Contacts of the helix formed by residues 1703 - 1720 (chain X) in PDB entry 3HM6
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 VAL1703 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1698X PHE* 3.3 23.8 + - + +
1699X VAL* 4.0 9.9 - - + -
1702X SER* 1.3 75.8 - - - +
1704X GLY* 1.3 59.9 + - - +
1706X PRO* 3.3 5.8 - - + +
1707X LEU* 3.0 38.2 + - + +
1936X LEU* 3.6 23.3 - - + -
1939X VAL* 4.1 12.6 - - + -
1940X ILE* 3.9 11.2 - - + -
1986X TRP* 3.4 43.3 - - + -
1989X ILE* 5.5 0.4 - - + -
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Residues in contact with GLY1704 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1563X ILE* 4.3 0.8 - - - +
1565X PHE* 3.8 21.5 - - - -
1699X VAL* 2.7 29.8 + - - -
1702X SER 3.4 0.4 - - - -
1703X VAL* 1.3 72.8 - - - +
1705X GLU* 1.3 63.1 + - - +
1707X LEU* 4.4 0.9 - - - -
1708X TYR* 3.0 27.4 + - - +
1997X PHE* 3.3 12.0 - - - -
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Residues in contact with GLU1705 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1563X ILE* 3.8 25.4 - - + +
1565X PHE* 4.6 1.4 - - - -
1700X ARG 5.6 0.6 + - - -
1701X ASP 5.9 2.0 - - - +
1702X SER* 4.1 5.3 + - - +
1704X GLY* 1.3 77.4 - - - +
1706X PRO* 1.4 69.3 - - + +
1708X TYR* 3.7 2.4 - - - +
1709X MET* 3.0 42.3 + - + +
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Residues in contact with PRO1706 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18X UNX 2.7 29.7 - - - -
1702X SER 3.2 21.1 - - - +
1703X VAL* 3.3 13.9 - - - +
1705X GLU* 1.4 95.2 - - + +
1707X LEU* 1.3 61.9 + - - +
1709X MET* 4.1 4.9 - - + -
1710X LEU* 3.0 16.5 + - - +
1932X PHE 4.5 0.3 - - - +
1935X ASP* 4.1 8.7 - - + +
1936X LEU* 3.9 19.5 - - + +
1939X VAL* 4.1 20.4 - - + -
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Residues in contact with LEU1707 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1699X VAL* 5.2 2.9 - - + -
1703X VAL* 3.0 25.5 + - + +
1704X GLY 4.1 2.2 - - - +
1706X PRO* 1.3 77.4 - - - +
1708X TYR* 1.3 57.8 + - - +
1710X LEU* 3.5 8.5 + - + +
1711X PHE* 3.1 24.6 + - - +
1936X LEU* 3.7 32.9 - - + +
1940X ILE* 6.2 0.2 - - + -
1989X ILE* 3.2 45.5 - - + +
1990X ILE* 4.3 14.6 - - + +
1993X PRO* 5.4 6.7 - - + +
1996X VAL* 4.6 8.5 - - + -
1997X PHE* 3.9 21.5 - - + -
2009X LEU* 5.9 2.0 - - + -
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Residues in contact with TYR1708 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1563X ILE* 3.9 26.7 - - + -
1564X PRO* 3.3 36.5 - - + +
1704X GLY 3.0 19.9 + - - +
1705X GLU 3.7 2.9 - - - +
1707X LEU* 1.3 74.5 - - - +
1709X MET* 1.3 71.9 + - - +
1710X LEU 3.2 0.2 - - - -
1711X PHE* 3.2 24.2 + + - +
1712X ARG* 2.9 45.6 + - + +
1997X PHE* 3.6 28.2 - + + -
1999X VAL* 4.1 6.9 - - + +
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Residues in contact with MET1709 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18X UNX 3.9 8.7 - - - -
1705X GLU* 3.0 36.0 + - + +
1706X PRO* 3.5 7.8 + - + +
1708X TYR* 1.3 82.7 - - - +
1710X LEU* 1.3 52.4 + - - +
1712X ARG* 3.6 6.3 - - + +
1713X GLY* 2.8 33.1 + - - -
1932X PHE* 3.9 31.4 - - + -
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Residues in contact with LEU1710 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18X UNX 4.1 1.5 - - - -
1706X PRO 3.0 13.8 + - - +
1707X LEU* 3.5 13.0 - - + +
1708X TYR 3.2 0.2 - - - -
1709X MET* 1.3 73.0 - - - +
1711X PHE* 1.3 65.6 + - - +
1713X GLY* 3.2 0.5 + - - -
1714X ILE* 2.9 46.6 + - + +
1929X LEU* 4.6 6.7 - - + +
1932X PHE* 3.7 30.5 - - + +
1933X VAL* 4.2 18.6 - - + -
1936X LEU* 3.7 26.9 - - + -
1990X ILE* 5.4 1.1 - - + -
2009X LEU* 4.1 20.0 - - + -
2012X ILE* 4.2 17.3 - - + -
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Residues in contact with PHE1711 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1707X LEU 3.1 12.7 + - - +
1708X TYR* 3.2 29.8 + + + +
1710X LEU* 1.3 78.9 - - - +
1712X ARG* 1.3 64.3 + - + +
1714X ILE* 3.4 2.1 + - - +
1715X LYS* 2.9 48.9 + - + +
1993X PRO* 4.0 26.9 - - + -
1997X PHE* 5.3 1.6 - + + -
1999X VAL* 3.6 33.9 - - + -
2000X GLN 3.5 26.2 - - - -
2001X THR* 4.8 0.2 - - - -
2005X MET* 3.4 44.6 - - + +
2009X LEU* 5.1 3.4 - - + -
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Residues in contact with ARG1712 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1708X TYR* 2.9 51.8 + - + +
1709X MET* 3.8 8.1 - - + +
1711X PHE* 1.3 83.1 - - + +
1713X GLY* 1.3 56.2 + - - +
1715X LYS* 3.7 8.8 - - + +
1716X HIS* 3.0 37.5 + - + -
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Residues in contact with GLY1713 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1709X MET 2.8 21.0 + - - -
1710X LEU 3.6 1.3 - - - -
1712X ARG* 1.3 70.7 - - - +
1714X ILE* 1.3 63.5 + - - +
1716X HIS* 3.5 4.1 + - - +
1717X GLN* 3.1 27.2 + - - +
1929X LEU* 3.9 8.1 - - - +
1932X PHE* 4.0 22.0 - - - -
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Residues in contact with ILE1714 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1710X LEU* 2.9 33.9 + - + +
1711X PHE* 3.7 4.0 - - - +
1713X GLY* 1.3 74.3 - - - +
1715X LYS* 1.3 62.3 + - - +
1717X GLN* 4.0 0.9 - - - +
1718X VAL* 3.1 36.6 + - + +
1925X MET* 4.8 2.9 - - + -
1929X LEU* 3.7 19.9 - - + +
2005X MET* 3.5 25.6 - - + -
2008X VAL* 3.5 39.7 - - + -
2009X LEU* 3.6 29.8 - - + -
2012X ILE* 4.1 1.8 - - + -
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Residues in contact with LYS1715 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1711X PHE* 2.9 40.2 + - + +
1712X ARG* 3.7 11.9 - - + +
1713X GLY 3.3 0.2 - - - -
1714X ILE* 1.3 78.1 - - - +
1716X HIS* 1.3 60.2 + - + +
1718X VAL* 3.5 3.5 + - - +
1719X ASP* 3.1 53.8 + - - +
1786X ASP* 2.7 39.2 + - - +
2000X GLN 5.5 3.1 - - - -
2005X MET* 3.8 12.8 - - + -
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Residues in contact with HIS1716 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1712X ARG* 3.0 24.2 + - + +
1713X GLY* 4.1 4.3 - - - +
1715X LYS* 1.3 77.6 - - + +
1717X GLN* 1.3 65.9 + - - +
1719X ASP* 4.0 7.3 - - - +
1720X LYS* 3.3 34.0 + - - +
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Residues in contact with GLN1717 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1713X GLY 3.1 18.7 + - - +
1714X ILE 4.0 3.1 - - - +
1716X HIS* 1.3 77.0 - - - +
1718X VAL* 1.3 63.5 + - - +
1720X LYS* 3.3 34.2 + - - +
1732X TYR* 3.1 48.6 - - - +
1925X MET* 4.2 22.6 - - + -
1928X THR* 3.7 33.2 + - + +
1929X LEU* 4.8 2.7 - - + -
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Residues in contact with VAL1718 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1714X ILE* 3.1 30.9 + - + +
1715X LYS* 3.9 4.3 - - - +
1717X GLN* 1.3 75.5 - - - +
1719X ASP* 1.3 61.3 + - - +
1721X GLY* 2.9 30.3 + - - +
1722X PRO 5.0 0.3 - - - +
1723X VAL* 3.5 26.4 - - + +
1730X ALA* 4.9 0.9 - - + -
1732X TYR* 3.7 18.7 + - - +
1925X MET* 4.2 11.2 - - + -
2004X ASN* 3.7 30.5 - - + +
2005X MET* 5.4 3.6 - - + +
2008X VAL* 5.1 0.9 - - + -
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Residues in contact with ASP1719 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1715X LYS* 3.1 44.4 + - - +
1716X HIS* 4.0 7.8 - - - +
1718X VAL* 1.3 80.3 - - - +
1720X LYS* 1.3 59.6 + - - +
1721X GLY 3.3 0.9 - - - -
1723X VAL* 5.6 2.2 - - - +
1770X LYS 5.2 4.7 - - - +
1772X LEU* 3.6 7.1 - - - +
1783X LYS* 2.9 50.4 + - - +
1786X ASP* 5.3 1.4 - - - +
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Residues in contact with LYS1720 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1716X HIS* 3.3 21.0 + - - +
1717X GLN* 3.3 34.2 + - - +
1718X VAL 3.0 1.4 + - - -
1719X ASP* 1.3 77.0 - - - +
1721X GLY* 1.3 55.8 + - - +
1732X TYR* 3.9 9.9 + - + +
1746X TYR* 3.4 15.4 + - - -
1772X LEU* 3.7 16.8 - - - +
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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
------------------------------------------------------------
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