Contacts of the helix formed by residues 313 - 324 (chain A) in PDB entry 2VGO
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 SER 313 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A GLU* 2.6 36.1 + - - -
311A PHE 3.6 3.4 + - - -
312A LEU* 1.3 75.6 - - - +
314A ASP* 1.3 65.0 + - - +
315A GLY 3.6 3.3 + - - -
316A SER* 3.0 34.6 + - - -
317A LYS* 3.1 11.1 + - - +
342A TRP* 3.6 2.9 + - - -
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Residues in contact with ASP 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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312A LEU 3.9 0.9 + - - +
313A SER* 1.3 71.9 - - - +
315A GLY* 1.3 56.7 + - - +
317A LYS* 3.4 24.1 + - - +
318A ASP* 2.9 30.1 + - - +
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Residues in contact with GLY 315 (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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313A SER* 3.2 3.8 + - - -
314A ASP* 1.3 78.3 - - - +
316A SER* 1.3 62.2 + - - +
318A ASP* 3.2 8.6 + - - +
319A LEU* 3.1 18.5 + - - +
340A HIS* 3.5 10.2 - - - -
342A TRP* 3.7 24.1 - - - +
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Residues in contact with SER 316 (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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190A GLU* 4.5 1.9 - - - +
279A CYS* 5.2 0.2 - - - -
283A LEU* 3.6 29.3 - - - +
312A LEU* 3.8 12.3 - - - +
313A SER* 3.0 35.8 + - - -
315A GLY* 1.3 73.7 - - - +
317A LYS* 1.3 62.4 + - - +
319A LEU* 3.3 2.6 + - - +
320A ILE* 3.0 30.8 + - - +
342A TRP* 3.6 24.9 - - - -
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Residues in contact with LYS 317 (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 PHE* 3.6 54.2 - - + +
309A PRO 4.9 3.2 + - - +
310A PRO* 5.6 3.2 + - - +
312A LEU* 3.7 29.4 + - + -
313A SER 3.1 17.1 + - - +
314A ASP* 3.8 22.6 + - - +
316A SER* 1.3 73.9 + - - +
318A ASP* 1.3 60.7 + - - +
321A SER* 2.9 36.2 + - - -
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Residues in contact with ASP 318 (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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314A ASP 2.9 15.1 + - - +
315A GLY* 3.2 12.5 + - - +
317A LYS* 1.3 76.1 - - - +
319A LEU* 1.3 63.0 + - - +
321A SER* 3.7 4.5 - - - -
322A LYS* 2.8 65.3 + - - +
340A HIS* 2.8 20.0 + - + +
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Residues in contact with LEU 319 (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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197A MET* 4.7 6.1 - - + -
279A CYS* 4.2 11.7 - - - -
315A GLY 3.1 12.6 + - - +
316A SER 3.8 6.7 - - - +
318A ASP* 1.3 78.1 - - - +
320A ILE* 1.3 63.7 + - - +
322A LYS* 3.1 4.2 + - - +
323A LEU* 3.1 35.3 + - + +
332A LEU* 3.7 26.5 - - + -
337A VAL* 4.2 15.9 - - + -
340A HIS* 3.6 24.1 + - + +
342A TRP* 3.6 33.4 - - + -
343A VAL* 3.8 14.1 - - + -
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Residues in contact with ILE 320 (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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276A GLY* 4.0 9.6 - - - +
279A CYS* 3.9 22.9 - - + -
280A TYR* 3.8 30.7 - - + +
283A LEU* 4.1 15.9 - - + -
306A LEU* 4.4 0.2 - - + -
308A PHE* 3.7 28.9 - - + -
312A LEU* 4.7 7.6 - - + -
316A SER 3.0 26.4 + - - +
317A LYS 4.6 0.4 - - - +
319A LEU* 1.3 75.2 - - - +
321A SER* 1.3 59.1 + - - +
323A LEU* 3.1 6.6 + - - +
324A LEU* 2.9 52.3 + - + +
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Residues in contact with SER 321 (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 LEU* 4.4 10.8 - - - +
308A PHE* 3.3 22.0 - - - -
317A LYS 2.9 23.4 + - - -
318A ASP* 3.7 5.4 - - - -
320A ILE* 1.3 77.2 - - - +
322A LYS* 1.3 61.7 + - - +
323A LEU 3.5 0.3 + - - -
324A LEU* 3.8 8.4 + - - +
325A ARG* 3.2 19.9 - - - -
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Residues in contact with LYS 322 (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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318A ASP* 2.8 51.7 + - - +
319A LEU 3.1 5.1 + - - +
321A SER* 1.3 78.5 - - - +
323A LEU* 1.3 59.0 + - - +
325A ARG* 3.4 23.4 - - - +
330A GLN 4.2 1.0 - - - +
332A LEU* 3.0 47.1 + - + -
340A HIS* 4.4 13.2 + - + -
341A PRO* 6.2 0.6 - - - +
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Residues in contact with LEU 323 (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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197A MET* 4.3 10.1 - - + -
272A LEU* 3.7 24.0 - - + +
273A TRP* 4.0 6.1 + - - -
275A ALA* 4.2 6.7 - - + -
276A GLY* 3.7 32.5 - - - +
279A CYS* 5.3 0.9 - - + -
319A LEU* 3.1 38.7 + - + +
320A ILE* 3.1 4.2 + - - +
322A LYS* 1.3 77.0 - - - +
324A LEU* 1.3 59.0 + - - +
325A ARG 3.0 11.2 + - - -
331A ARG* 3.2 23.3 + - - +
332A LEU* 3.5 28.0 - - + +
337A VAL* 3.7 21.1 - - + -
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Residues in contact with LEU 324 (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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273A TRP* 3.3 56.5 - - + +
276A GLY* 3.9 11.2 - - - +
277A VAL* 3.7 13.9 - - + +
288A PRO* 4.3 10.3 - - + -
289A PHE* 4.2 12.3 - - + -
304A VAL* 3.4 19.5 - - + +
306A LEU* 4.0 29.4 - - + +
320A ILE* 2.9 36.7 + - + +
321A SER 3.9 9.3 - - - +
322A LYS 3.7 0.4 - - - -
323A LEU* 1.3 71.8 - - - +
325A ARG* 1.3 57.9 + - - +
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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