Contacts of the helix formed by residues 1688 - 1696 (chain B) in PDB entry 5V7W
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 SER1688 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1684B THR* 3.3 16.5 + - - -
1685B ASP* 3.0 29.8 + - - -
1687B GLY* 1.3 76.4 - - - +
1689B VAL* 1.3 62.9 + - - +
1690B PRO 3.5 0.7 - - - -
1691B HIS* 3.4 10.3 + - - +
1692B VAL* 3.1 26.2 + - - +
1701B TYR* 4.1 14.9 - - - -
1901B 91J 4.1 13.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1689 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1690A PRO* 4.1 17.7 - - + -
1684B THR* 4.4 5.6 - - + -
1685B ASP 3.8 11.0 - - - +
1686B ALA* 2.9 25.9 + - - +
1688B SER* 1.3 76.9 - - - +
1690B PRO* 1.3 65.3 - - + +
1692B VAL* 3.3 1.1 + - - -
1693B ASN* 3.0 43.5 + - - +
1737B HIS* 4.3 22.7 - - + -
1739B TYR* 3.1 18.9 + - + +
1796B LEU* 3.8 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1690 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1647A LYS* 5.6 10.3 + - - +
1649A GLU* 6.0 1.8 - - - +
1686A ALA 5.0 0.9 - - - +
1689A VAL* 3.8 34.8 - - + -
1690A PRO* 4.3 7.4 - - + -
1693A ASN* 5.8 0.9 - - - +
1796A LEU* 6.1 2.0 - - + -
1617B PHE* 4.0 12.2 - - + -
1686B ALA 3.5 5.4 - - - +
1687B GLY* 3.4 16.6 - - - +
1689B VAL* 1.3 94.4 - - + +
1691B HIS* 1.3 60.4 + - - +
1693B ASN* 3.4 10.8 + - + +
1694B ARG* 3.3 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1691 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1647A LYS* 6.1 1.6 - - - +
1735A ARG* 4.5 21.5 - - - +
1687B GLY 4.8 1.7 + - - +
1688B SER* 3.4 16.6 + - - +
1689B VAL 3.2 0.4 - - - -
1690B PRO* 1.3 77.6 - - - +
1692B VAL* 1.3 60.7 + - - +
1694B ARG* 3.3 1.3 + - - -
1695B ASN* 2.8 63.3 + - + +
1696B GLY 4.2 2.0 + - - -
1698B ASN* 3.3 26.6 + - - -
1700B SER* 3.8 17.2 + - - -
1701B TYR* 3.6 30.9 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1692 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1684B THR* 4.9 1.6 - - + -
1688B SER* 3.1 18.6 + - - +
1691B HIS* 1.3 74.2 - - - +
1693B ASN* 1.3 60.1 + - - +
1696B GLY* 2.7 34.4 + - - +
1697B PHE* 3.7 30.7 - - + -
1701B TYR* 3.6 34.1 - - + +
1739B TYR* 3.6 35.4 - - + +
1793B PRO* 3.7 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1693 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1617A PHE* 6.1 0.4 - - - -
1617B PHE* 3.7 38.6 - - + +
1619B VAL* 4.1 5.3 - - - +
1651B ILE* 3.2 39.6 - - + +
1653B ASN* 2.8 22.7 + - - +
1656B LEU* 4.0 2.6 - - - +
1689B VAL* 3.0 32.7 + - - +
1690B PRO* 3.7 5.3 - - - +
1691B HIS 3.2 0.4 - - - -
1692B VAL* 1.3 78.3 - - - +
1694B ARG* 1.3 56.6 + - - +
1739B TYR* 2.7 24.1 + - - -
1793B PRO* 4.9 0.9 - - - -
1796B LEU* 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1694 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1619A VAL* 2.9 30.3 + - - +
1621A GLU* 3.6 29.5 + - - +
1647A LYS* 4.5 11.1 - - - +
1649A GLU* 3.0 28.4 + - - -
1614B GLN 2.9 27.5 + - - +
1615B GLN* 2.9 33.2 + - + +
1616B ASN* 2.9 19.7 + - - +
1617B PHE* 3.8 8.8 - - + -
1653B ASN* 3.0 18.4 + - - +
1656B LEU* 4.2 0.9 - - - +
1690B PRO 3.3 13.4 + - - +
1691B HIS* 4.0 2.5 - - - +
1692B VAL 3.3 0.2 - - - -
1693B ASN* 1.3 78.6 - - - +
1695B ASN* 1.3 80.8 + - - +
1696B GLY 3.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1695 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1647A LYS* 6.4 0.2 - - - +
1615B GLN* 3.8 9.7 - - - +
1656B LEU* 3.5 15.7 - - - +
1691B HIS* 2.8 51.9 + - + +
1694B ARG* 1.3 99.9 - - - +
1696B GLY* 1.3 60.7 + - - +
1697B PHE 3.9 0.2 + - - -
1698B ASN* 3.8 37.0 + - - +
1789B TYR* 4.9 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1696 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1656B LEU* 3.8 15.7 - - - +
1691B HIS* 4.2 0.7 + - - -
1692B VAL* 2.7 36.8 + - - -
1694B ARG 3.8 0.6 - - - -
1695B ASN* 1.3 77.7 - - - +
1697B PHE* 1.3 65.5 + - - -
1698B ASN* 3.3 8.2 + - - +
1701B TYR* 4.1 6.9 - - - +
1791B ALA 4.8 3.1 - - - -
1793B PRO* 4.4 9.6 - - - -
----------------------------------------------------------
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