Contacts of the helix formed by residues 80 - 89 (chain C) in PDB entry 2YPA
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 CYS 80 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57C CYS* 3.2 9.1 - - - +
60C CYS* 3.8 4.9 - - - -
62C CYS* 3.8 17.5 - - - -
64C LEU* 3.7 16.1 - - + +
69C ARG* 5.2 7.0 - - - -
70C ARG 4.1 0.4 - - - -
72C TYR* 4.4 0.9 - - - -
79C LEU* 1.3 76.6 - - - +
81C ARG* 1.3 59.5 + - - +
82C ARG* 3.2 12.9 + - - +
83C ASP* 2.9 21.2 + - - -
84C TYR* 2.9 27.4 + - - +
1158C ZN 2.4 35.0 - - - -
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Residues in contact with ARG 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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69C ARG* 6.1 1.2 - - - +
70C ARG* 3.0 61.2 + - + +
72C TYR* 3.3 31.0 + - + -
80C CYS* 1.3 72.7 - - - +
82C ARG* 1.3 62.9 + - - +
84C TYR* 3.7 0.7 + - - +
85C LEU* 3.2 36.6 + - + +
309D LEU* 3.4 31.3 - - + +
312D GLY 3.1 26.4 + - - -
313D GLU* 5.3 1.0 - - - +
314D PHE 4.5 8.1 + - - -
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Residues in contact with ARG 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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216A THR 5.5 3.8 + - - -
219A PRO* 3.7 38.5 - - - +
80C CYS* 3.2 12.7 - - - -
81C ARG* 1.3 79.4 - - - +
83C ASP* 1.3 65.9 + - - +
85C LEU 3.3 2.1 + - - -
86C ARG* 2.8 41.0 + - - +
104C TYR* 3.3 66.5 + - + +
105C GLU* 5.7 0.4 - - - +
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Residues in contact with ASP 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A PRO* 3.6 6.7 - - - +
57C CYS* 3.2 7.6 - - - -
59C LEU* 3.7 23.9 - - + +
60C CYS* 3.1 7.4 - - - +
79C LEU* 4.3 3.8 - - + -
80C CYS* 3.3 7.4 + - - +
82C ARG* 1.3 74.4 - - - +
84C TYR* 1.3 67.7 + - - +
86C ARG* 3.1 31.3 + - - +
87C LEU* 3.0 30.9 + - - +
1158C ZN 1.7 43.6 - - - -
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Residues in contact with TYR 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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607B ASN* 5.3 1.9 + - - -
72C TYR* 3.7 44.0 - + + -
74C LYS* 4.6 12.3 - - + -
79C LEU* 4.2 16.8 - - + +
80C CYS 2.9 16.8 + - - +
81C ARG* 3.9 4.0 - - - +
83C ASP* 1.3 79.1 - - - +
85C LEU* 1.3 76.3 + - + +
88C PHE* 3.0 62.0 + + + +
314D PHE* 4.4 13.5 - + - -
315D GLY* 3.5 30.1 - - - -
318D ASP* 3.1 31.1 + - + -
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Residues in contact with LEU 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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72C TYR* 6.4 0.7 - - + -
81C ARG* 3.2 34.9 + - + +
82C ARG* 3.8 3.6 - - - +
84C TYR* 1.3 94.6 - - + +
86C ARG* 1.3 63.1 + - - +
89C GLY* 2.9 32.7 + - - +
103C ALA* 3.6 34.0 - - + +
104C TYR* 4.2 3.6 - - - +
309D LEU* 4.2 19.1 - - + -
311D GLY* 4.1 14.4 - - - -
312D GLY 5.1 0.2 - - - +
314D PHE* 4.1 35.9 - - + +
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Residues in contact with ARG 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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212A LYS 4.2 9.3 + - - -
213A LEU 3.9 14.7 + - - -
214A ILE 4.6 1.6 + - - -
215A PRO* 3.3 25.0 - - - +
216A THR 4.9 0.6 - - - +
235A TYR* 3.8 20.3 + - - +
600B GLU* 4.3 4.3 + - - +
604B ARG* 4.6 12.1 + - - -
59C LEU* 4.2 8.7 - - - -
82C ARG* 2.8 29.8 + - - +
83C ASP* 3.1 35.2 + - - +
85C LEU* 1.3 78.3 - - - +
87C LEU* 1.3 70.9 + - + +
89C GLY 5.3 0.2 - - - +
102C ARG* 3.7 25.7 + - - +
103C ALA* 5.6 0.9 - - - +
104C TYR* 3.5 51.6 + - + -
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Residues in contact with LEU 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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235A TYR* 3.9 13.0 - - - +
238A PHE* 4.0 14.1 - - + -
239A LEU* 3.7 29.6 - - + -
242A LEU* 4.3 10.1 - - + -
600B GLU* 4.3 8.8 - - + +
603B VAL* 4.1 9.9 - - + +
604B ARG* 3.9 23.4 + - - +
59C LEU* 3.7 20.0 - - + -
79C LEU* 4.1 19.5 - - + -
83C ASP 3.0 19.2 + - - +
86C ARG* 1.3 85.9 - - + +
88C PHE* 1.3 83.2 + - + +
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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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242A LEU* 4.5 15.7 - - + -
246A GLN* 4.0 8.7 - - - -
603B VAL* 3.7 22.0 - - + -
604B ARG* 4.0 8.6 - - - +
607B ASN* 3.4 44.8 + - + +
74C LYS* 3.9 24.2 - - + -
75C LEU* 5.1 0.9 - - + -
79C LEU* 4.3 4.7 - - + -
84C TYR* 3.0 57.9 + + + +
87C LEU* 1.3 99.1 - - + +
89C GLY* 1.3 67.5 + - - +
90C GLN* 3.7 13.3 + - - -
314D PHE* 3.9 12.4 - - + -
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Residues in contact with GLY 89 (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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604B ARG* 3.3 18.1 + - - -
85C LEU* 2.9 31.5 + - - +
86C ARG 5.3 0.3 - - - +
87C LEU 5.3 0.2 - - - -
88C PHE* 1.3 80.9 - - - +
90C GLN* 1.3 64.3 + - - -
91C ASP* 3.9 2.6 - - - +
103C ALA* 3.5 15.5 - - - +
311D GLY* 5.8 0.4 - - - -
314D PHE* 4.4 9.5 - - - -
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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