Contacts of the helix formed by residues 81 - 91 (chain C) in PDB entry 3DVA
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 GLN 81 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78C THR* 2.9 17.4 + - - +
80C GLY* 1.3 80.5 - - - +
82C GLU* 1.3 56.7 + - - -
83C ALA 3.4 2.5 - - - -
84C SER* 3.3 10.4 + - - +
85C GLN* 2.9 46.7 + - + +
103C ARG* 3.9 16.7 - - - +
200C GLN* 3.3 33.7 + - - +
202C ASN* 3.0 31.0 + - - +
235C GLY 5.3 0.2 - - - -
265C CYS* 4.1 17.6 - - - -
266C PHE 4.1 10.5 - - - +
267C ARG* 3.8 10.0 - - + +
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Residues in contact with GLU 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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53C MET* 3.4 41.7 - - + +
56C THR* 4.3 15.1 - - + +
57C ARG* 2.5 55.8 + - - +
78C THR 4.4 2.1 - - - -
79C ALA* 3.4 12.7 + - - -
80C GLY* 2.8 19.8 + - - -
81C GLN* 1.3 77.5 - - - +
83C ALA* 1.3 57.2 + - - +
85C GLN* 4.9 2.0 - - - -
86C ILE* 2.7 42.6 + - - +
295C PRO* 3.7 8.7 - - + +
296C LEU* 5.1 2.0 - - + -
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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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53C MET* 4.2 8.7 - - - -
81C GLN 3.4 0.6 - - - -
82C GLU* 1.3 76.3 - - - +
84C SER* 1.3 64.2 + - - +
87C ALA* 3.0 30.3 + - - +
235C GLY 3.3 17.5 + - - +
236C MET 3.8 7.6 - - - -
237C ASP 3.8 6.5 - - - +
238C PRO* 3.6 29.2 - - + -
241C VAL* 3.5 6.5 - - + +
295C PRO* 3.9 12.5 - - + +
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Residues in contact with SER 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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81C GLN* 3.3 9.1 + - - -
83C ALA* 1.3 80.6 - - - +
85C GLN* 1.3 51.2 + - - +
88C SER* 2.6 32.6 + - - -
170C TYR* 4.2 4.7 - - - -
198C VAL* 4.8 0.7 - - - +
200C GLN* 2.8 27.2 + - - +
235C GLY 3.5 12.9 + - - -
241C VAL* 3.9 11.4 - - - +
263C THR* 2.8 30.6 + - - +
265C CYS* 4.1 11.0 - - - -
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Residues in contact with GLN 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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56C THR* 4.7 3.3 - - - +
78C THR* 3.5 18.2 - - - +
81C GLN* 2.9 33.0 + - + +
82C GLU* 4.3 0.7 - - - +
84C SER* 1.3 77.3 - - - +
86C ILE* 1.3 69.5 + - + +
88C SER* 2.9 15.9 + - - -
89C HIS* 3.3 7.8 + - - +
103C ARG* 3.0 29.9 + - - +
104C ASP* 3.3 12.9 + - - -
106C PRO* 3.4 18.9 - - - +
107C GLN* 3.3 42.5 + - + +
200C GLN* 3.5 12.3 - - - +
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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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49C LEU* 4.0 12.6 - - + -
52C ARG* 3.6 36.8 - - + +
53C MET* 3.9 11.0 - - + -
56C THR* 3.3 31.0 - - + +
82C GLU* 2.7 32.7 + - - +
85C GLN* 1.3 75.7 - - + +
87C ALA* 1.3 59.0 + - - +
89C HIS* 3.3 7.3 + - + +
90C PHE* 2.8 26.0 + - - +
106C PRO* 4.0 16.6 - - + -
107C GLN* 5.0 0.4 - - - +
110C TRP* 3.6 21.5 - - + +
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Residues in contact with ALA 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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49C LEU* 3.8 19.4 - - + +
53C MET* 5.3 0.4 - - - +
82C GLU 3.7 0.6 + - - -
83C ALA* 3.0 20.0 + - - +
86C ILE* 1.3 75.8 - - - +
88C SER* 1.3 64.7 + - - +
90C PHE* 3.3 10.9 + - - +
91C ALA 3.6 6.8 + - - -
238C PRO* 3.3 37.9 - - + +
241C VAL* 4.1 0.7 - - + -
242C TYR* 3.6 20.7 - - + +
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Residues in contact with SER 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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83C ALA 3.6 3.4 + - - -
84C SER 2.6 27.0 + - - -
85C GLN 2.9 11.3 + - - -
87C ALA* 1.3 77.2 - - - +
89C HIS* 1.3 59.9 + - - +
91C ALA* 3.3 9.5 + - - +
92C LEU* 3.8 5.2 - - - +
168C ILE* 5.0 1.1 - - - -
170C TYR* 2.7 32.0 + - - -
198C VAL* 5.2 2.9 - - - -
241C VAL* 3.7 6.8 - - - +
245C VAL* 3.5 44.3 - - - +
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Residues in contact with HIS 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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52C ARG* 3.5 20.4 + - - -
85C GLN 3.3 13.9 + - - +
86C ILE* 3.3 7.7 + - - +
88C SER* 1.3 78.9 + - - +
90C PHE* 1.3 61.6 + - - +
91C ALA 3.0 5.4 - - - -
92C LEU* 3.0 26.2 + - + +
98C ILE* 3.8 10.1 - - + -
107C GLN* 3.6 26.7 - - + -
110C TRP* 3.3 36.0 - - + +
111C HIS* 3.0 38.9 + + - +
170C TYR* 4.3 2.0 - - - +
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Residues in contact with PHE 90 (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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41C LEU* 4.5 9.6 - - + -
45C GLN* 3.5 49.4 - - + -
48C GLU* 3.7 28.0 - - + -
49C LEU* 3.9 29.2 - - + -
52C ARG* 3.9 27.6 - - - +
86C ILE 2.8 17.0 + - - +
87C ALA 3.6 8.1 - - - +
88C SER 3.2 0.6 - - - -
89C HIS* 1.3 77.6 + - - +
91C ALA* 1.3 59.2 + - - +
92C LEU 3.7 4.6 + - - +
242C TYR* 3.5 21.8 + + + -
246C LYS* 5.1 1.4 + - - -
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Residues in contact with ALA 91 (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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87C ALA 3.6 2.3 + - - +
88C SER 3.3 11.4 + - - +
89C HIS 3.0 1.2 - - - -
90C PHE* 1.3 79.3 - - - +
92C LEU* 1.3 61.0 + - - +
242C TYR* 3.5 26.2 - - + +
245C VAL* 3.8 17.9 - - + -
246C LYS* 2.8 45.3 + - + +
249C ARG* 3.5 9.8 - - - -
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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