Contacts of the helix formed by residues 77 - 88 (chain C) in PDB entry 1YAA
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 PRO 77 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71C LEU* 6.0 0.4 - - + -
75C GLY 3.3 10.3 - - - +
76C LEU* 1.3 95.0 - - + +
78C SER* 1.3 57.0 + - - +
80C THR* 3.3 7.1 + - - +
81C SER* 3.0 34.3 + - - -
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Residues in contact with SER 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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76C LEU* 3.4 13.9 - - - +
77C PRO* 1.3 79.7 - - - +
79C LEU* 1.3 62.3 + - - +
81C SER* 4.2 3.6 - - - -
82C ASN* 2.9 34.0 + - - +
307C ALA* 3.5 20.4 - - - +
308C LYS* 5.4 0.3 + - - -
311C GLU* 3.7 29.6 + - - -
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Residues in contact with LEU 79 (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 LEU* 3.0 19.2 + - + +
78C SER* 1.3 81.5 + - - +
80C THR* 1.3 60.2 + - - +
82C ASN* 3.8 0.7 - - - +
83C ALA* 2.9 32.7 + - + +
104C GLN* 3.9 22.7 - - + +
256C PHE* 4.5 9.6 - - + -
267C VAL* 4.3 9.0 - - + -
268C GLY 4.2 3.6 - - - +
269C CYS* 4.1 20.6 - - - -
303C ALA* 3.7 38.4 - - + +
306C VAL* 4.1 28.3 - - + -
307C ALA* 4.4 6.5 - - - +
310C LEU* 4.8 2.9 - - + +
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Residues in contact with THR 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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74C THR 4.2 6.1 - - - +
76C LEU 3.2 11.8 + - - +
77C PRO* 3.3 12.3 + - - +
79C LEU* 1.3 74.6 - - + +
81C SER* 1.3 65.1 + - - +
83C ALA* 3.8 0.9 - - - +
84C ALA* 3.1 25.6 + - - +
102C SER* 4.0 22.8 + - - +
103C VAL* 3.7 10.3 - - - -
104C GLN* 3.7 31.6 - - + +
269C CYS* 3.9 19.7 - - - -
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Residues in contact with SER 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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77C PRO 3.0 16.9 + - - -
78C SER* 4.4 4.5 - - - -
80C THR* 1.3 83.3 + - - +
82C ASN* 1.3 65.9 + - - +
84C ALA* 3.5 9.6 + - - +
85C LYS* 3.5 24.0 + - - +
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Residues in contact with ASN 82 (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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78C SER* 2.9 29.4 + - - +
81C SER* 1.3 81.1 + - - +
83C ALA* 1.3 62.5 + - - +
84C ALA 3.4 0.2 - - - -
85C LYS* 3.5 34.9 + - - +
86C ILE* 3.2 22.7 + - - +
307C ALA 4.8 0.2 + - - -
310C LEU* 3.9 30.2 - - + +
311C GLU* 3.2 34.2 + - - +
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Residues in contact with ALA 83 (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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79C LEU* 2.9 20.7 + - + +
80C THR 3.8 1.6 - - - +
81C SER 3.3 0.2 - - - -
82C ASN* 1.3 74.4 - - - +
84C ALA* 1.3 64.9 + - - +
85C LYS 3.2 0.7 + - - -
86C ILE* 3.4 11.7 + - - +
87C ILE* 3.6 2.4 - - - +
254C GLN* 3.1 42.7 + - - +
256C PHE* 3.8 14.8 - - + -
269C HIS* 3.6 18.6 - - - -
310C LEU* 4.2 7.4 - - + -
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Residues in contact with ALA 84 (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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80C THR 3.1 16.7 + - - +
81C SER* 3.7 7.4 - - - +
83C ALA* 1.3 76.8 - - - +
85C LYS* 1.3 57.5 + - - +
87C ILE* 4.3 0.4 - - - -
88C PHE* 3.0 47.1 + - + +
95C LEU* 4.3 16.2 - - + -
100C VAL* 4.8 0.4 - - + -
102C SER* 3.9 10.1 - - - +
269C HIS* 3.5 19.9 - - - +
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Residues in contact with LYS 85 (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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81C SER* 3.5 21.3 + - - +
82C ASN* 3.5 30.6 + - - +
83C ALA 3.2 0.8 - - - -
84C ALA* 1.3 76.9 - - + +
86C ILE* 1.3 60.1 + - + +
89C GLY* 3.0 27.9 + - - -
90C THR* 3.7 31.2 + - + +
95C LEU* 4.1 20.0 - - + -
241C ARG* 4.7 0.2 + - - -
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Residues in contact with ILE 86 (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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82C ASN 3.2 16.4 - - - +
83C ALA* 3.4 10.7 + - - +
85C LYS* 1.3 76.3 - - + +
87C ILE* 1.3 61.2 + - - +
226C GLN* 3.2 22.9 + - - +
233C LEU* 4.6 16.6 - - + +
234C ASP* 4.8 0.5 - - - +
241C ARG* 3.2 19.5 + - - +
254C GLN* 3.7 17.7 - - - +
256C PHE* 3.8 24.2 - - + -
259C ASN* 5.4 2.5 - - - +
310C LEU* 4.0 20.2 - - + -
319C TRP* 4.2 19.1 - - + -
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Residues in contact with ILE 87 (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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83C ALA 3.6 13.7 - - - +
84C ALA* 3.7 6.5 - - - +
86C ILE* 1.3 80.5 - - - +
88C PHE* 1.3 79.1 + - + +
89C GLY 3.3 0.4 - - - -
223C THR* 3.4 29.2 - - + +
226C GLN* 3.7 19.3 - - - +
237C ALA* 3.4 9.0 - - + +
240C VAL* 4.1 19.0 - - + +
241C ARG* 3.0 23.7 + - - +
252C VAL* 3.4 29.8 - - + -
254C GLN* 3.9 15.9 - - + +
269C HIS* 4.4 5.8 - - - +
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Residues in contact with PHE 88 (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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84C ALA* 3.0 31.7 + - + +
87C ILE* 1.3 83.3 - - + +
89C GLY* 1.3 57.7 - - - +
92C SER* 3.3 21.6 - - - -
94C ALA* 5.2 0.2 - - + -
95C LEU* 4.0 16.6 - - + -
100C VAL* 3.7 25.6 - - + -
240C VAL* 4.5 6.3 - - + -
241C ARG* 3.6 19.0 + - - +
242C VAL* 3.5 39.0 - - - -
252C VAL* 3.9 18.4 - - + -
269C ALA* 3.6 52.5 - + - -
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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