Contacts of the helix formed by residues 61 - 72 (chain X) in PDB entry 6FF7
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 GLU 61 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10X HIS* 5.0 0.6 - - - +
38X GLY* 6.2 0.9 - - - -
39X HIS 4.9 0.8 + - - +
59X PHE* 3.3 22.9 - - - +
60X LYS* 1.3 80.9 - - + +
62X LEU* 1.3 62.6 + - - +
63X GLY* 3.4 2.5 - - - +
64X SER* 3.3 23.0 - - - +
65X SER 3.5 1.4 + - - -
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Residues in contact with LEU 62 (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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8X PRO* 6.4 2.7 - - + -
9X ASN 4.9 2.9 - - - +
10X HIS* 4.7 15.0 - - + +
60X LYS 4.0 1.2 + - - -
61X GLU* 1.3 69.4 - - - +
63X GLY* 1.3 67.2 + - - +
64X SER 3.1 1.8 - - - -
65X SER* 3.0 19.2 + - - +
66X THR* 3.1 12.8 + - - -
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Residues in contact with GLY 63 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61X GLU* 3.4 3.6 - - - +
62X LEU* 1.3 78.4 - - - +
64X SER* 1.3 56.8 + - - +
66X THR* 3.3 7.6 + - - -
67X ASN* 3.0 29.3 + - - +
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Residues in contact with SER 64 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37X PHE* 3.2 35.3 - - - +
38X GLY* 4.0 9.0 - - - -
59X PHE* 4.2 10.8 - - - -
61X GLU* 3.3 23.8 + - - +
62X LEU 3.1 0.6 - - - -
63X GLY* 1.3 76.4 - - - +
65X SER* 1.3 60.7 + - - +
67X ASN* 3.4 5.4 + - - +
68X ALA* 3.0 24.9 + - - +
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Residues in contact with SER 65 (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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9X ASN 3.1 27.8 - - - -
10X HIS* 3.5 20.4 - - - -
11X THR 5.3 2.9 - - - -
12X ILE* 5.4 5.8 - - - -
59X PHE* 4.4 4.0 - - - +
61X GLU 3.5 3.8 + - - -
62X LEU 3.0 8.8 + - - -
64X SER* 1.3 79.4 - - - +
66X THR* 1.3 60.8 + - - +
68X ALA* 3.4 7.1 + - - +
69X LEU* 2.9 23.6 + - - +
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Residues in contact with THR 66 (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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8X PRO* 5.7 9.6 - - - -
62X LEU 3.1 10.8 + - - -
63X GLY* 3.7 10.1 - - - -
65X SER* 1.3 77.4 - - - +
67X ASN* 1.3 61.4 + - - +
69X LEU* 3.4 8.0 + - - +
70X ARG* 3.2 23.4 + - - +
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Residues in contact with ASN 67 (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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37X PHE* 4.8 8.7 - - + +
63X GLY 3.0 16.7 + - - +
64X SER* 3.8 7.4 - - - +
65X SER 3.3 0.2 - - - -
66X THR* 1.3 73.2 - - - +
68X ALA* 1.3 65.8 + - - +
70X ARG* 3.5 4.1 + - - +
71X GLN* 3.0 29.0 + - + +
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Residues in contact with ALA 68 (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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34X PHE* 5.7 9.6 - - + +
37X PHE* 4.3 14.8 - - + +
64X SER 3.0 17.5 + - - +
65X SER* 3.6 7.4 - - - +
67X ASN* 1.3 75.9 - - - +
69X LEU* 1.3 62.6 + - - +
71X GLN* 4.9 2.2 - - - -
72X LEU* 2.9 32.7 + - + +
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Residues in contact with LEU 69 (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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65X SER 2.9 14.4 + - - +
66X THR* 3.5 11.7 - - - +
68X ALA* 1.3 77.4 - - - +
70X ARG* 1.3 60.8 + - - +
72X LEU 4.3 0.2 - - - -
73X GLN* 3.5 22.3 + - - +
84X ILE* 4.6 22.0 - - + +
85X GLN* 5.9 5.2 - - - +
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Residues in contact with ARG 70 (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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66X THR 3.2 13.1 + - - +
67X ASN* 4.0 4.3 - - - +
69X LEU* 1.3 79.4 - - - +
71X GLN* 1.3 62.9 + - - +
73X GLN* 3.9 11.3 + - - +
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Residues in contact with GLN 71 (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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67X ASN 3.0 19.7 + - - +
68X ALA* 4.1 1.3 - - - +
70X ARG* 1.3 79.0 - - - +
72X LEU* 1.3 59.2 + - + +
73X GLN 3.5 1.8 + - - +
75X PHE* 5.6 0.2 - - - +
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Residues in contact with LEU 72 (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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68X ALA* 2.9 17.2 + - + +
69X LEU 4.3 1.8 - - - -
71X GLN* 1.3 76.8 - - + +
73X GLN* 1.3 64.7 + - - +
74X GLY 3.2 1.2 + - - -
75X PHE* 3.2 29.1 + - + +
82X MET* 4.4 5.4 - - - +
84X ILE* 5.3 5.3 - - - +
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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