Contacts of the helix formed by residues 311 - 317 (chain A) in PDB entry 1W8D
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 PHE 311 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A GLU* 1.3 109.6 - - + +
312A ASN* 1.3 59.2 + - - +
313A ASP* 3.1 7.4 - - - -
314A LEU* 3.0 54.0 + - + +
148D ASN* 5.5 3.6 - - - -
150D ILE* 4.8 20.2 - - + -
199D TYR* 3.5 23.3 - + - -
204D SER* 3.0 12.7 + - - +
205D GLY 3.7 10.5 - - - +
206D PHE* 3.4 5.7 - - + -
207D VAL* 4.0 17.9 - - + -
262D MSE 5.5 11.4 - - + -
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Residues in contact with ASN 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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305A VAL 3.1 16.8 + - - -
306A LEU* 2.9 38.9 + - + +
309A GLY* 3.0 18.6 + - - +
310A GLU 3.4 0.2 - - - -
311A PHE* 1.3 73.0 - - - +
313A ASP* 1.3 55.7 + - - +
314A LEU 3.0 6.1 - - - -
315A ARG* 3.1 38.4 + - - +
226B ALA* 3.4 20.7 - - - +
227B GLU* 4.6 1.7 + - - -
204D SER* 3.8 1.4 + - - +
205D GLY* 2.9 32.0 + - - +
206D PHE* 4.2 6.4 - - - -
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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
----------------------------------------------------------
309A GLY 4.8 0.6 + - - -
310A GLU 3.5 5.7 - - - +
311A PHE* 3.3 14.6 - - - +
312A ASN* 1.3 69.0 - - - +
314A LEU* 1.3 69.8 + - - +
315A ARG* 3.1 21.5 + - - +
316A LYS* 3.3 25.7 + - + +
317A VAL* 5.3 0.5 - - - +
260D LYS* 5.9 1.0 + - - -
265D ARG* 3.5 39.3 + - - +
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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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311A PHE* 3.0 36.8 + - + +
313A ASP* 1.3 88.7 + - - +
315A ARG* 1.3 58.2 + - - +
316A LYS 3.0 7.5 + - - -
317A VAL* 3.3 32.2 + - + +
322A TRP* 3.9 16.7 + - + -
150D ILE* 3.5 31.9 - - + -
206D PHE* 3.6 20.6 - - + -
260D LYS* 5.5 9.4 - - - +
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Residues in contact with ARG 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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264A GLY 3.4 26.3 + - - -
265A ARG* 4.1 16.4 - - - +
306A LEU* 3.8 35.8 - - - +
312A ASN* 3.1 29.7 + - - +
313A ASP* 3.1 14.8 - - - +
314A LEU* 1.3 79.1 - - - +
316A LYS* 1.3 94.0 + - + +
317A VAL 3.4 6.1 - - - +
226B ALA 5.9 0.4 - - - +
227B GLU* 6.1 1.3 - - - +
230B LYS* 5.2 16.4 + - + +
206D PHE* 3.4 19.5 - - + -
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Residues in contact with LYS 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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264A GLY* 5.3 2.8 + - - -
313A ASP* 3.3 19.7 - - - +
314A LEU 3.0 0.4 - - - -
315A ARG* 1.3 113.1 - - + +
317A VAL* 1.3 66.7 + - + +
318A THR* 3.4 9.4 + - - +
321A GLN* 4.5 2.1 + - - -
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Residues in contact with VAL 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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313A ASP 5.3 0.2 - - - +
314A LEU* 3.3 35.9 + - + +
315A ARG 3.9 6.9 - - - +
316A LYS* 1.3 79.1 - - + +
318A THR* 1.3 70.3 + - - +
321A GLN* 3.5 27.1 - - + +
322A TRP* 3.4 43.6 + - + +
325A ILE* 4.5 7.9 - - + -
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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