Contacts of the helix formed by residues 69 - 80 (chain C) in PDB entry 3RCY
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 69 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65C GLU* 2.8 28.8 + - + +
66C ASN* 3.0 26.7 + - - +
67C PRO 3.1 0.6 - - - -
68C GLU* 1.3 82.1 - - - +
70C ILE* 1.3 57.7 + - - +
71C GLU 3.4 2.5 - - - -
72C LEU* 3.4 21.7 + - + +
73C MET* 2.9 34.3 + - - +
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Residues in contact with ILE 70 (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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67C PRO 3.2 23.8 - - - +
68C GLU 2.9 13.5 + - - +
69C ASN* 1.3 70.8 - - - +
71C GLU* 1.3 66.3 + - + +
73C MET* 4.2 9.7 - - + +
74C PHE* 3.1 25.1 + - + +
94C PHE* 4.4 2.1 - - + -
98C GLU* 3.6 22.0 - - + +
101C CYS* 3.8 22.7 - - + -
102C TRP* 4.0 26.0 - - + +
105C LEU* 4.3 6.7 - - + -
291C TRP* 3.5 36.8 - - + -
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Residues in contact with GLU 71 (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 ASN 3.4 0.6 - - - -
70C ILE* 1.3 78.1 - - - +
72C LEU* 1.3 63.8 + - - +
74C PHE* 3.4 5.4 + - - +
75C ARG* 3.1 33.0 + - + +
291C TRP* 2.7 36.1 + - + +
295C LYS* 2.8 32.1 + - - -
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Residues in contact with LEU 72 (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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174A LEU* 4.1 18.2 - - + -
175A ARG* 5.8 5.8 - - - +
390A GLU* 3.8 27.4 - - + +
65C GLU* 4.4 13.0 - - - +
69C ASN* 3.4 21.1 + - + +
70C ILE 3.3 0.4 - - - -
71C GLU* 1.3 80.0 - - - +
73C MET* 1.3 63.4 + - - +
75C ARG* 3.2 6.4 + - + +
76C ARG* 2.9 55.7 + - - +
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Residues in contact with MET 73 (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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3C LEU* 3.9 10.1 - - - -
61C HIS* 3.9 9.8 - - - +
62C MET* 3.7 31.9 - - + -
65C GLU* 3.8 24.7 - - + -
66C ASN 3.8 15.7 - - - +
67C PRO* 3.9 20.6 - - + +
69C ASN 2.9 25.3 + - - +
70C ILE* 4.2 7.4 - - + +
71C GLU 3.4 0.2 - - - -
72C LEU* 1.3 76.6 - - - +
74C PHE* 1.3 62.3 + - - +
76C ARG* 3.3 10.1 + - - +
77C VAL* 3.1 27.7 + - - +
94C PHE* 3.8 16.6 - - + -
101C CYS* 4.0 14.8 - - - -
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Residues in contact with PHE 74 (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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70C ILE* 3.1 18.5 + - + +
71C GLU* 3.7 4.7 - - - +
73C MET* 1.3 76.5 - - - +
75C ARG* 1.3 72.5 + - - +
76C ARG 3.2 0.2 + - - -
77C VAL* 3.3 1.6 + - - +
78C TYR* 2.8 69.3 + + - +
91C ILE* 4.3 11.0 - - + -
94C PHE* 3.6 32.6 - + + -
264C THR* 3.9 13.9 - - + -
265C LYS* 3.5 20.2 - - - -
288C GLY* 4.3 9.6 - - - -
292C GLU* 3.5 37.0 - - + -
295C LYS* 5.9 2.2 - - - -
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Residues in contact with ARG 75 (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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174A LEU* 2.8 43.8 + - + +
175A ARG* 3.5 19.1 + - + -
176A GLY* 3.4 14.1 - - - -
240A ASP* 5.2 2.6 + - - -
71C GLU* 3.1 24.7 + - + +
72C LEU* 3.2 9.4 + - + +
74C PHE* 1.3 91.6 - - - +
76C ARG* 1.3 63.1 + - - +
78C TYR* 3.9 23.9 - - - -
79C SER* 2.8 31.4 + - - -
84C GLN* 3.4 29.3 - - - +
265C LYS* 4.6 10.3 - - - +
295C LYS* 6.3 1.3 - - - +
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Residues in contact with ARG 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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174A LEU* 3.7 25.4 - - + -
390A GLU* 2.8 35.3 + - - -
61C HIS* 3.0 53.8 + - + +
65C GLU* 2.7 40.0 + - - +
72C LEU* 2.9 30.7 + - + +
73C MET* 3.6 10.9 - - - +
74C PHE 3.2 0.2 - - - -
75C ARG* 1.3 77.4 - - - +
77C VAL* 1.3 61.9 + - - +
79C SER* 3.7 1.6 - - - -
80C SER* 3.0 24.4 + - - -
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Residues in contact with VAL 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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44A SER* 5.7 1.2 - - - -
57C VAL* 3.8 24.9 - - + -
61C HIS* 3.8 24.0 - - + -
62C MET* 5.0 1.3 - - + -
73C MET 3.1 16.1 + - - +
74C PHE 4.1 1.8 - - - +
76C ARG* 1.3 74.6 - - - +
78C TYR* 1.3 64.0 + - - +
80C SER* 3.0 18.7 + - - -
83C THR* 4.5 1.2 + - - -
90C ALA* 3.9 31.7 - - + +
91C ILE* 4.1 9.3 - - + +
94C PHE* 3.6 31.4 - - + -
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Residues in contact with TYR 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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240A ASP* 2.6 43.9 + - - +
74C PHE* 2.8 44.5 + + + +
75C ARG* 3.9 31.4 - - - +
77C VAL* 1.3 77.8 - - - +
79C SER* 1.3 56.3 + - - +
83C THR* 3.1 5.9 + - - -
84C GLN* 2.9 38.9 + - + -
85C ARG* 3.8 13.8 + - - +
86C PRO* 3.6 28.1 - - + +
91C ILE* 4.0 13.8 - - + +
264C THR* 4.0 14.6 - - + -
265C LYS* 6.0 1.3 - - - -
266C ALA* 3.5 13.1 - - + +
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Residues in contact with SER 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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174A LEU* 3.1 19.8 + - - -
388A MET* 3.3 27.4 - - - +
75C ARG* 2.8 23.1 + - - -
76C ARG 3.7 1.6 - - - -
78C TYR* 1.3 73.6 - - - +
80C SER* 1.3 65.8 - - - +
81C GLY 3.3 0.2 + - - -
82C PHE 3.1 14.2 + - - -
83C THR* 3.2 8.8 + - - -
84C GLN* 2.8 32.9 + - - +
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Residues in contact with SER 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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43A ALA 4.1 1.1 - - - -
44A SER* 2.7 32.8 + - - -
384A LEU* 3.2 11.3 - - - +
61C HIS* 2.8 31.7 + - - -
76C ARG 3.0 7.5 + - - -
77C VAL* 3.0 19.9 + - - -
78C TYR 3.4 0.4 - - - -
79C SER* 1.3 75.3 - - - +
81C GLY* 1.3 58.8 + - - +
83C THR* 2.7 27.6 + - - +
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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