Contacts of the strand formed by residues 1582 - 1586 (chain D) in PDB entry 1UKJ
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 ALA1582 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1575D ALA* 3.9 8.5 - - - -
1580D GLY 3.5 0.4 - - - -
1581D GLU* 1.3 76.0 - - - +
1583D GLY* 1.3 59.9 + - - +
1725D VAL* 3.2 5.2 - - - +
1726D GLY 2.7 41.6 + - - +
1727D SER 4.0 9.9 - - - +
1728D GLN* 3.5 31.2 - - - +
1731D VAL* 3.8 10.9 - - + +
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Residues in contact with GLY1583 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1571D GLU* 3.6 33.9 + - - +
1572D ALA* 5.8 0.2 - - - +
1574D MET* 5.8 0.4 - - - -
1582D ALA* 1.3 75.5 - - - +
1584D LEU* 1.3 64.6 + - - +
1723D ILE* 5.7 0.4 - - - -
1724D VAL 3.1 12.6 - - - -
1725D VAL* 4.2 7.0 - - - -
1731D VAL* 3.8 6.9 - - - +
1735D ARG* 3.7 13.2 + - - -
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Residues in contact with LEU1584 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1571D GLU* 3.4 13.9 - - - +
1583D GLY* 1.3 73.7 - - - +
1585D ALA* 1.3 62.5 + - - +
1586D LEU* 3.3 21.4 - - + +
1723D ILE* 3.5 6.2 - - - +
1724D VAL* 2.9 33.1 + - + +
1731D VAL* 4.0 11.7 - - + +
1734D ILE* 3.9 18.4 - - + -
1735D ARG* 3.4 70.9 - - + +
1739D LEU* 4.4 18.8 - - + -
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Residues in contact with ALA1585 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1567D LEU* 4.2 18.0 - - + +
1570D LEU* 3.9 17.3 - - + -
1571D GLU* 2.8 23.6 + - + +
1584D LEU* 1.3 75.9 - - - +
1586D LEU* 1.3 66.8 + - - +
1722D GLY 3.7 4.5 - - - +
1723D ILE* 4.1 6.7 - - + -
1739D LEU* 4.7 6.4 - - - +
1745D ALA 4.7 0.5 - - - +
1747D LEU* 3.5 28.8 + - + +
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Residues in contact with LEU1586 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1584D LEU* 3.3 31.2 - - + +
1585D ALA* 1.3 78.1 - - - +
1587D ALA* 1.3 56.5 + - - +
1588D SER 2.7 16.9 + - - +
1591D GLY 3.2 33.0 - - - +
1592D ALA* 3.9 22.0 - - + +
1595D SER* 3.4 18.2 - - - +
1721D ALA* 3.5 3.6 - - - +
1722D GLY 2.7 27.3 + - - +
1724D VAL* 4.0 9.4 - - + -
1739D LEU* 3.6 26.2 - - + -
1745D ALA* 3.3 9.0 - - + +
1747D LEU* 3.8 10.2 - - - +
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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