Contacts of the helix formed by residues 2083 - 2098 (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 GLY2083 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1585X LEU* 3.5 20.3 - - - +
1643X VAL* 3.7 3.8 - - - -
2081X ASP* 2.8 21.0 + - - -
2082X LEU* 1.4 78.4 - - - +
2084X ALA* 1.3 50.8 + - - +
2085X ARG* 3.4 2.9 - - - -
2086X VAL* 3.4 7.0 + - - +
2087X ALA* 2.8 34.1 + - - +
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Residues in contact with ALA2084 (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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1643X VAL* 3.6 27.2 - - + +
1644X ALA* 4.6 8.2 - - - +
2081X ASP* 3.6 9.2 + - - +
2082X LEU* 6.3 0.2 - - + -
2083X GLY* 1.3 72.9 - - - +
2085X ARG* 1.3 57.2 + - - +
2087X ALA* 3.5 2.0 - - - +
2088X LEU* 2.8 46.5 + - + +
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Residues in contact with ARG2085 (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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1587X ARG 4.9 3.0 + - - -
1588X ASP* 5.5 0.8 - - - +
1589X LEU* 3.7 40.5 - - + +
1596X ARG* 3.9 19.5 - - - +
1600X GLU* 2.8 32.0 + - + +
1603X LEU* 3.6 18.6 - - + +
2081X ASP* 5.7 3.3 + - - +
2083X GLY 5.1 0.7 - - - -
2084X ALA* 1.3 77.8 - - - +
2086X VAL* 1.3 75.2 + - + +
2088X LEU* 3.6 8.9 + - - +
2089X HIS* 3.2 15.9 + - - +
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Residues in contact with VAL2086 (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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1584X PRO 4.0 0.9 - - - +
1585X LEU* 3.4 46.0 - - + +
1587X ARG* 3.6 47.8 - - + +
1589X LEU* 4.4 8.1 - - + -
2083X GLY* 3.4 9.1 + - - +
2085X ARG* 1.3 91.5 - - + +
2087X ALA* 1.3 58.2 + - - +
2089X HIS* 3.2 7.0 + - - +
2090X GLU* 2.8 27.9 + - + +
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Residues in contact with ALA2087 (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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1585X LEU* 4.0 6.6 - - + +
1640X LEU* 3.7 42.4 - - + +
1643X VAL* 4.0 14.4 - - + -
1644X ALA* 4.6 2.2 - - + +
2083X GLY 2.8 21.2 + - - +
2084X ALA* 3.3 5.6 + - - +
2086X VAL* 1.3 72.5 - - - +
2088X LEU* 1.3 56.9 + - - +
2090X GLU* 3.2 1.7 + - - +
2091X LEU* 2.8 35.7 + - - +
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Residues in contact with LEU2088 (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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1603X LEU* 3.4 37.0 - - + +
1604X GLY* 5.2 0.4 - - - -
1606X LEU* 3.6 17.0 - - + +
1607X SER* 3.8 28.9 - - - +
1610X LEU* 3.7 29.8 - - + -
1644X ALA* 4.2 13.2 - - + -
2084X ALA* 2.8 29.9 + - + +
2085X ARG* 3.6 9.4 - - - +
2087X ALA* 1.3 75.8 - - - +
2089X HIS* 1.3 58.2 + - - +
2091X LEU* 3.3 4.1 + - + +
2092X TYR* 2.9 24.1 + - - +
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Residues in contact with HIS2089 (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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1587X ARG* 3.0 22.8 + - - +
1589X LEU* 3.6 46.6 - - + +
1591X VAL* 4.0 15.1 - - + +
1599X VAL* 4.5 9.3 - - + +
1603X LEU* 3.9 22.1 - - + +
2085X ARG 3.2 4.8 + - - +
2086X VAL 3.2 9.5 + - - +
2088X LEU* 1.3 76.2 - - - +
2090X GLU* 1.3 64.9 + - - +
2092X TYR* 3.2 9.5 + + + +
2093X LYS* 3.2 39.5 + - - +
2128X VAL* 4.7 9.6 - - + +
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Residues in contact with GLU2090 (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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1584X PRO 5.2 1.3 - - - +
1585X LEU* 4.4 1.6 - - + -
1587X ARG* 2.8 20.8 + - - +
1636X TYR* 2.7 33.6 + - - +
1640X LEU* 3.6 23.3 - - + -
2086X VAL* 2.8 30.9 + - + +
2087X ALA 3.2 4.9 + - - +
2089X HIS* 1.3 69.3 - - - +
2091X LEU* 1.3 65.6 + - - +
2093X LYS* 2.7 50.7 + - - +
2094X TYR* 3.4 19.4 - - - -
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Residues in contact with LEU2091 (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* 4.5 7.0 - - + -
1610X LEU* 4.0 19.5 - - + -
1619X PHE* 4.1 17.4 - - + -
1637X VAL* 3.8 30.7 - - + -
1640X LEU* 3.7 33.7 - - + +
1641X LEU* 3.8 28.0 - - + -
1644X ALA* 4.3 5.6 - - + -
2087X ALA 2.8 24.1 + - - +
2088X LEU* 3.6 6.5 - - + +
2090X GLU* 1.3 72.8 - - - +
2092X TYR* 1.3 64.8 + - - +
2094X TYR* 3.2 9.5 + - + +
2095X ILE* 3.1 22.7 + - + +
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Residues in contact with TYR2092 (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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1603X LEU* 4.5 5.6 - - + -
1606X LEU* 4.1 6.4 - - + +
2088X LEU 2.9 13.7 + - - +
2089X HIS* 3.2 17.7 + + - +
2091X LEU* 1.3 77.2 - - - +
2093X LYS* 1.3 54.5 + - + +
2095X ILE* 2.8 37.0 + - + +
2096X ASN* 2.7 43.7 + - + +
2099X TYR* 5.7 0.3 - - - -
2124X ILE* 4.6 8.3 - - + -
2125X ALA* 3.1 35.3 - - + +
2128X VAL* 3.6 33.9 - - + -
2129X GLU* 2.6 43.6 + - - -
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Residues in contact with LYS2093 (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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14X UNX 3.4 22.2 - - - -
1587X ARG* 3.7 16.1 - - - +
2089X HIS* 3.2 27.0 + - + +
2090X GLU* 2.7 43.9 + - - +
2091X LEU 3.3 0.2 - - - -
2092X TYR* 1.3 77.1 - - + +
2094X TYR* 1.3 57.7 + - - +
2096X ASN* 3.5 10.0 + - - +
2097X LYS* 2.9 28.6 + - - +
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Residues in contact with TYR2094 (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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14X UNX 4.0 14.8 - - - -
17X UNX 4.1 5.0 - - - -
1619X PHE* 4.8 3.1 - - + -
1623X LEU* 4.1 13.6 - - + +
1629X PHE* 3.7 28.7 - + - -
1633X ASP* 2.7 37.7 + - - -
1636X TYR* 3.8 29.3 - + - -
1637X VAL* 3.8 24.7 - - + -
1640X LEU* 4.5 2.5 - - + -
2090X GLU* 3.4 21.1 - - - -
2091X LEU* 3.2 9.3 + - - +
2092X TYR 3.1 0.6 - - - -
2093X LYS* 1.3 74.8 - - - +
2095X ILE* 1.3 64.5 + - - +
2097X LYS* 4.4 12.8 - - + -
2098X TYR* 3.3 40.1 + + - +
2102X ILE* 4.3 0.3 - - - +
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Residues in contact with ILE2095 (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* 3.7 41.3 - - + -
1615X PHE* 4.8 3.4 - - + -
1619X PHE* 3.7 27.1 - - + -
2091X LEU* 3.1 14.1 + - + +
2092X TYR* 2.8 25.4 + - + +
2094X TYR* 1.3 73.7 - - - +
2096X ASN* 1.3 60.1 + - - +
2098X TYR 3.4 0.3 - - - -
2099X TYR* 2.8 44.0 + - + -
2102X ILE* 3.9 10.3 - - + +
2121X LEU* 3.7 36.3 - - + -
2125X ALA* 5.5 0.2 - - + -
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Residues in contact with ASN2096 (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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15X UNX 3.7 5.2 - - - -
2092X TYR* 2.7 29.4 + - + +
2093X LYS* 3.6 12.6 + - - +
2095X ILE* 1.3 74.3 - - - +
2097X LYS* 1.3 65.0 + - - +
2099X TYR* 3.2 20.6 + - - +
2129X GLU* 3.0 29.7 + - - +
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Residues in contact with LYS2097 (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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15X UNX 4.0 6.6 - - - -
1628X THR* 4.4 14.0 + - - -
1633X ASP* 5.0 6.9 + - - -
2093X LYS 2.9 18.7 + - - +
2094X TYR* 4.0 15.2 - - + +
2095X ILE 3.5 0.2 - - - -
2096X ASN* 1.3 79.2 - - - +
2098X TYR* 1.3 97.8 + - + +
2099X TYR 3.9 0.7 + - - -
2101X GLN* 4.2 2.3 + - - +
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Residues in contact with TYR2098 (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* 5.9 0.4 - - + -
1623X LEU* 3.4 27.6 - - + -
1626X GLN* 3.5 32.8 - - + -
1628X THR* 3.0 47.5 + - - -
1629X PHE* 3.5 15.3 + + + -
1633X ASP* 4.8 0.7 + - - -
2094X TYR* 3.3 20.6 + + - +
2095X ILE 3.4 3.1 - - - -
2096X ASN 3.3 0.2 - - - -
2097X LYS* 1.3 110.8 + - + +
2099X TYR* 1.3 65.4 + - - +
2101X GLN* 3.2 27.7 + - + +
2102X ILE* 3.0 29.9 + - + +
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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