Contacts of the helix formed by residues 1612 - 1626 (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 SER1612 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1608X ASN 4.0 1.6 + - - -
1609X LEU 2.9 13.5 + - - +
1610X LEU 3.7 0.5 - - - +
1611X ASN* 1.3 76.7 - - - +
1613X LYS* 1.3 62.5 + - - +
1614X LEU* 3.4 8.1 + - - +
1615X PHE* 2.8 27.0 + - - +
1616X LEU* 3.0 18.2 + - - +
1651X TYR* 3.3 4.8 + - - -
2117X LEU* 4.0 7.9 - - - +
2120X ARG* 4.3 17.7 - - - -
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Residues in contact with LYS1613 (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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1611X ASN 3.5 3.6 + - - -
1612X SER* 1.3 71.4 - - - +
1614X LEU* 1.3 61.4 + - - +
1617X THR* 2.9 38.5 + - + +
1651X TYR* 3.4 19.0 + - + -
1654X ASP* 2.8 35.8 + - - +
1655X ILE* 3.8 16.6 - - + -
1658X THR* 2.7 40.3 + - - -
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Residues in contact with LEU1614 (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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1612X SER* 3.2 6.6 + - - +
1613X LYS* 1.3 76.2 - - - +
1615X PHE* 1.3 66.5 + - - +
1617X THR* 3.1 8.8 + - - +
1618X LYS* 3.1 41.3 + - + +
2109X ASP* 4.0 13.2 - - - +
2111X THR* 3.7 22.9 - - + +
2112X ALA* 3.5 28.7 - - + +
2115X MET* 5.8 1.1 - - + -
2117X LEU* 3.8 14.1 - - + -
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Residues in contact with PHE1615 (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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1606X LEU* 4.6 7.0 - - + -
1609X LEU* 3.7 51.4 - - + +
1610X LEU* 3.9 24.5 - - + -
1612X SER* 2.8 28.5 + - - +
1614X LEU* 1.3 74.8 - - - +
1616X LEU* 1.3 57.5 + - - +
1618X LYS* 3.3 1.4 + - - +
1619X PHE* 2.7 60.3 + + + +
2095X ILE* 4.8 2.2 - - + -
2102X ILE* 4.6 3.6 - - + -
2106X LEU* 4.0 24.5 - - + -
2117X LEU* 3.7 15.3 - - + +
2121X LEU* 4.1 27.1 - - + -
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Residues in contact with LEU1616 (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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1610X LEU* 3.7 23.1 - - + +
1612X SER 3.0 17.3 + - - +
1613X LYS* 4.0 2.7 - - - +
1615X PHE* 1.3 83.4 - - + +
1617X THR* 1.3 58.0 + - - +
1619X PHE* 3.5 6.4 + - + +
1620X ILE* 3.0 36.4 + - + +
1641X LEU* 3.7 37.5 - - + -
1645X LEU* 3.8 18.6 - - + -
1651X TYR* 3.6 15.9 - - - +
1655X ILE* 3.7 29.2 - - + -
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Residues in contact with THR1617 (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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1613X LYS* 2.9 35.9 + - + +
1614X LEU* 3.1 13.0 + - - +
1616X LEU* 1.3 73.0 - - - +
1618X LYS* 1.3 62.5 + - - +
1620X ILE* 3.9 6.9 - - - +
1621X HIS* 3.0 31.3 + - - +
1655X ILE* 4.3 13.7 - - + -
1658X THR* 4.7 14.6 - - + -
1659X LEU* 4.7 19.5 - - + +
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Residues in contact with LYS1618 (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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1614X LEU* 3.1 35.4 + - + +
1615X PHE 3.5 2.9 - - - +
1617X THR* 1.3 74.0 + - - +
1619X PHE* 1.3 58.9 + - - +
1621X HIS* 3.9 7.6 + - + +
1622X THR* 2.6 41.7 + - - +
2102X ILE* 6.0 1.1 - - - -
2105X ALA* 4.0 26.0 + - + +
2106X LEU* 4.1 20.2 - - + -
2108X GLU 5.3 1.8 + - - -
2109X ASP* 3.2 37.7 + - + +
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Residues in contact with PHE1619 (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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1610X LEU* 4.4 5.6 - - + -
1615X PHE* 2.7 47.8 + + + +
1616X LEU* 3.6 17.9 - - + +
1618X LYS* 1.3 73.7 - - - +
1620X ILE* 1.3 64.2 + - - +
1622X THR* 3.8 3.4 - - - -
1623X LEU* 3.1 54.4 + - + +
1637X VAL* 4.9 2.0 - - + -
1641X LEU* 4.6 7.9 - - + -
2091X LEU* 4.1 32.5 - - + -
2094X TYR* 4.8 1.3 - - + -
2095X ILE* 3.7 26.2 - - + -
2102X ILE* 3.6 38.1 - - + +
2106X LEU* 5.7 0.4 - - - +
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Residues in contact with ILE1620 (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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1616X LEU* 3.0 39.9 + - + +
1617X THR* 3.9 6.5 - - - +
1619X PHE* 1.3 76.7 - - + +
1621X HIS* 1.3 65.5 + - - +
1623X LEU* 3.5 7.2 + - - +
1624X GLU* 3.1 42.0 + - - +
1637X VAL* 5.9 1.3 - - + -
1641X LEU* 4.1 24.0 - - + -
1655X ILE* 4.5 8.1 - - + -
1659X LEU* 4.0 33.2 - - + -
1682X VAL* 3.9 23.5 - - + +
1683X VAL 5.9 0.2 - - - +
1686X LEU* 4.7 2.0 - - + -
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Residues in contact with HIS1621 (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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1617X THR 3.0 19.2 + - - +
1618X LYS* 3.9 8.0 - - + +
1620X ILE* 1.3 78.7 - - - +
1622X THR* 1.3 67.3 + - - +
1624X GLU* 3.3 6.3 + - - +
1625X THR* 3.0 44.2 + - - -
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Residues in contact with THR1622 (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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1618X LYS* 2.6 25.0 + - - +
1619X PHE* 3.8 3.5 - - - -
1621X HIS* 1.3 82.7 + - - +
1623X LEU* 1.3 63.2 + - - +
1625X THR* 3.3 10.6 + - + -
1626X GLN* 3.1 34.6 + - + +
2098X TYR* 5.9 0.7 - - + -
2101X GLN* 3.5 33.7 - - + +
2102X ILE* 3.9 17.6 - - + +
2105X ALA* 3.4 21.4 - - + +
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Residues in contact with LEU1623 (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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1619X PHE* 3.1 51.7 + - + +
1620X ILE* 3.7 6.3 - - - +
1622X THR* 1.3 80.3 - - - +
1624X GLU* 1.3 56.0 + - - +
1626X GLN* 3.0 15.9 + - - +
1629X PHE* 3.0 56.2 - - + +
1637X VAL* 4.1 16.6 - - + -
1682X VAL* 6.2 0.7 - - + -
2094X TYR* 4.1 12.6 - - + +
2098X TYR* 3.4 39.5 - - + -
2102X ILE* 4.6 2.7 - - + -
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Residues in contact with GLU1624 (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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1X UNX 2.3 26.8 - - - -
1620X ILE* 3.1 24.9 + - - +
1621X HIS* 3.3 6.3 + - - +
1622X THR 3.3 0.2 - - - -
1623X LEU* 1.3 76.3 - - - +
1625X THR* 1.3 61.4 + - - +
1626X GLN 3.3 0.2 - - - -
1629X PHE* 3.8 7.2 - - + -
1634X ARG* 2.9 50.6 + - - +
1681X THR* 3.5 9.1 - - - +
1682X VAL* 3.2 39.6 + - + +
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Residues in contact with THR1625 (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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1621X HIS* 3.0 32.0 + - - -
1622X THR* 3.4 12.3 - - - -
1623X LEU 3.2 0.2 - - - -
1624X GLU* 1.3 76.8 - - - +
1626X GLN* 1.3 74.8 + - - +
1627X ARG* 3.4 15.6 + - - +
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Residues in contact with GLN1626 (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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1622X THR* 3.1 26.8 + - - +
1623X LEU* 3.0 11.5 + - - +
1625X THR* 1.3 90.5 - - - +
1627X ARG* 1.3 60.5 + - - +
1628X THR* 3.2 2.0 - - - +
1629X PHE* 3.0 26.9 + - + +
1634X ARG* 3.6 9.4 + - - -
2098X TYR* 3.5 41.1 - - + -
2101X GLN* 3.5 38.7 + - - +
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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