Contacts of the helix formed by residues 303 - 314 (chain A) in PDB entry 1GVJ
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 THR 303 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A HIS* 3.9 13.2 - - + -
302A GLY* 1.3 74.9 - - - +
304A PHE* 1.3 65.8 + - - +
305A LYS* 3.4 9.2 + - - +
306A ASP* 2.8 33.2 + - - +
307A TYR* 3.0 20.6 + - - +
329B TYR* 3.2 9.8 - - - -
419B GLN 5.1 0.2 - - - +
420B SER* 3.7 19.1 - - - +
421B LEU 3.7 6.7 - - - -
423B GLY* 3.8 20.7 - - - -
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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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303A THR* 1.3 74.0 - - - +
305A LYS* 1.3 67.0 + - - +
307A TYR* 3.0 9.2 + + - +
308A VAL* 2.9 50.5 + - + +
320B VAL 4.0 8.1 - - - -
321B ILE* 3.6 42.2 - - + -
322B PRO* 4.1 7.4 - - + -
325B ALA* 3.7 22.2 - - + -
326B LEU* 3.6 33.0 - - + -
329B TYR* 3.5 29.1 + + + -
421B LEU 2.9 17.9 + - - +
422B LEU* 3.7 14.6 - - + +
424B TYR* 5.1 1.6 - + - -
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Residues in contact with LYS 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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303A THR* 3.2 6.7 - - - +
304A PHE* 1.3 78.8 - - - +
306A ASP* 1.3 63.0 + - - +
308A VAL* 3.5 5.7 + - - +
309A ARG* 3.0 25.5 + - + +
422B LEU 3.1 18.7 + - - +
423B GLY* 4.0 17.2 + - - +
424B TYR* 3.9 39.1 - - + +
428B GLU* 5.5 6.1 + - - -
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Residues in contact with ASP 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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302A GLY* 3.5 12.4 - - - -
303A THR* 2.8 38.9 + - - +
305A LYS* 1.3 77.7 - - - +
307A TYR* 1.3 59.9 + - - +
309A ARG* 2.9 28.7 + - - +
310A ASP* 2.8 43.0 + - - +
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Residues in contact with TYR 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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302A GLY* 5.8 0.2 - - - -
303A THR 3.0 7.8 + - - +
304A PHE* 3.2 18.6 - + - +
306A ASP* 1.3 77.5 - - - +
308A VAL* 1.3 66.3 + - + +
310A ASP* 3.4 6.0 + - - +
311A ARG* 3.1 67.0 + - + +
325B ALA* 3.5 26.4 + - + -
328B GLY* 3.6 20.1 - - - -
329B TYR* 3.6 49.4 - + + -
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Residues in contact with VAL 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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304A PHE* 2.9 55.1 + - + +
305A LYS* 3.9 5.8 - - - +
307A TYR* 1.3 79.7 - - + +
309A ARG* 1.3 60.4 + - - +
311A ARG* 3.4 5.7 + - - +
312A ALA* 2.9 31.8 + - + +
317A ASP* 5.0 5.5 - - - +
320B VAL 5.4 2.2 - - - +
322B PRO* 5.5 2.7 - - + -
325B ALA* 5.0 4.5 - - + -
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Residues in contact with ARG 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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305A LYS* 3.0 20.6 + - + +
306A ASP* 2.9 40.9 + - - +
308A VAL* 1.3 77.5 - - - +
310A ASP* 1.3 89.4 + - - +
312A ALA* 3.3 7.1 + - + +
313A ASP* 3.0 28.5 + - + +
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Residues in contact with ASP 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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306A ASP* 2.8 26.5 + - - +
307A TYR* 3.7 6.7 + - - +
309A ARG* 1.3 106.7 + - - +
311A ARG* 1.3 64.1 + - + +
313A ASP* 3.3 15.2 + - - +
314A LEU* 3.4 21.8 + - + +
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Residues in contact with ARG 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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307A TYR* 3.1 64.6 + - + +
308A VAL* 3.8 3.8 - - - +
310A ASP* 1.3 74.6 - - + +
312A ALA* 1.3 66.4 + - - +
314A LEU* 3.0 15.2 + - + -
316A LYS* 3.0 60.6 + - + +
317A ASP* 2.9 45.5 + - - +
325B ALA* 6.1 1.0 - - - +
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Residues in contact with ALA 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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308A VAL* 2.9 21.5 + - + +
309A ARG* 3.6 9.0 - - + +
311A ARG* 1.3 77.1 - - - +
313A ASP* 1.3 57.6 + - - +
315A ASN* 2.9 22.9 + - - +
316A LYS 4.2 10.5 - - - -
317A ASP* 4.9 1.0 + - - -
318A LYS* 3.9 22.7 + - - +
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Residues in contact with ASP 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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309A ARG* 3.0 13.7 + - + +
310A ASP* 3.5 12.8 - - - +
311A ARG 3.1 0.2 - - - -
312A ALA* 1.3 76.4 - - - +
314A LEU* 1.3 63.2 + - + +
315A ASN* 3.2 9.3 + - - +
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Residues in contact with LEU 314 (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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310A ASP* 3.4 17.9 + - + +
311A ARG* 3.0 10.5 + - + +
313A ASP* 1.3 82.7 - - + +
315A ASN* 1.3 74.3 + - - +
316A LYS* 3.2 29.5 + - + +
349A SER* 3.4 14.7 - - - -
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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