Contacts of the strand formed by residues 247 - 257 (chain J) in PDB entry 6G2T
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 247 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233C SER* 6.1 3.1 - - - -
156J LEU* 4.7 0.2 - - - -
240J GLU* 5.1 12.3 - - - +
241J VAL 4.1 2.2 - - - -
242J SER* 3.5 26.0 - - - -
243J THR 4.2 8.5 - - - -
244J LYS 6.0 0.2 - - - -
245J ASP 6.2 0.4 - - - -
246J LYS* 1.3 87.9 - - - +
248J ASP* 1.3 63.8 + - - +
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Residues in contact with ASP 248 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155J GLY* 3.4 11.3 - - - -
156J LEU* 2.8 46.0 + - + -
157J PHE* 4.3 10.3 + - + -
240J GLU* 3.5 6.3 - - - +
241J VAL* 3.0 31.9 + - - -
246J LYS* 5.9 0.2 - - + -
247J PHE* 1.3 76.9 - - - +
249J CYS* 1.3 89.6 + - - +
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Residues in contact with CYS 249 (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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157J PHE* 3.9 5.9 - - - -
160J ARG* 5.6 2.4 + - - -
238J ARG* 3.5 41.1 - - + +
239J CYS 3.0 15.5 - - - +
240J GLU* 4.1 11.4 - - + -
248J ASP* 1.3 92.7 + - - +
250J SER* 1.3 63.6 + - - +
251J ASN* 5.4 2.7 - - - -
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Residues in contact with SER 250 (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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157J PHE* 3.5 21.5 - - - -
160J ARG* 3.9 27.9 + - - +
161J PRO* 3.7 25.3 + - - +
237J TYR 4.1 0.2 - - - +
238J ARG* 3.5 1.9 - - - +
239J CYS* 3.0 29.9 + - - +
249J CYS* 1.3 76.8 - - - +
251J ASN* 1.3 77.2 + - - +
252J PHE* 4.2 2.0 + - - -
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Residues in contact with ASN 251 (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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160J ARG* 5.6 3.2 + - - +
161J PRO 5.0 1.7 - - - +
163J ASP* 4.8 0.9 - - - +
236J SER* 6.3 2.7 - - - -
237J TYR 3.8 3.1 - - - +
238J ARG* 3.4 31.1 + - - +
249J CYS* 5.4 2.2 - - - -
250J SER* 1.3 87.3 + - - +
252J PHE* 1.3 62.5 + - - +
253J ASN* 5.7 1.1 - - - +
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Residues in contact with PHE 252 (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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161J PRO* 3.4 36.1 - - + +
162J GLN 4.3 9.2 - - - -
163J ASP* 3.4 12.6 - - - +
174J PHE* 3.5 34.8 - + - -
191J TRP* 3.5 37.9 - + - -
224J LEU* 4.2 3.1 - - + -
236J SER* 3.7 0.9 - - - -
237J TYR* 2.8 74.1 + + + +
239J CYS* 4.0 10.1 - - + -
250J SER 4.5 2.9 - - - -
251J ASN* 1.3 76.9 - - - +
253J ASN* 1.3 70.6 + - - +
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Residues in contact with ASN 253 (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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163J ASP* 2.8 27.3 + - - +
164J GLY 3.6 22.9 + - - +
174J PHE* 4.8 0.5 - - - -
235J GLY 3.6 6.6 - - - +
236J SER* 3.3 27.2 + - - -
251J ASN* 6.0 0.5 - - - +
252J PHE* 1.3 80.2 - - - +
254J LEU* 1.3 61.8 + - - +
255J THR* 4.0 6.6 + - - +
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Residues in contact with LEU 254 (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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164J GLY 3.8 4.3 - - - +
166J VAL* 3.7 30.3 - - + -
172J ILE* 4.0 3.6 - - + -
174J PHE* 3.7 25.4 - - + -
226J ILE* 3.4 34.5 - - + -
233J PHE* 4.0 15.0 - - + +
234J THR* 3.2 4.9 - - - -
235J GLY 3.0 32.2 + - - +
237J TYR* 3.5 32.0 - - + +
252J PHE* 4.3 1.0 + - - -
253J ASN* 1.3 73.2 - - - +
255J THR* 1.3 67.3 + - - +
256J VAL* 4.8 6.1 - - + -
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Residues in contact with THR 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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164J GLY 3.6 9.8 + - - +
165J GLU* 3.8 5.6 - - - -
166J VAL* 3.1 24.1 + - - +
234J THR* 4.0 18.3 - - + +
253J ASN* 4.0 7.3 + - - +
254J LEU* 1.3 79.1 + - - +
256J VAL* 1.3 67.8 + - - +
257J HIS* 3.4 37.2 + - + +
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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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166J VAL* 3.1 29.8 - - + +
167J THR 5.3 1.1 - - - +
168J VAL* 5.3 4.9 - - + -
229J ALA* 3.9 21.1 - - + -
230J GLN 3.1 26.7 - - - +
231J PRO* 3.6 14.1 - - + +
233J PHE* 4.8 4.5 - - + -
234J THR* 3.1 28.3 + - - +
254J LEU* 4.3 10.1 - - + -
255J THR* 1.3 78.6 - - - +
257J HIS* 1.3 65.5 + - - +
258J GLU* 4.9 1.9 - - - +
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Residues in contact with HIS 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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165J GLU* 3.7 38.1 + - + +
166J VAL 3.2 9.7 + - - +
167J THR* 4.3 4.3 - - + -
168J VAL* 3.4 19.2 + - - +
255J THR* 3.4 28.3 - - + +
256J VAL* 1.3 76.4 + - - +
258J GLU* 1.3 82.8 + - + +
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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