Contacts of the helix formed by residues 71 - 81 (chain C) in PDB entry 5FLZ
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 SER 71 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C ASP* 1.3 85.1 + - - +
72C GLU* 1.3 75.4 + - - +
73C PRO* 3.3 15.2 - - - +
75C VAL* 3.1 22.3 + - - +
94C VAL* 3.4 8.5 - - - -
95C ALA 3.6 20.2 - - - -
96C SER* 4.3 3.6 - - - -
100C SER* 6.1 0.9 - - - -
146C THR* 4.6 4.9 + - - -
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Residues in contact with GLU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C SER* 1.3 85.1 + - - +
73C PRO* 1.3 67.5 - - + +
74C SER 3.3 0.3 + - - -
75C VAL* 3.3 4.3 + - - +
76C ILE* 3.0 38.7 + - + +
94C VAL* 3.3 26.9 - - + +
95C ALA* 3.7 9.5 - - - +
96C SER* 2.8 31.8 + - - -
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Residues in contact with PRO 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C GLN* 6.4 1.8 - - + -
70C ASP* 4.3 4.0 - - - +
71C SER* 3.3 14.8 - - - +
72C GLU* 1.3 92.5 - - + +
74C SER* 1.4 62.5 + - - +
76C ILE* 3.4 11.2 + - + +
77C ALA* 3.3 19.8 + - - +
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Residues in contact with SER 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C GLN* 3.8 15.4 + - - +
15C ASN* 3.1 43.5 - - - +
16C HIS* 4.2 13.2 - - - -
19C LYS* 5.1 1.6 + - - +
68C MET* 4.7 2.1 - - - +
70C ASP* 3.3 20.0 + - - -
72C GLU 3.6 0.4 - - - -
73C PRO* 1.4 74.8 - - - +
75C VAL* 1.4 65.6 + - - +
77C ALA* 3.2 17.2 + - - +
78C ASP* 3.3 11.8 + - - +
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Residues in contact with VAL 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C MET* 3.6 27.1 - - + -
70C ASP* 4.6 5.8 - - + -
71C SER 3.1 20.2 - - - +
72C GLU* 3.3 6.2 + - - +
74C SER* 1.4 76.5 - - - +
76C ILE* 1.3 60.0 + - + +
78C ASP* 3.2 4.7 + - - +
79C VAL* 3.0 33.3 + - + +
84C ARG* 4.6 5.8 - - - +
92C THR* 4.2 20.2 - - + -
93C TRP 4.9 2.2 - - - +
94C VAL* 4.1 27.4 - - + -
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Residues in contact with ILE 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C GLU* 3.0 32.7 + - + +
73C PRO* 3.5 12.3 - - + +
74C SER 3.2 0.2 - - - -
75C VAL* 1.3 76.7 - - + +
77C ALA* 1.3 59.0 + - - +
79C VAL* 3.3 12.4 + - + +
80C GLU* 3.1 37.4 + - + +
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Residues in contact with ALA 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C HIS* 5.8 7.2 - - + +
19C LYS* 3.4 17.9 - - - +
73C PRO 3.3 8.4 + - - +
74C SER* 3.2 12.6 + - - +
76C ILE* 1.3 76.0 - - - +
78C ASP* 1.4 60.2 + - - +
80C GLU* 3.3 22.4 + - - +
81C ASN* 3.3 18.7 + - - +
225C GLN* 6.4 0.2 - - - +
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Residues in contact with ASP 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LYS* 3.7 15.7 - - + +
68C MET* 3.6 25.9 - - + +
74C SER 3.3 6.8 + - - +
75C VAL 3.2 10.1 + - - +
77C ALA* 1.4 73.8 - - - +
79C VAL* 1.3 60.9 + - - +
81C ASN* 3.3 20.5 + - - +
83C PHE* 3.0 36.4 - - - +
84C ARG* 3.4 40.5 + - - +
87C PHE* 3.6 12.2 - - - -
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Residues in contact with VAL 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C VAL* 3.0 26.0 + - + +
76C ILE* 3.4 15.7 - - + +
78C ASP* 1.3 73.2 - - - +
80C GLU* 1.3 67.7 + - + +
81C ASN 3.2 7.1 - - - +
84C ARG* 3.5 33.2 - - + +
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Residues in contact with GLU 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C ILE* 3.1 29.6 + - + +
77C ALA* 3.3 14.0 + - - +
78C ASP 3.3 0.6 - - - -
79C VAL* 1.3 79.2 - - + +
81C ASN* 1.4 64.0 + - - +
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Residues in contact with ASN 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LYS* 3.2 28.1 + - - +
77C ALA 3.3 4.8 - - - +
78C ASP 3.3 9.9 + - - +
79C VAL 3.2 13.6 - - - +
80C GLU* 1.4 82.7 - - - +
82C THR* 1.3 61.6 + - - +
83C PHE* 3.1 37.3 + - + +
84C ARG* 3.8 7.1 - - - +
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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