Contacts of the strand formed by residues 160 - 166 (chain 6) in PDB entry 1MVW
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 THR 160 (chain 6).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1536 LEU* 4.4 6.7 - - + -
1546 ASP 3.2 9.0 - - - +
1556 SER* 2.6 25.4 + - - +
1596 VAL* 1.4 71.6 - - - +
1616 HIS* 1.3 74.9 + - - +
1626 ASN* 5.0 2.7 - - - +
1776 ARG* 3.3 6.8 - - - +
1786 LEU* 2.9 47.1 + - + -
1806 LEU 3.1 16.5 + - - -
2616 LEU* 5.1 0.3 - - - +
2746 ILE* 3.6 30.3 - - + +
2776 THR* 6.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 161 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736 HIS 5.2 0.9 - - - -
1086 ALA* 4.9 7.4 - - + -
1096 PRO* 3.6 42.4 - - + +
1106 LEU* 5.2 3.2 + - - +
1526 VAL 4.1 0.4 - - - -
1536 LEU* 3.4 5.0 - - - -
1546 ASP* 2.7 41.2 + - + +
1596 VAL* 4.0 32.2 - - + +
1606 THR* 1.3 80.3 + - - +
1626 ASN* 1.3 66.1 + - - +
1636 VAL* 4.2 11.7 - - + -
1756 ILE* 4.0 8.7 - - + +
1766 MET 3.0 17.0 - - - -
1776 ARG* 3.7 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 162 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1516 ILE* 4.5 6.1 - - + +
1526 VAL 3.2 6.7 - - - -
1536 LEU* 3.6 21.4 - - - +
1606 THR* 5.0 2.1 - - - +
1616 HIS* 1.3 75.4 - - - +
1636 VAL* 1.3 63.9 + - - +
1646 PRO* 3.5 1.8 - - - +
1756 ILE* 3.2 24.1 - - - +
1766 MET* 2.9 14.8 + - + +
1786 LEU* 5.8 0.5 + - - +
2776 THR* 2.9 31.4 - - - +
2786 THR* 3.4 34.1 + - - +
2816 SER* 3.6 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 163 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096 PRO* 3.5 33.9 - - + -
1366 ILE* 5.1 2.5 - - + -
1386 ALA* 3.4 21.1 - - + -
1396 VAL* 5.0 0.9 - - + -
1516 ILE* 4.2 1.1 - - - +
1526 VAL 2.9 28.4 + - - +
1546 ASP* 5.8 0.7 - - + -
1616 HIS* 4.2 9.4 - - + -
1626 ASN* 1.3 79.4 - - - +
1646 PRO* 1.3 61.9 - - - +
1656 ILE* 3.5 17.8 + - + +
1706 ALA* 3.6 31.0 - - + -
1756 ILE* 3.9 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 164 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1506 GLY 3.7 7.2 - - - +
1516 ILE* 3.9 16.2 - - + -
1626 ASN 3.5 7.2 - - - +
1636 VAL* 1.3 83.8 - - - +
1656 ILE* 1.3 58.6 + - - +
1706 ALA* 3.6 0.2 - - - -
1716 LEU* 2.8 36.6 + - + +
1746 ALA* 3.7 15.5 - - + -
1756 ILE* 4.0 17.3 - - + +
2816 SER* 3.4 20.6 - - - +
2856 CYS* 3.8 21.3 - - - -
2936 LEU* 4.4 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 165 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1386 ALA* 3.7 10.1 - - + +
1396 VAL* 3.5 39.7 - - + +
1426 LEU* 3.9 18.8 - - + -
1486 THR* 3.4 16.8 - - - +
1496 THR* 3.1 23.4 - - - +
1506 GLY 2.9 13.9 + - - +
1526 VAL* 4.5 2.7 - - + -
1636 VAL* 3.6 20.2 - - + +
1646 PRO* 1.3 75.1 - - - +
1666 TYR* 1.3 61.0 + - - +
1686 GLY* 3.6 25.8 - - - +
1696 TYR 3.7 3.1 - - - +
1706 ALA* 3.6 15.7 - - + -
1716 LEU* 4.7 1.1 - - - -
2936 LEU* 4.3 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 166 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1496 THR* 3.6 18.4 - - + -
1656 ILE* 1.3 73.2 - - - +
1676 GLU* 1.3 91.0 + - + +
1686 GLY 2.9 4.2 + - - -
1696 TYR* 3.1 26.6 + - + +
1716 LEU* 4.3 21.0 - - + +
2896 ILE* 3.7 35.4 - - + -
2926 ASP* 4.0 16.8 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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