Contacts of the strand formed by residues 1606 - 1610 (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 GLU1606 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1601D LEU* 4.7 0.2 - - - +
1605D ASP* 1.3 75.8 - - - +
1607D VAL* 1.3 68.4 + - - +
1608D LEU* 3.0 26.0 + - - +
1631D LYS* 3.2 24.9 - - + +
1633D ARG* 3.5 18.3 - - + +
1646D ALA 4.1 3.7 - - - +
1648D THR* 3.1 18.2 + - - +
1650D ALA* 2.7 23.8 + - + +
1651D THR* 2.4 30.8 + - - -
1652D ARG* 3.0 23.6 + - - +
1653D VAL 3.7 5.7 + - - +
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Residues in contact with VAL1607 (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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1597D LEU* 5.4 2.0 - - + -
1601D LEU* 3.7 23.3 - - + -
1606D GLU* 1.3 76.5 - - - +
1608D LEU* 1.3 65.9 + - - +
1609D LEU* 3.3 28.8 + - + +
1621D LEU* 4.9 5.6 - - + -
1625D ILE* 6.3 0.2 - - + -
1630D VAL* 3.4 29.6 - - + -
1631D LYS 2.6 10.9 + - - +
1632D LEU* 3.4 9.1 - - + -
1633D ARG 2.8 26.9 + - - -
1653D VAL* 3.5 25.6 - - + +
1655D TYR* 4.4 4.7 - - + -
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Residues in contact with LEU1608 (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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1606D GLU* 3.0 29.3 + - - +
1607D VAL* 1.3 71.2 - - - +
1609D LEU* 1.3 60.0 + - - +
1633D ARG* 3.2 23.3 - - + -
1635D VAL* 4.1 13.0 - - + -
1637D MET* 3.6 9.7 - - + +
1643D LEU* 3.8 11.9 - - + -
1646D ALA* 4.2 14.1 - - + +
1647D MET* 3.5 34.1 - - + -
1651D THR* 3.5 16.8 - - + +
1653D VAL 3.2 6.8 + - - +
1654D ILE* 3.4 13.9 - - + -
1655D TYR 3.0 25.5 + - - +
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Residues in contact with LEU1609 (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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1607D VAL* 3.3 38.6 - - + +
1608D LEU* 1.3 73.5 - - - +
1610D GLY* 1.3 66.6 + - - +
1613D LEU* 4.1 5.8 - - + -
1621D LEU* 4.0 34.1 - - + -
1622D HIS* 4.8 1.1 - - - +
1632D LEU* 3.8 24.9 - - + -
1633D ARG 2.6 12.8 + - - +
1634D HIS* 3.0 31.1 - - + +
1635D VAL 2.6 34.1 + - - +
1637D MET* 3.3 5.8 - - - -
1655D TYR* 3.3 18.2 - - + +
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Residues in contact with GLY1610 (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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1609D LEU* 1.3 74.6 - - - +
1611D ASN* 1.3 58.1 + - - +
1612D THR 3.6 6.1 - - - -
1613D LEU* 4.1 6.5 - - - +
1634D HIS* 2.7 28.8 + - - -
1635D VAL 3.4 7.9 - - - -
1637D MET* 3.4 11.1 - - - +
1655D TYR 3.0 12.7 + - - -
1656D PHE* 4.0 14.9 - - - +
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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