Contacts of the helix formed by residues 315 - 320 (chain A) in PDB entry 2W8D
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 315 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A GLN 5.1 0.4 - - - -
295A GLY* 4.0 11.6 - - - -
298A SER* 4.1 3.1 + - - -
299A ASP* 4.6 0.4 + - - -
311A LEU* 3.9 2.9 - - - -
314A GLY* 1.3 73.7 - - - -
316A VAL* 1.3 58.5 + - - +
317A PHE* 3.3 9.7 + - - +
318A VAL* 3.1 34.1 + - - +
319A ASN* 3.0 37.2 + - - +
350A TRP* 3.8 22.2 - - - -
478B ASN* 3.9 7.6 + - - -
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Residues in contact with VAL 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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299A ASP* 3.8 17.9 + - - +
302A PHE* 3.7 59.0 - - + -
310A PRO* 3.9 8.5 - - + -
311A LEU* 3.9 26.6 - - + +
314A GLY 4.0 0.8 + - - -
315A SER* 1.3 70.2 + - - +
317A PHE* 1.3 65.7 + - + +
319A ASN 4.5 0.2 - - - +
320A LYS* 2.9 48.6 + - + -
355A MSE 3.3 4.6 - - + +
609A ILE* 5.0 5.8 - - + -
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Residues in contact with PHE 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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298A SER* 3.2 41.7 + - - +
301A GLU* 4.0 14.8 - - + -
302A PHE* 3.8 22.9 - + + -
315A SER* 3.3 8.0 + - - +
316A VAL* 1.3 84.8 - - + +
318A VAL* 1.3 58.0 + - - +
321A ALA* 3.6 12.3 - - - +
350A TRP 3.3 24.2 - - - +
351A ASN* 3.0 20.1 + - - +
352A ARG* 3.9 15.0 - - + -
355A MSE 3.5 42.7 - - + +
356A TYR* 3.7 30.3 - + - -
359A GLU* 4.2 6.7 - - - -
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Residues in contact with VAL 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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315A SER* 3.1 28.0 + - - +
317A PHE* 1.3 76.4 - - - +
319A ASN* 1.3 74.4 + - - +
320A LYS 3.7 0.2 - - - -
321A ALA* 4.8 1.4 + - - +
350A TRP* 4.2 17.5 - - + +
351A ASN* 3.7 27.6 + - + +
354A GLU* 5.0 1.4 - - - +
477B GLU 4.5 4.0 - - - +
478B ASN* 3.7 37.9 - - + +
480B ASN* 5.7 2.9 - - + +
481B LYS* 5.9 5.3 - - + +
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Residues in contact with ASN 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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311A LEU* 4.2 16.9 - - + +
314A GLY* 4.7 4.4 - - - -
315A SER 3.0 31.3 + - - +
318A VAL* 1.3 94.6 - - - +
320A LYS* 1.3 70.5 + - + +
321A ALA 3.6 1.5 + - - -
322A GLN 5.3 0.5 + - - -
477B GLU 5.4 3.3 + - - +
480B ASN* 5.8 1.9 + - - -
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Residues in contact with LYS 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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302A PHE* 5.9 0.4 - - + -
311A LEU* 4.1 28.5 - - + -
316A VAL* 2.9 35.4 + - + +
319A ASN* 1.3 85.3 + - - +
321A ALA* 1.3 57.4 + - - +
322A GLN 3.1 6.3 - - - +
323A ASN* 3.0 48.1 + - - +
325A LEU* 5.3 0.5 - - - +
355A MSE 3.7 10.6 - - + +
609A ILE* 4.1 22.6 + - + +
610A ASN* 4.7 13.0 + - - +
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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