A LEU* 3.8 35.7 - - + -
1559A ASN 2.9 7.2 + - - +
1560A VAL* 3.3 12.9 - - + -
1561A SER* 2.9 26.9 + - - -
1583A VAL* 5.1 0.4 - - + -
1587A ILE* 4.6 0.2 - - + -
1608A LEU* 3.7 34.3 - - + -
1609A GLU 3.3 5.2 - - - +
1610A TRP* 3.5 41.7 - - + -
1611A PHE* 4.8 3.1 - - - -
1620A LEU* 4.0 11.7 - - + -
1639A LEU* 5.3 2.9 - - + -
1644A ILE* 4.7 8.1 - - + -
1648A ALA* 4.5 7.0 - - + +
1649A SER* 1.3 75.9 - - - +
1651A ALA* 1.3 61.5 + - - +
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Residues in contact with ALA1651 (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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1561A SER* 3.3 15.3 - - - +
1563A GLN* 3.8 21.1 - - + +
1607A ASP 3.8 0.7 - - - +
1608A LEU* 3.5 4.9 - - - +
1609A GLU* 2.8 43.9 + - + +
1611A PHE* 3.3 31.5 - - + -
1650A LEU* 1.3 73.1 - - - +
1652A MSE 1.3 59.5 + - - +
1653A SER* 5.3 1.6 + - - +
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Residues in contact with MSE1652 (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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1560A VAL* 4.3 6.5 - - + +
1561A SER 2.7 14.8 + - - +
1562A PHE* 3.5 33.9 - - + -
1563A GLN* 2.8 32.6 + - - +
1584A LYS* 4.1 23.6 - - + +
1587A ILE* 3.4 41.1 - - + -
1588A LEU* 4.0 15.3 - - - -
1606A VAL* 3.9 26.9 - - + -
1607A ASP 3.3 8.1 - - - +
1608A LEU* 4.1 11.4 - - + +
1651A ALA* 1.3 74.8 - - - +
1653A SER* 1.3 62.5 + - - +
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Residues in contact with SER1653 (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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1562A PHE* 4.5 1.3 - - - -
1563A GLN* 3.8 25.3 + - - +
1606A VAL* 3.0 10.0 - - - -
1607A ASP* 2.9 43.7 + - - -
1651A ALA* 5.3 1.8 - - - +
1652A MSE 1.3 76.5 + - - +
1654A LEU* 1.3 65.7 + - - +
1655A ILE* 3.7 3.0 - - - +
1679A UNX 4.4 4.0 - - - -
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Residues in contact with LEU1654 (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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2A ARS 4.6 13.7 - - - -
1562A PHE* 4.0 24.1 - - + -
1563A GLN 4.8 1.3 + - - +
1601A PRO* 3.7 34.5 - - + -
1605A ASP* 3.5 16.8 - - + +
1606A VAL* 3.8 2.7 - - + -
1653A SER* 1.3 73.5 - - - +
1655A ILE* 1.3 62.6 + - - +
1679A UNX 2.9 24.8 - - - -
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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