Contacts of the strand formed by residues 161 - 166 (chain 1) in PDB entry 3EXG
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 CYS 161 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841 HIS 3.1 9.9 - - - +
851 LEU 4.8 0.2 - - - -
861 ILE* 4.8 3.4 - - - -
1451 GLY* 3.6 22.9 - - - -
1481 ILE* 3.6 24.0 - - + -
1491 ALA* 3.8 26.7 - - + +
1521 CYS* 4.9 0.2 - - - -
1601 VAL* 1.3 79.1 - - - +
1621 LEU* 1.3 79.0 + - - +
1631 THR* 3.8 6.4 + - - -
1881 PRO 3.0 4.9 + - - -
1891 CYS* 3.5 3.3 - - - -
1901 ILE* 3.0 23.3 + - - +
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Residues in contact with LEU 162 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751 LEU* 3.9 18.8 - - + -
791 ILE* 3.8 37.0 - - + -
831 ASP* 5.4 0.4 - - + -
841 HIS 2.9 10.5 + - - +
851 LEU* 3.6 25.3 - - + +
861 ILE* 3.1 25.9 + - - +
1601 VAL* 4.3 8.5 - - + +
1611 CYS* 1.3 83.0 - - - +
1631 THR* 1.3 60.6 + - - +
1641 LEU* 3.9 2.2 - - + -
1901 ILE* 3.4 27.6 - - + -
1921 ILE* 3.8 27.4 - - + -
2371 THR* 4.7 4.5 - - + -
2531 MET* 6.0 0.2 - - + -
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Residues in contact with THR 163 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861 ILE* 3.7 5.6 - - + -
1411 GLN 3.5 10.5 - - - +
1421 VAL* 3.5 47.3 - - + +
1451 GLY* 3.2 21.4 + - - -
1611 CYS* 4.0 1.2 - - - -
1621 LEU* 1.3 75.6 - - - +
1641 LEU* 1.3 60.4 + - - +
1651 TYR* 3.8 4.7 - - - -
1891 CYS* 3.4 15.6 - - - -
1901 ILE 2.9 12.7 + - - -
1911 PHE* 3.7 11.1 - - - -
1921 ILE* 3.0 20.8 + - - +
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Residues in contact with LEU 164 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711 CYS* 6.0 0.2 - - + -
751 LEU* 3.9 11.2 - - + -
851 LEU* 3.8 33.4 - - + -
861 ILE 3.1 20.7 + - - +
871 THR* 3.8 15.4 - - - +
881 ALA 3.9 0.3 + - - -
941 PHE* 3.1 32.5 - - + -
1411 GLN* 3.2 19.8 + - - +
1621 LEU* 4.3 6.3 - - + +
1631 THR* 1.3 74.2 - - - +
1651 TYR* 1.3 64.9 + - - +
1921 ILE* 3.0 24.5 - - + +
1941 GLU* 3.6 28.0 - - + +
2551 LEU* 5.8 0.7 - - + -
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Residues in contact with TYR 165 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881 ALA* 5.1 2.9 - - - +
1411 GLN* 3.5 18.4 - - - +
1421 VAL* 3.9 22.7 - - + -
1631 THR 3.8 9.4 - - - -
1641 LEU* 1.3 79.9 - - - +
1661 GLY* 1.3 76.2 - - - +
1691 ALA* 4.3 7.0 - - + -
1701 ALA* 3.9 24.6 - - + +
1751 ILE* 3.9 14.6 - - + -
1791 TYR* 2.5 30.5 + - - -
1911 PHE* 4.5 11.7 - + + -
1921 ILE 2.9 23.2 + - - -
1931 CYS* 3.3 25.6 - - + +
1941 GLU* 2.8 33.8 + - - -
2131 TYR 5.2 0.7 + - - -
2521 LEU* 3.9 13.9 - - - +
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Residues in contact with GLY 166 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881 ALA* 5.3 4.8 - - - +
1411 GLN* 5.2 0.2 - - - +
1651 TYR* 1.3 91.1 - - - +
1671 ASP* 1.3 69.1 + - - +
1681 GLY 3.0 3.8 - - - -
1691 ALA* 3.0 18.3 + - - +
1701 ALA 3.5 0.5 + - - -
1931 CYS* 4.4 0.9 - - - -
1941 GLU* 3.9 9.4 - - - -
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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