Contacts of the helix formed by residues 2063 - 2077 (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 SER2063 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2061X PRO 3.7 3.2 + - - -
2062X ALA* 1.3 74.6 - - - +
2064X ASP* 1.3 59.1 + - - +
2065X GLN* 3.6 7.5 + - - +
2066X GLU* 3.1 40.3 + - - +
2067X MET* 2.8 26.2 + - - +
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Residues in contact with ASP2064 (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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1953X TYR* 4.7 14.2 - - - -
2062X ALA 3.7 2.5 + - - +
2063X SER* 1.3 72.1 - - - +
2065X GLN* 1.3 58.5 + - - +
2067X MET* 3.1 6.5 + - - +
2068X ASN* 2.8 45.9 + - - +
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Residues in contact with GLN2065 (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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2063X SER* 3.2 7.4 + - - +
2064X ASP* 1.3 78.1 - - - +
2066X GLU* 1.3 58.3 + - + +
2068X ASN* 3.8 6.1 - - - +
2069X SER* 2.9 41.0 + - - +
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Residues in contact with GLU2066 (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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1949X LEU* 4.0 21.1 - - + +
2061X PRO 3.9 5.2 - - - +
2062X ALA* 3.7 7.6 - - - -
2063X SER* 3.1 39.4 + - - +
2065X GLN* 1.3 77.4 - - + +
2067X MET* 1.3 63.4 + - - +
2069X SER* 3.5 6.0 + - - -
2070X VAL* 3.1 29.9 + - - +
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Residues in contact with MET2067 (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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3X UNX 4.2 8.1 - - - -
1690X TRP* 5.3 2.9 - - + -
1949X LEU* 3.2 30.3 - - + +
1950X ALA* 4.0 15.0 - - - -
1953X TYR* 3.7 37.2 - - + -
2062X ALA* 3.2 32.8 - - + -
2063X SER 2.8 14.4 + - - +
2064X ASP* 3.7 6.3 - - - +
2066X GLU* 1.3 77.7 - - - +
2068X ASN* 1.3 57.4 + - - +
2070X VAL* 3.3 11.6 + - - +
2071X LEU* 2.8 50.9 + - + +
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Residues in contact with ASN2068 (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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3X UNX 2.6 25.9 - - - -
1650X GLU* 3.4 46.1 + - - +
2064X ASP* 2.8 35.6 + - - +
2065X GLN* 4.0 5.8 - - - +
2067X MET* 1.3 70.4 - - - +
2069X SER* 1.3 60.2 + - - +
2071X LEU* 3.8 6.4 - - - +
2072X ALA* 2.8 30.7 + - - +
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Residues in contact with SER2069 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2065X GLN* 2.9 26.1 + - - +
2066X GLU* 3.7 6.9 - - - -
2067X MET 3.3 0.2 - - - -
2068X ASN* 1.3 73.9 - - - +
2070X VAL* 1.3 67.2 + - - +
2072X ALA* 3.3 5.7 + - - +
2073X GLU* 3.0 24.4 + - - +
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Residues in contact with VAL2070 (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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1694X CYS* 6.0 0.4 - - - +
1949X LEU* 4.2 24.7 - - + -
1950X ALA* 5.7 6.7 - - + +
2066X GLU 3.1 14.9 + - - +
2067X MET* 3.5 18.4 - - - +
2069X SER* 1.3 79.8 - - - +
2071X LEU* 1.3 64.4 + - + +
2073X GLU* 3.3 6.3 + - - +
2074X LEU* 3.0 44.2 + - + +
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Residues in contact with LEU2071 (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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3X UNX 4.0 15.7 - - - -
1649X LEU* 3.7 17.1 - - + +
1650X GLU* 4.1 20.2 - - - +
1653X THR* 3.2 42.6 - - + +
1690X TRP* 4.2 14.4 - - + +
1694X CYS* 4.2 17.0 - - - -
2067X MET* 2.8 36.2 + - + +
2068X ASN* 3.4 7.6 + - - +
2069X SER 3.3 0.2 - - - -
2070X VAL* 1.3 73.1 - - + +
2072X ALA* 1.3 61.3 + - - +
2074X LEU* 3.3 14.1 + - + +
2075X SER* 3.3 21.1 + - - -
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Residues in contact with ALA2072 (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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1650X GLU* 5.5 5.5 - - + +
2068X ASN 2.8 22.1 + - - +
2069X SER* 3.8 6.3 - - - +
2070X VAL 3.3 0.2 - - - -
2071X LEU* 1.3 70.5 - - - +
2073X GLU* 1.3 64.4 + - - +
2075X SER* 3.2 18.2 + - - -
2076X TRP* 3.1 24.6 + - + +
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Residues in contact with GLU2073 (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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2069X SER 3.0 16.2 + - - +
2070X VAL* 3.3 6.1 + - - +
2072X ALA* 1.3 74.8 - - - +
2074X LEU* 1.3 68.0 + - + +
2076X TRP* 3.2 34.0 + - + +
2077X ASN* 3.0 52.7 + - + +
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Residues in contact with LEU2074 (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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12X UNX 2.5 30.1 - - - -
1646X HIS* 3.9 10.0 - - - -
1649X LEU* 3.6 12.8 - - + -
1693X ILE* 3.8 25.4 - - + +
1694X CYS* 3.9 39.9 - - + +
1696X TYR* 6.1 0.9 - - + -
1697X THR* 5.5 11.7 - - + +
2070X VAL* 3.0 35.8 + - + +
2071X LEU* 3.6 16.4 - - + +
2072X ALA 3.3 0.4 - - - -
2073X GLU* 1.3 79.6 - - + +
2075X SER* 1.4 60.6 + - - +
2076X TRP 3.3 0.9 + - - -
2077X ASN* 3.9 2.1 + - + -
2078X TYR* 4.0 0.9 - - - -
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Residues in contact with SER2075 (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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1646X HIS* 3.3 26.7 + - - +
1647X GLY* 3.3 29.0 + - - -
1649X LEU* 3.5 10.5 + - - +
2071X LEU 3.3 14.3 + - - -
2072X ALA* 3.2 15.4 + - - -
2073X GLU 3.2 1.2 - - - -
2074X LEU* 1.4 75.6 - - - +
2076X TRP* 1.3 61.9 + - - +
2078X TYR* 3.5 16.1 + - - -
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Residues in contact with TRP2076 (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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2072X ALA* 3.1 25.4 + - + +
2073X GLU* 3.2 38.7 + - + -
2075X SER* 1.3 82.3 - - - +
2077X ASN* 1.3 77.8 + - - +
2078X TYR* 2.9 23.9 + - - +
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Residues in contact with ASN2077 (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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12X UNX 4.0 10.3 - - - -
1568X TYR* 5.6 0.7 - - - +
1697X THR* 5.1 12.9 - - - +
2073X GLU* 3.0 40.8 + - + +
2074X LEU* 3.9 4.9 + - + -
2076X TRP* 1.3 88.3 - - + +
2078X TYR* 1.3 59.8 + - - +
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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
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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