Contacts of the helix formed by residues 254 - 262 (chain J) in PDB entry 6K71
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 PRO 254 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144J VAL* 3.6 32.5 - - + +
145J ARG 3.3 27.8 - - - +
146J SER* 3.7 8.3 - - - +
148J PHE* 5.2 3.4 - - + -
172J ARG* 5.9 0.4 - - - +
253J SER* 1.3 82.1 - - - +
255J GLN* 1.3 61.1 + - - +
256J VAL* 3.1 4.7 - - + +
257J ALA* 3.2 29.4 + - + +
258J GLN* 3.5 5.9 + - - +
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Residues in contact with GLN 255 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172J ARG* 4.1 22.1 - - - +
177J ASN* 3.3 44.6 + - - +
179J SER 5.3 0.4 + - - -
180J VAL* 4.0 28.9 - - + +
253J SER* 2.6 12.1 + - - +
254J PRO* 1.3 73.2 - - - +
256J VAL* 1.3 56.7 + - - +
258J GLN* 3.0 11.9 + - - +
259J LEU* 2.9 26.0 + - + +
285J ASN* 4.2 5.4 - - - +
72P GLU* 3.1 38.8 + - - +
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Residues in contact with VAL 256 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135J LEU* 5.4 12.8 - - + -
148J PHE* 5.8 2.9 - - + -
180J VAL* 3.7 27.1 - - + -
181J MET* 3.7 16.4 - - + -
252J CYS* 3.8 26.2 - - + -
253J SER 3.3 6.9 + - - +
254J PRO* 4.7 1.1 - - + -
255J GLN* 1.3 74.0 - - - +
257J ALA* 1.3 57.0 + - - +
258J GLN 3.2 0.2 - - - -
259J LEU* 3.5 8.2 - - + +
260J PHE* 2.7 41.1 + - + +
272J PHE* 4.0 25.6 - - + -
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Residues in contact with ALA 257 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135J LEU* 5.5 6.1 - - + +
138J VAL* 5.6 4.9 - - + -
139J ASP* 2.9 44.5 - - + +
144J VAL* 5.5 2.7 - - + -
254J PRO* 3.2 25.6 + - + +
255J GLN 3.2 0.4 - - - -
256J VAL* 1.3 81.8 - - - +
258J GLN* 1.3 55.9 + - - +
260J PHE* 4.3 3.1 - - - -
261J THR* 3.0 22.7 + - - -
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Residues in contact with GLN 258 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254J PRO 3.5 5.3 + - - +
255J GLN* 3.0 12.6 + - - +
257J ALA* 1.3 73.7 - - - +
259J LEU* 1.3 61.2 + - + +
260J PHE 3.1 9.3 + - - -
261J THR* 5.3 0.7 - - - -
262J ASP* 3.1 38.5 + - + +
72P GLU* 2.9 36.6 + - - +
73P LEU 2.7 31.1 + - - -
74P GLU* 4.6 3.2 - - - +
351P ASP* 5.1 13.3 + - - +
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Residues in contact with LEU 259 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180J VAL* 4.7 12.3 - - + -
255J GLN 2.9 19.1 + - - +
256J VAL* 3.4 8.0 + - + -
258J GLN* 1.3 75.1 - - + +
260J PHE* 1.3 55.5 + - - +
262J ASP* 5.9 2.2 - - + +
263J ASN* 3.6 32.6 - - - +
266J TYR* 4.3 1.6 - - - -
272J PHE* 3.2 21.7 - - + -
276J LEU* 3.8 25.8 - - + -
285J ASN* 3.7 24.5 - - - +
72P GLU* 4.3 16.4 - - + +
75P ARG* 3.4 32.1 - - + +
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Residues in contact with PHE 260 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131J LEU* 4.5 7.4 - - + -
132J GLY* 3.9 9.2 - - - -
135J LEU* 3.5 48.2 - - + -
136J ARG* 3.0 42.9 + - - -
256J VAL* 2.7 18.0 + - + +
257J ALA* 3.9 4.9 - - - +
259J LEU* 1.3 77.4 - - - +
261J THR* 1.3 61.9 + - - +
262J ASP 3.5 0.2 - - - -
263J ASN 2.9 22.4 - - - +
266J TYR 4.4 4.7 - - - +
267J GLN* 3.3 31.0 - - - -
268J THR 4.8 1.1 - - - -
269J ARG* 5.5 1.6 - - - -
272J PHE* 3.5 36.3 - + + -
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Residues in contact with THR 261 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135J LEU 4.6 1.0 + - - -
136J ARG* 4.1 25.8 - - + +
139J ASP* 2.4 35.0 + - - +
257J ALA 3.0 10.7 + - - -
258J GLN* 5.3 0.7 - - - -
260J PHE* 1.3 75.9 - - - +
262J ASP* 1.3 65.7 + - - +
264J PHE* 3.2 34.5 - - + -
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Residues in contact with ASP 262 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258J GLN* 3.1 27.9 + - + +
259J LEU* 5.0 1.9 - - + +
261J THR* 1.3 78.7 - - - +
263J ASN* 1.3 67.0 + - - +
264J PHE* 3.4 13.4 + - - -
74P GLU* 3.2 43.1 - - - +
75P ARG* 3.6 16.9 + - - +
78P THR* 4.0 13.0 + - - +
405P MET* 4.3 6.8 - - - +
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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