Contacts of the helix formed by residues 294 - 306 (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 ASP 294 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57C ARG* 2.9 41.3 + - - -
268C TYR* 3.2 18.2 + - + +
290C TRP 3.4 4.4 + - - -
291C ALA* 3.3 17.0 - - - +
292C LYS 3.2 1.4 - - - +
293C LYS* 1.3 77.0 - - - +
295C PRO* 1.3 71.3 - - - +
296C LEU* 2.9 19.7 + - - +
297C VAL* 3.0 31.8 + - + +
298C ARG* 3.6 6.1 + - - +
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Residues in contact with PRO 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C MET* 4.8 2.9 - - - -
57C ARG* 4.3 1.3 - - - +
80C GLY 3.9 9.0 - - - +
82C GLU* 3.7 24.0 - - + +
83C ALA* 3.9 28.7 - - + +
236C MET* 3.3 47.6 - - + +
238C PRO* 4.3 6.6 - - + +
268C TYR* 4.3 1.1 - - - +
293C LYS 3.1 0.6 - - - -
294C ASP* 1.3 89.7 - - - +
296C LEU* 1.3 62.2 + - - +
298C ARG* 3.7 3.5 - - + +
299C PHE* 3.3 26.5 + - - +
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Residues in contact with LEU 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C MET* 3.8 10.7 - - + +
53C MET* 3.7 39.9 - - + +
54C VAL* 3.8 20.2 - - + +
57C ARG* 3.5 49.8 - - + +
82C GLU* 5.1 2.9 - - + -
294C ASP* 2.9 12.6 + - - +
295C PRO* 1.3 79.9 - - + +
297C VAL* 1.3 58.6 + - + +
299C PHE* 4.9 1.3 - - - -
300C ARG* 3.0 50.9 + - - +
314C GLU* 5.5 0.4 - - - +
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Residues in contact with VAL 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C GLU 4.6 2.9 - - - +
291C ALA 4.5 6.7 - - - +
292C LYS* 4.6 13.5 - - - +
294C ASP* 3.0 31.1 + - + +
296C LEU* 1.3 74.7 - - + +
298C ARG* 1.3 68.3 + - - +
300C ARG* 3.1 20.3 + - - +
301C LYS* 3.1 52.3 + - + +
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Residues in contact with ARG 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLN* 3.9 3.0 - - - +
26C LEU* 2.9 30.9 + - + +
27C ASN 3.2 26.8 + - - +
28C GLU* 3.8 20.6 + - - +
29C GLU 4.7 0.2 - - - -
30C GLY* 3.3 19.1 - - - +
234C ASP* 2.9 31.1 + - - -
236C MET* 3.3 25.9 + - - +
237C ASP* 3.7 9.4 - - - +
238C PRO* 4.5 3.4 - - + -
292C LYS 5.6 0.6 + - - +
293C LYS* 3.2 43.9 + - - +
294C ASP 3.6 1.9 + - - +
295C PRO 3.7 10.5 - - - +
297C VAL* 1.3 79.2 - - - +
299C PHE* 1.3 63.0 + - - +
301C LYS* 3.6 2.0 + - - +
302C PHE* 3.0 24.1 + - - +
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Residues in contact with PHE 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 3.8 13.0 - - + -
46C LEU* 3.5 42.2 - - + -
49C LEU* 4.1 10.8 - - + -
50C MET* 3.6 23.8 - - + -
53C MET* 3.5 19.1 - - + -
238C PRO* 3.7 21.5 - - + -
239C LEU* 3.8 25.1 - - + -
295C PRO 3.3 16.0 + - - +
296C LEU 4.3 1.3 - - - +
297C VAL 3.2 0.8 - - - -
298C ARG* 1.3 79.8 - - + +
300C ARG* 1.3 60.6 + - - +
302C PHE* 3.6 11.3 - + - +
303C LEU* 2.9 51.2 + - + +
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Residues in contact with ARG 300 (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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50C MET* 3.8 12.7 - - + +
296C LEU* 3.0 48.6 + - - +
297C VAL* 3.4 25.2 - - - +
299C PHE* 1.3 77.8 - - - +
301C LYS* 1.3 58.6 + - + +
303C LEU* 3.3 4.5 + - - +
304C GLU* 2.9 57.5 + - - +
309C TRP* 4.0 12.5 - - + +
314C GLU* 2.6 39.6 + - - -
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Residues in contact with LYS 301 (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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28C GLU 4.4 7.3 + - - -
29C GLU* 3.6 37.8 - - - +
30C GLY 5.0 0.7 - - - -
297C VAL* 3.1 38.4 + - + +
298C ARG 3.9 2.2 - - - +
300C ARG* 1.3 76.6 - - + +
302C PHE* 1.3 63.9 + - - +
304C GLU* 3.3 12.9 + - - +
305C ALA* 3.0 26.0 + - - +
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Residues in contact with PHE 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 3.5 25.1 - - + -
30C GLY 3.8 17.6 + - - +
32C VAL* 3.8 22.9 - - + -
38C MET* 3.9 21.1 - - + -
46C LEU* 4.2 9.6 - - + -
239C LEU* 4.0 12.3 - - + -
298C ARG 3.0 18.6 + - - +
299C PHE* 3.6 17.7 - + - +
301C LYS* 1.3 77.3 - - - +
303C LEU* 1.3 81.6 + - + +
305C ALA* 3.7 5.7 + - - +
306C LYS* 3.4 52.1 + - + +
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Residues in contact with LEU 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C LEU* 3.8 34.5 - - + +
47C LYS* 4.8 1.1 - - - -
50C MET* 3.5 25.4 - - + -
299C PHE* 2.9 44.3 + - + +
300C ARG* 3.8 1.6 - - - +
302C PHE* 1.3 91.7 - - + +
304C GLU* 1.3 60.7 + - - +
306C LYS* 3.0 6.8 + - - +
307C GLY 3.0 8.0 + - - -
308C LEU* 2.9 36.5 + - + +
309C TRP* 3.5 28.3 - - + +
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Residues in contact with GLU 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C ARG* 2.9 49.8 + - + +
301C LYS* 3.3 14.1 + - - +
303C LEU* 1.3 72.4 - - - +
305C ALA* 1.3 55.9 + - - +
306C LYS 3.0 4.5 - - - -
307C GLY* 2.7 24.1 + - - +
309C TRP* 3.9 29.3 - - + +
310C SER* 4.9 6.2 - - - -
311C GLU 5.3 0.9 + - - -
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Residues in contact with ALA 305 (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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301C LYS 3.0 17.0 + - - +
302C PHE* 4.0 7.4 - - - +
304C GLU* 1.3 76.4 - - - +
306C LYS* 1.3 60.1 + - + +
307C GLY 3.3 0.4 + - - -
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Residues in contact with LYS 306 (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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38C MET* 5.4 3.9 - - - +
43C ASP* 5.4 2.8 + - - -
46C LEU* 4.5 7.4 - - + +
302C PHE* 3.4 51.1 + - + +
303C LEU* 3.0 9.6 + - - +
304C GLU 3.0 1.0 - - - -
305C ALA* 1.3 77.9 - - + +
307C GLY* 1.3 63.3 + - - +
308C LEU* 3.4 33.3 + - + +
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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