Contacts of the helix formed by residues 274 - 279 (chain B) in PDB entry 1W98
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 VAL 274 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B GLN* 3.7 18.9 - - - +
118B PHE* 4.0 16.6 - - + +
119B LEU* 4.1 12.8 - - + -
127B PRO* 4.0 33.4 - - + +
130B ARG* 3.2 52.0 - - + +
272B LEU 4.3 2.7 - - - +
273B ASP* 1.3 74.2 + - - +
275B ASP* 1.3 61.4 + - - +
276B CYS 3.2 2.0 - - - -
277B LEU* 3.4 22.8 + - + +
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Residues in contact with ASP 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLN* 4.2 18.6 - - - +
117B HIS* 5.2 6.8 + - - -
273B ASP* 2.8 15.4 + - - +
274B VAL* 1.3 74.5 - - - +
276B CYS* 1.3 62.8 + - - +
277B LEU 3.0 3.7 + - - -
278B GLU* 3.1 34.7 + - - +
279B PHE* 4.2 3.3 - - - -
315B TRP* 4.2 17.4 + - + +
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Residues in contact with CYS 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ARG* 4.4 1.6 - - - -
231B ILE* 5.1 0.2 - - - -
270B CYS 3.3 22.9 - - - +
271B VAL* 3.8 21.8 - - - -
273B ASP 3.1 16.7 + - - +
275B ASP* 1.3 76.7 - - - +
277B LEU* 1.3 75.6 + - - +
278B GLU 3.0 0.2 - - - -
279B PHE* 3.0 34.4 + - - +
281B TYR* 6.1 0.2 - - - -
284B LEU* 3.9 23.9 - - + +
315B TRP* 3.5 24.2 - - + -
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Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ARG* 4.1 19.7 - - + +
115B ASP 3.8 16.8 - - - +
116B GLN* 3.4 22.0 - - - +
118B PHE* 3.7 30.3 - - + -
130B ARG* 4.3 3.6 - - - +
155B GLN* 4.5 1.6 - - - +
159B ASP* 3.8 28.0 - - + +
274B VAL* 3.4 16.4 - - + +
275B ASP 3.0 1.0 - - - -
276B CYS* 1.3 91.5 - - - +
278B GLU* 1.3 59.6 + - - +
279B PHE 3.3 6.8 + - - +
281B TYR* 4.1 27.8 - - + +
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Residues in contact with GLU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLN* 3.5 35.9 + - + +
275B ASP* 3.1 21.7 + - - +
276B CYS 3.0 1.2 + - - -
277B LEU* 1.3 79.5 - - - +
279B PHE* 1.3 99.1 + - + +
280B PRO* 3.7 7.1 - - - +
311B ASN* 5.2 4.9 + - - -
315B TRP* 5.8 1.6 - - - -
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Residues in contact with PHE 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ASP 4.2 4.0 - - - -
276B CYS* 3.0 22.7 + - - +
277B LEU* 4.2 5.0 - - - +
278B GLU* 1.3 112.7 - - + +
280B PRO* 1.3 75.8 - - + +
281B TYR* 3.4 7.1 + - - -
283B ILE* 4.1 9.2 - - + -
284B LEU* 4.2 8.3 - - + +
308B ASP 6.2 0.2 - - - -
311B ASN* 3.8 16.6 - - + -
312B CYS* 3.5 50.0 - - + -
315B TRP* 3.7 49.1 - + + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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