Contacts of the helix formed by residues 299 - 313 (chain A) in PDB entry 3VAS
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 GLY 299 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ASN* 4.9 0.9 - - - -
132A ARG* 5.8 0.8 - - - +
297A THR 3.2 0.6 + - - -
298A ASN* 1.3 77.9 + - - +
300A ALA* 1.3 64.4 + - - +
301A GLY 3.2 3.4 - - - -
302A ASP* 3.0 13.6 + - - +
303A ALA* 3.0 19.2 + - - +
332A ILE* 4.0 5.2 - - - -
338A PHE* 3.6 15.3 - - - -
401A ADN 3.8 22.8 + - - -
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Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A THR* 3.1 19.8 + - - +
298A ASN 3.4 1.2 + - - -
299A GLY* 1.3 76.7 - - - +
301A GLY* 1.3 58.2 + - - +
303A ALA* 3.3 2.9 + - - +
304A PHE* 2.8 29.7 + - - +
329A ALA* 3.5 13.4 - - + +
332A ILE* 4.0 9.8 - - + +
333A ILE* 3.9 29.8 - - + -
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Residues in contact with GLY 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ASN* 4.6 8.6 + - - -
265A THR* 5.8 4.9 - - - -
299A GLY 3.2 0.6 - - - -
300A ALA* 1.3 75.3 - - - +
302A ASP* 1.3 65.7 + - - +
304A PHE* 3.4 9.3 + - - +
305A ALA* 3.1 22.3 + - - +
401A ADN 5.8 0.2 + - - -
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Residues in contact with ASP 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ALA* 3.7 25.0 - - - +
68A ASN* 3.1 34.4 + - + -
69A THR* 2.8 30.2 + - - +
165A TYR* 4.9 4.7 + - - -
195A ASN* 5.2 2.9 + - - -
299A GLY* 3.0 8.7 + - - +
301A GLY* 1.3 76.1 - - - +
303A ALA* 1.3 63.3 + - - +
305A ALA* 3.4 2.5 + - - -
306A ALA* 3.1 14.4 + - - +
338A PHE* 4.0 2.7 - - + -
401A ADN 2.7 31.5 + - - +
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Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A MET* 3.7 16.6 - - - -
299A GLY 3.0 8.3 + - - +
300A ALA 3.5 7.6 - - - +
302A ASP* 1.3 75.2 - - - +
304A PHE* 1.3 55.1 + - - +
306A ALA* 3.1 1.9 + - - +
307A GLY 2.8 32.2 + - - -
328A ALA* 3.2 24.0 - - - +
329A ALA* 3.8 2.2 - - - -
332A ILE* 3.5 32.8 - - + -
338A PHE* 3.8 1.9 - - + -
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Residues in contact with PHE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A PHE* 4.2 20.0 - + - -
263A ILE* 3.8 21.1 - - + -
265A THR* 3.7 26.7 - - + -
271A LEU* 3.6 33.4 - - + -
300A ALA 2.8 18.3 + - - +
301A GLY* 3.5 10.8 - - - +
303A ALA* 1.3 75.9 - - - +
305A ALA* 1.3 64.0 + - - +
308A PHE* 3.0 20.8 + - + +
322A LEU* 4.3 6.1 - - + -
325A ALA* 3.2 50.0 - - + +
326A VAL* 4.1 13.0 - - + -
329A ALA* 4.2 6.5 - - + +
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Residues in contact with ALA 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A THR* 4.0 3.1 - - + -
165A TYR* 3.8 37.0 - - + +
195A ASN* 4.4 1.3 - - - +
220A PHE* 3.9 26.0 - - + -
301A GLY 3.1 9.1 + - - +
302A ASP 3.7 8.3 - - - +
303A ALA 3.2 0.2 - - - -
304A PHE* 1.3 80.2 - - - +
306A ALA* 1.3 62.8 + - - +
308A PHE* 3.3 1.4 + - - +
309A ILE* 3.0 30.0 + - - +
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Residues in contact with ALA 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A THR* 3.3 26.3 - - - +
72A MET* 3.7 24.5 - - + -
73A ILE* 3.7 15.7 - - + +
76A ILE* 4.2 2.2 - - - -
302A ASP 3.1 10.6 + - - +
303A ALA 3.1 8.6 + - - +
305A ALA* 1.3 78.7 - - - +
307A GLY* 1.3 62.8 + - - +
310A ALA* 2.9 29.5 + - - +
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Residues in contact with GLY 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ILE* 3.9 10.7 - - - +
303A ALA 2.8 14.7 + - - -
304A PHE 3.8 0.7 - - - -
306A ALA* 1.3 74.4 - - - +
308A PHE* 1.3 62.8 + - - +
310A ALA* 4.2 1.2 - - - +
311A ASP* 3.6 10.0 + - - +
324A ALA* 3.6 23.1 - - - +
325A ALA* 3.8 6.7 - - - -
328A ALA* 3.6 23.5 - - - +
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Residues in contact with PHE 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ILE* 4.2 11.4 - - + -
220A PHE* 3.9 25.1 - + + -
261A LEU* 3.7 25.4 - - + -
263A ILE* 3.7 17.0 - - + -
304A PHE* 3.0 17.9 + + + +
305A ALA 3.7 3.1 - - - +
307A GLY* 1.3 78.7 - - - +
309A ILE* 1.3 63.2 + - + +
311A ASP* 3.3 2.3 + - - +
312A TYR* 2.9 63.2 + + + +
318A MET* 3.9 9.4 - - - -
321A SER* 3.6 35.4 - - - -
322A LEU* 3.8 22.0 - - + -
325A ALA* 3.5 7.0 - - + +
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Residues in contact with ILE 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 5.5 0.2 - - + -
69A THR* 4.8 0.2 - - + -
73A ILE* 3.9 21.5 - - + -
163A VAL* 4.3 14.6 - - + -
165A TYR* 3.6 36.1 - - + -
191A LEU* 6.1 0.2 - - + -
193A CYS* 4.0 16.8 - - - -
218A ILE* 5.6 1.6 - - + -
220A PHE* 4.0 21.8 - - + -
305A ALA 3.0 21.3 + - - +
306A ALA 4.1 1.8 - - - +
308A PHE* 1.3 76.7 - - + +
310A ALA* 1.3 66.1 + - - +
312A TYR* 4.3 3.4 - - - -
313A ILE* 2.9 51.5 + - + +
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Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ILE* 4.3 10.2 - - + +
76A ILE* 3.8 33.0 - - + -
77A ILE* 4.0 21.6 - - + +
306A ALA 2.9 17.9 + - - +
307A GLY 4.2 3.4 - - - +
309A ILE* 1.3 77.1 - - - +
311A ASP* 1.3 57.5 + - - +
313A ILE* 3.7 4.2 - - - +
314A ARG* 2.8 35.6 + - - +
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Residues in contact with ASP 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ILE* 5.0 2.4 - - - +
307A GLY 3.6 10.6 + - - +
308A PHE 3.3 1.7 + - - +
309A ILE 3.1 0.4 - - - -
310A ALA* 1.3 81.4 - - - +
312A TYR* 1.3 64.6 + - - +
313A ILE 3.3 0.2 - - - -
314A ARG* 3.0 36.3 + - - +
316A LYS* 3.3 43.9 + - + +
320A THR* 4.1 11.4 - - - +
321A SER* 3.8 13.7 - - - +
324A ALA* 3.3 28.4 - - + +
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Residues in contact with TYR 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A LEU* 4.8 17.0 - - + -
218A ILE* 4.1 24.7 - - + -
259A LYS* 4.7 15.1 + - - -
261A LEU* 4.8 12.6 - - + +
308A PHE* 2.9 46.3 + + + +
309A ILE* 3.9 3.8 - - - +
311A ASP* 1.3 77.6 - - - +
313A ILE* 1.3 61.7 + - + +
315A GLY* 3.2 13.9 + - - -
316A LYS 4.0 12.9 + - - +
317A PRO* 5.7 0.4 - - + -
318A MET* 4.8 15.0 - - + -
321A SER* 3.4 13.6 + - - +
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Residues in contact with ILE 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LEU* 3.7 35.2 - - + +
8A TYR* 4.2 13.2 + - + +
9A VAL* 3.7 30.1 - - + -
73A ILE* 5.0 0.4 - - + -
77A ILE* 4.2 8.7 - - + -
163A VAL* 3.7 23.6 - - + -
191A LEU* 4.0 15.5 - - + -
309A ILE* 2.9 40.0 + - + +
310A ALA* 3.7 7.9 - - - +
312A TYR* 1.3 76.9 - - + +
314A ARG* 1.3 59.6 + - - +
315A GLY 3.3 1.7 + - - -
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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