Contacts of the helix formed by residues 2116 - 2129 (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 GLN2116 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2112X ALA 2.9 5.4 + - - -
2113X GLN* 3.0 16.4 + - - +
2114X LYS 4.4 8.4 + - - +
2115X MET* 1.3 77.8 - - - +
2117X LEU* 1.3 59.2 + - - +
2118X GLY 3.3 2.9 - - - +
2119X TYR* 3.2 26.3 + - + +
2120X ARG* 2.9 34.6 + - + +
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Residues in contact with LEU2117 (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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1609X LEU* 4.1 10.7 - - + +
1612X SER* 4.0 11.7 - - - +
1614X LEU* 3.8 21.1 - - + -
1615X PHE* 3.7 34.3 - - + +
2106X LEU* 3.9 19.9 - - + +
2112X ALA* 2.8 32.0 + - + +
2115X MET* 3.0 22.4 + - + +
2116X GLN* 1.3 73.0 - - - +
2118X GLY* 1.3 62.2 + - - +
2120X ARG* 3.2 28.1 + - - +
2121X LEU* 3.1 23.7 + - - +
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Residues in contact with GLY2118 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2103X ILE* 3.6 18.8 - - - +
2106X LEU* 3.9 21.7 - - - +
2107X GLU* 4.3 20.5 + - - -
2112X ALA 4.2 3.4 + - - -
2113X GLN* 5.7 0.6 - - - +
2116X GLN 3.3 0.6 - - - -
2117X LEU* 1.3 79.4 - - - +
2119X TYR* 1.3 59.9 + - - +
2121X LEU* 3.4 0.7 + - - +
2122X GLN* 3.1 22.0 + - - +
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Residues in contact with TYR2119 (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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2107X GLU* 5.2 0.6 + - - -
2116X GLN* 3.2 30.1 + - + +
2118X GLY* 1.3 75.6 - - - +
2120X ARG* 1.3 62.4 + - + +
2122X GLN* 3.1 27.5 - - - +
2123X GLN* 2.9 50.9 + - + +
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Residues in contact with ARG2120 (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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1605X GLN* 5.0 5.2 + - - -
1608X ASN* 4.3 12.9 + - - +
1609X LEU* 3.2 49.8 - - + +
1612X SER* 4.3 11.9 - - - -
2115X MET* 4.4 9.5 + - - +
2116X GLN* 2.9 23.7 + - + +
2117X LEU* 3.2 19.1 + - - +
2119X TYR* 1.3 80.3 - - + +
2121X LEU* 1.3 58.4 + - - +
2123X GLN* 3.4 9.0 + - + +
2124X ILE* 3.0 35.4 + - + +
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Residues in contact with LEU2121 (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* 4.8 0.2 - - + -
1609X LEU* 4.0 19.7 - - + +
1615X PHE* 4.1 10.8 - - + -
2095X ILE* 3.7 46.0 - - + -
2099X TYR* 4.4 7.4 - - + -
2102X ILE* 3.5 33.7 - - + -
2103X ILE* 4.4 10.3 - - + -
2106X LEU* 4.2 5.8 - - + -
2117X LEU 3.1 12.9 + - - +
2118X GLY 3.8 7.6 - - - +
2120X ARG* 1.3 73.2 - - - +
2122X GLN* 1.3 55.4 + - - +
2124X ILE* 3.3 13.2 + - + +
2125X ALA* 2.9 35.1 + - - +
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Residues in contact with GLN2122 (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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2099X TYR* 3.1 26.1 + - - +
2103X ILE* 4.4 10.4 - - + +
2107X GLU* 5.4 5.9 + - - -
2118X GLY 3.1 15.1 + - - +
2119X TYR* 3.1 31.1 - - + +
2121X LEU* 1.3 76.0 - - - +
2123X GLN* 1.3 57.0 + - + +
2125X ALA* 3.5 2.3 + - - +
2126X ALA* 2.8 30.2 + - - +
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Residues in contact with GLN2123 (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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2119X TYR* 2.9 48.1 + - + +
2120X ARG* 3.6 10.3 - - + +
2121X LEU 3.3 0.2 - - - -
2122X GLN* 1.3 72.7 - - + +
2124X ILE* 1.3 67.0 + - + +
2126X ALA* 3.3 8.6 + - - +
2127X ALA* 3.0 23.4 + - - +
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Residues in contact with ILE2124 (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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1602X GLY* 3.4 19.3 - - - +
1605X GLN* 3.7 25.6 - - + +
1606X LEU* 3.6 32.1 - - + -
1609X LEU* 3.4 34.1 - - + -
2092X TYR* 4.6 11.0 - - + -
2120X ARG* 3.0 18.2 + - + +
2121X LEU* 3.3 10.3 + - + +
2123X GLN* 1.3 75.6 - - + +
2125X ALA* 1.3 58.3 + - - +
2127X ALA* 3.1 6.9 + - - +
2128X VAL* 2.9 44.0 + - + +
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Residues in contact with ALA2125 (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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2092X TYR* 3.1 31.2 - - + +
2095X ILE* 5.5 0.2 - - + -
2099X TYR* 4.1 24.0 - - + +
2121X LEU 2.9 20.3 + - - +
2122X GLN 3.7 4.0 - - - +
2124X ILE* 1.3 70.8 - - - +
2126X ALA* 1.3 64.7 + - - +
2129X GLU* 3.1 33.6 + - - +
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Residues in contact with ALA2126 (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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1595X ARG* 3.9 3.8 + - - -
2122X GLN 2.8 21.5 + - - +
2123X GLN* 3.5 10.5 - - - +
2124X ILE 3.3 0.2 - - - -
2125X ALA* 1.3 71.1 - - - +
2127X ALA* 1.3 62.2 + - - +
2129X GLU 3.3 22.2 - - - +
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Residues in contact with ALA2127 (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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1595X ARG* 2.8 20.8 + - - +
1598X THR* 3.3 33.2 - - + +
1599X VAL* 3.9 0.9 + - - -
1601X GLN* 5.3 2.9 - - + -
1602X GLY* 4.0 20.6 - - - +
2123X GLN 3.0 13.6 + - - +
2124X ILE* 3.1 8.9 + - - +
2126X ALA* 1.3 76.9 - - - +
2128X VAL* 1.3 58.8 + - - +
2129X GLU 3.2 0.2 - - - -
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Residues in contact with VAL2128 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1595X ARG* 4.2 2.0 - - - -
1599X VAL* 3.9 36.5 - - + +
1602X GLY* 3.9 17.3 - - - -
1603X LEU* 4.3 9.9 - - + +
2089X HIS* 4.7 7.2 - - + +
2092X TYR* 3.6 35.8 - - + -
2124X ILE* 2.9 34.6 + - + +
2125X ALA 3.3 0.6 + - - +
2127X ALA* 1.3 76.7 - - - +
2129X GLU* 1.3 63.5 + - - +
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Residues in contact with GLU2129 (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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1595X ARG* 3.3 20.4 + - - +
2092X TYR* 2.6 36.7 + - - -
2096X ASN* 3.0 25.0 - - - +
2125X ALA* 3.1 17.5 + - - +
2126X ALA* 3.3 17.7 - - - +
2127X ALA 3.2 2.4 - - - -
2128X VAL* 1.3 78.0 - - - +
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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