Contacts of the helix formed by residues 315 - 319 (chain A) in PDB entry 6VSU
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 ASN 315 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A LEU* 3.7 14.6 - - - +
81A GLY* 3.4 28.0 - - - +
82A PRO* 3.8 6.3 - - + +
281A GLY* 2.7 22.7 + - - +
282A VAL* 3.9 11.2 - - - -
283A SER* 3.0 27.8 + - - +
313A GLU 3.4 0.6 + - - +
314A PHE* 1.3 74.7 - - - +
316A PRO* 1.4 64.3 - - - +
317A GLN* 2.8 19.6 + - - +
318A ARG* 2.9 26.6 + - - +
319A ASP 3.5 6.2 + - - -
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Residues in contact with PRO 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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81A GLY 3.3 20.4 - - - +
84A PHE* 3.9 7.6 - - + -
85A ALA* 3.8 25.1 - - - +
88A ARG* 4.0 16.7 + - + +
314A PHE* 3.4 35.0 - - + +
315A ASN* 1.4 84.0 - - - +
317A GLN* 1.3 57.1 + - - +
319A ASP* 3.2 23.2 + - + +
88D ARG* 4.0 20.0 - - - +
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Residues in contact with GLN 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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79A LEU* 6.1 0.2 - - - +
81A GLY* 3.3 22.2 + - - -
84A PHE* 3.7 16.7 - - + -
315A ASN* 2.8 11.7 + - - +
316A PRO* 1.3 76.4 - - + +
318A ARG* 1.3 62.8 + - + +
319A ASP 3.5 1.7 + - - +
322B ASP* 4.8 2.3 - - - +
88D ARG* 3.9 28.5 - - - +
91D GLU* 2.8 36.9 + - - +
321D VAL* 4.7 9.9 - - - +
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Residues in contact with ARG 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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78A PHE* 3.6 27.3 - - - -
79A LEU* 3.5 26.1 - - + +
280A PRO* 3.4 18.4 - - - +
281A GLY* 3.6 2.9 - - - -
282A VAL 3.2 36.1 + - - +
283A SER 4.0 7.7 + - - -
285A ILE* 4.0 20.2 - - - +
315A ASN* 2.9 17.2 + - - +
317A GLN* 1.3 82.1 - - + +
319A ASP* 1.3 62.1 + - - +
322B ASP* 3.2 54.4 + - - +
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Residues in contact with ASP 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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280A PRO 4.9 0.4 - - - -
281A GLY* 3.8 5.8 - - - +
314A PHE* 3.6 7.1 - - - -
315A ASN 3.5 2.6 + - - +
316A PRO* 3.2 25.1 + - + +
317A GLN 3.5 2.1 - - - +
318A ARG* 1.3 81.7 - - - +
320A THR* 1.3 77.7 + - - +
321A VAL* 5.6 0.5 - - - +
323A GLY* 3.2 19.6 - - - -
324A MET* 3.6 1.7 + - - -
325A THR* 2.6 41.2 + - - -
326A ALA* 3.1 20.4 + - - +
321B VAL* 6.1 0.7 - - - +
322B ASP* 5.1 1.0 - - - +
321D VAL* 5.9 3.1 - - - +
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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