Contacts of the strand formed by residues 1701 - 1704 (chain D) in PDB entry 3SE2
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 LEU1701 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D 3AB 4.3 17.0 - - + +
1628D TYR* 3.8 39.7 - - + -
1633D TYR* 4.3 15.9 - - + -
1634D PHE 3.2 13.2 - - - +
1635D ALA* 4.4 0.2 - - - +
1636D VAL* 4.1 0.8 - - - +
1640D TYR* 3.9 23.1 - - + -
1693D THR* 2.9 25.1 + - - -
1694D ASP* 3.3 20.2 + - + +
1699D PRO 3.7 1.4 - - - -
1700D SER* 1.3 82.1 - - - +
1702D PHE* 1.3 74.8 + - - +
1703D VAL* 4.6 0.4 - - + -
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Residues in contact with PHE1702 (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 LYS* 4.0 20.4 - - + -
1599D LEU* 3.8 28.3 - - + -
1632D THR 3.6 0.5 - - - +
1633D TYR* 3.4 5.7 - - - +
1634D PHE* 2.8 37.8 + - + -
1636D VAL* 4.0 13.5 - - + -
1662D VAL* 5.5 0.9 - - + -
1664D THR* 3.6 21.8 - - + -
1667D TYR* 3.5 46.2 - + - -
1691D THR* 3.8 8.3 - - - +
1692D VAL 3.3 13.2 - - - +
1693D THR* 3.7 6.1 - - - -
1699D PRO* 3.5 31.2 - - + -
1701D LEU* 1.3 77.4 - - - +
1703D VAL* 1.3 66.4 + - - +
1704D ALA 4.1 0.4 - - - -
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Residues in contact with VAL1703 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1628D TYR* 4.0 12.3 - - + +
1629D GLY 4.7 2.2 - - - -
1630D LYS 4.4 0.7 - - - -
1631D GLY* 3.8 28.5 - - - +
1632D THR 3.3 6.1 - - - +
1633D TYR* 3.8 33.4 - - + -
1691D THR* 3.4 6.5 - - - -
1692D VAL* 2.8 49.9 + - + +
1701D LEU* 4.6 2.9 - - + -
1702D PHE* 1.3 77.4 - - - +
1704D ALA* 1.3 61.3 + - - +
1705D PHE* 3.3 27.6 - - + -
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Residues in contact with ALA1704 (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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1623D LYS* 5.3 0.7 + - - -
1631D GLY* 3.6 3.3 - - - -
1632D THR* 3.0 33.2 + - - -
1634D PHE* 3.7 25.5 - - + -
1662D VAL* 4.4 10.5 - - + -
1691D THR* 4.3 5.6 - - + -
1702D PHE 4.1 0.4 - - - -
1703D VAL* 1.3 73.7 - - - +
1705D PHE* 1.3 61.7 + - - +
1706D TYR 5.1 1.1 - - - +
1709D GLN* 3.7 25.8 - - + +
1710D ALA* 5.5 1.8 - - + -
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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