Contacts of the helix formed by residues 59 - 71 (chain H) in PDB entry 7C17
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 ASN 59 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382 A 4.5 14.4 + - - +
54H ARG* 3.5 20.2 - - - +
58H PHE* 1.3 73.5 - - - +
60H LEU* 1.3 58.1 + - - +
61H GLU* 3.8 24.7 - - - +
62H GLU* 3.7 11.6 + - - +
63H SER* 3.1 31.0 + - - -
87H LYS* 2.6 36.8 + - - +
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Residues in contact with LEU 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372 A 4.1 24.5 - - - +
382 A 3.3 24.3 + - + +
392 G 3.5 20.2 - - - +
19H PHE* 3.8 21.8 - - + -
20H TYR* 3.7 19.3 - - + -
23H LYS* 5.5 5.2 - - + -
25H LEU* 3.8 25.2 - - + +
54H ARG* 3.4 12.7 - - - +
59H ASN* 1.3 77.4 - - - +
61H GLU* 1.3 66.3 + - + +
63H SER* 4.7 2.9 - - - -
64H GLY* 2.9 28.1 + - - -
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Residues in contact with GLU 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372 A 3.6 30.4 + - - +
382 A 4.9 0.6 + - - +
59H ASN* 3.4 16.8 - - - +
60H LEU* 1.3 86.1 - - + +
62H GLU* 1.3 61.0 + - - +
64H GLY* 4.4 0.8 - - - -
65H GLU* 3.3 25.2 + - - +
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Residues in contact with GLU 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H PHE* 3.6 41.5 - - + -
59H ASN* 3.6 16.7 + - - +
60H LEU 3.2 0.4 - - - -
61H GLU* 1.3 81.1 - - - +
63H SER* 1.3 59.2 + - - +
64H GLY 3.2 1.6 - - - -
65H GLU* 3.2 15.5 + - - +
66H LEU* 2.9 38.7 + - + +
83H ARG* 3.4 36.9 - - - +
87H LYS* 4.6 11.5 - - + +
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Residues in contact with SER 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H LEU* 5.2 1.1 - - - -
49H LEU* 4.2 0.7 + - - +
50H LEU* 3.5 26.1 + - - +
53H ALA* 3.4 28.8 - - - +
54H ARG* 4.5 5.6 - - - -
58H PHE* 4.4 1.0 - - - +
59H ASN 3.1 20.0 + - - -
60H LEU* 4.4 3.1 - - - -
62H GLU* 1.3 74.8 - - - +
64H GLY* 1.3 59.7 + - - +
66H LEU* 3.6 11.6 - - - +
67H VAL* 2.9 31.2 + - - +
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Residues in contact with GLY 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H LEU* 3.8 31.4 - - - +
60H LEU 2.9 19.1 + - - -
61H GLU 5.0 0.4 - - - -
62H GLU 3.2 0.2 - - - -
63H SER* 1.3 77.5 - - - +
65H GLU* 1.3 56.9 + - - +
67H VAL* 3.3 1.2 - - - +
68H ASN* 2.9 36.9 + - - +
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Residues in contact with GLU 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61H GLU* 3.3 22.3 + - - +
62H GLU* 3.2 20.5 + - - +
64H GLY* 1.3 73.6 - - - +
66H LEU* 1.3 61.2 + - - +
68H ASN* 3.6 14.9 + - - +
69H LEU* 2.9 37.3 + - + +
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Residues in contact with LEU 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123G ILE* 5.6 8.1 - - + +
126G LEU* 6.1 4.7 - - + -
49H LEU* 4.3 21.9 - - + +
53H ALA* 4.8 8.3 - - + -
58H PHE* 3.6 32.5 - - + -
62H GLU* 2.9 29.3 + - - +
63H SER* 3.6 11.7 - - - +
65H GLU* 1.3 76.8 - - - +
67H VAL* 1.3 57.6 + - - +
69H LEU* 3.4 13.2 + - + +
70H PHE* 2.9 28.9 + - - +
80H VAL* 3.7 34.1 - - + -
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Residues in contact with VAL 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H LEU* 3.3 36.6 - - + +
26H VAL* 5.3 2.7 - - + -
46H GLU* 3.9 43.3 - - + +
49H LEU* 4.5 8.0 - - + +
50H LEU* 4.2 17.3 - - + -
63H SER 2.9 17.7 + - - +
64H GLY 3.3 11.0 - - - +
66H LEU* 1.3 73.1 - - - +
68H ASN* 1.3 53.1 + - - +
70H PHE* 3.8 6.0 - - + +
71H ASN* 2.4 36.8 + - - +
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Residues in contact with ASN 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H GLY 4.2 13.1 + - - -
25H LEU* 3.0 31.1 - - - +
64H GLY 2.9 22.0 + - - +
65H GLU* 3.6 16.8 + - - +
66H LEU 3.2 0.2 - - - -
67H VAL* 1.3 77.2 - - - +
69H LEU* 1.3 60.6 + - - +
71H ASN* 2.9 25.0 + - - +
72H ASP* 4.1 4.2 + - - +
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Residues in contact with LEU 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123G ILE* 5.6 7.9 - - + -
62H GLU* 6.1 0.2 - - - +
65H GLU* 2.9 28.9 + - + +
66H LEU* 3.4 16.4 - - + +
68H ASN* 1.3 73.5 - - - +
70H PHE* 1.3 65.0 + - + +
71H ASN 3.4 0.4 - - - -
72H ASP* 3.4 21.6 - - + +
74H GLN 4.3 2.4 - - - +
75H ARG* 4.2 15.6 - - + +
76H HIS* 4.6 26.7 - - + +
79H ASP* 4.9 15.3 - - + +
80H VAL* 3.8 33.2 - - + +
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Residues in contact with PHE 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G ILE* 3.6 26.7 - - + -
127G SER* 5.5 0.4 - - - -
42H GLN* 3.8 23.5 + - - -
45H ASN* 4.0 19.7 - - + -
46H GLU* 3.6 43.5 - - + -
49H LEU* 3.7 20.4 - - + -
66H LEU 2.9 17.6 + - - +
67H VAL* 3.9 6.5 - - + +
68H ASN 3.2 0.6 - - - -
69H LEU* 1.3 80.4 - - + +
71H ASN* 1.3 55.9 + - - +
72H ASP 3.2 5.3 + - - -
73H PRO* 3.6 16.3 - - + +
75H ARG* 3.6 37.0 - - - -
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Residues in contact with ASN 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H LEU 5.0 3.2 + - - -
27H THR* 5.3 15.3 - - + +
42H GLN* 5.8 1.8 - - - +
46H GLU* 3.7 23.7 + - - +
67H VAL* 2.4 33.1 + - - +
68H ASN* 2.9 22.9 + - - +
70H PHE* 1.3 77.0 - - - +
72H ASP* 1.3 63.3 + - - +
73H PRO* 3.6 3.7 - - - +
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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