Contacts of the helix formed by residues 255 - 260 (chain C) in PDB entry 6Q2J
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 ASP 255 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228C GLN* 5.5 1.0 - - - +
252C CYS* 4.0 10.1 + - + +
254C GLU* 1.3 77.7 - - - +
256C GLU* 1.3 61.5 + - - +
257C ASN* 3.1 18.7 + - - +
258C CYS* 2.8 39.6 + - + +
259C ILE* 2.9 41.2 + - - +
307C PHE* 5.6 0.9 - - - -
76E TYR* 4.6 18.6 + - - +
77E ARG 5.3 1.0 + - - -
122E TYR* 6.1 1.0 - - - -
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Residues in contact with GLU 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C LEU* 5.4 1.3 - - - +
224C ILE* 4.9 7.8 - - + +
225C ARG* 2.9 45.4 + - - -
228C GLN* 5.0 9.7 - - - +
255C ASP* 1.3 72.9 + - - +
257C ASN* 1.3 66.8 + - - +
258C CYS 3.1 0.2 - - - -
259C ILE* 4.8 0.4 - - - -
260C SER* 2.9 33.5 + - - -
303C LEU* 3.6 26.2 - - + +
307C PHE* 4.5 19.7 - - + -
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Residues in contact with ASN 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C ASP* 3.1 14.7 + - - +
256C GLU* 1.3 82.7 + - - +
258C CYS* 1.3 52.5 + - - +
260C SER* 4.2 7.7 - - - -
261C THR* 3.3 12.6 - - - +
303C LEU* 6.3 0.2 - - - +
77E ARG* 4.1 15.3 + - - +
136E GLU* 4.6 8.5 + - - +
137E CYS 4.6 3.2 + - - -
138E GLN* 5.2 8.9 - - - +
144E ARG* 3.4 41.1 + - - +
146E TYR* 2.7 21.1 + - - -
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Residues in contact with CYS 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C LYS* 3.8 9.2 - - - -
252C CYS* 2.0 57.7 - - + -
255C ASP* 2.8 17.4 + - + +
256C GLU 3.1 0.2 - - - -
257C ASN* 1.3 79.4 - - - +
259C ILE* 1.3 59.6 + - - +
260C SER 3.3 1.1 - - - -
261C THR* 2.9 21.2 + - - -
262C LEU* 4.0 5.5 - - - +
37E TRP* 5.0 4.3 - - - -
120E THR* 5.3 4.5 - - - -
146E TYR* 3.2 24.7 - - + +
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Residues in contact with ILE 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C TYR* 4.8 2.9 - - + +
241C GLN* 4.2 8.3 - - - +
248C VAL* 3.7 31.0 - - + -
252C CYS* 4.5 6.1 - - + -
254C GLU* 5.1 2.5 - - - -
255C ASP 2.9 31.8 + - - +
256C GLU 4.3 1.8 - - - +
258C CYS* 1.3 72.6 - - - +
260C SER* 1.3 57.3 + - - +
261C THR 3.0 10.8 + - - -
262C LEU* 3.3 18.0 + - + +
303C LEU* 4.1 9.0 - - + -
306C ILE* 3.4 36.1 - - + +
307C PHE* 3.9 26.0 - - + -
310C MET* 4.1 13.9 - - + -
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Residues in contact with SER 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C GLU 2.9 19.8 + - - -
257C ASN* 4.5 8.7 - - - -
258C CYS 3.3 0.8 - - - -
259C ILE* 1.3 75.9 - - - +
261C THR* 1.3 59.5 + - - +
262C LEU 4.9 1.6 - - - +
299C SER 5.4 3.6 + - - -
302C SER* 3.9 16.6 + - - -
303C LEU* 3.9 31.7 - - - +
306C ILE* 5.0 1.8 - - - -
34E ASP* 3.2 18.4 + - - +
175E ARG* 5.5 1.0 + - - -
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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