Contacts of the strand formed by residues 247 - 257 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156H LEU* 4.2 0.4 - - - -
240H GLU* 5.6 7.6 - - + +
241H VAL 4.2 2.0 - - - -
242H SER* 3.7 26.0 - - - -
243H THR 4.4 8.1 - - - -
245H ASP 6.3 0.2 - - - -
246H LYS* 1.3 85.8 - - - +
248H ASP* 1.3 65.6 + - - +
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Residues in contact with ASP 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155H GLY* 2.9 31.7 - - - -
156H LEU* 3.0 25.2 + - + +
157H PHE* 4.2 16.0 + - + +
240H GLU* 3.6 6.5 - - - +
241H VAL 3.1 31.7 + - - +
247H PHE* 1.3 77.9 - - - +
249H CYS* 1.3 89.5 + - - +
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Residues in contact with CYS 249 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157H PHE* 4.0 4.3 - - - -
160H ARG* 4.9 6.4 + - - -
238H ARG* 3.7 38.8 - - + +
239H CYS 3.2 11.9 - - - +
240H GLU* 4.4 11.2 - - + -
248H ASP* 1.3 93.3 + - - +
250H SER* 1.3 62.7 + - - +
251H ASN* 5.4 3.1 - - - -
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Residues in contact with SER 250 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157H PHE* 3.5 23.3 - - - -
160H ARG* 4.1 25.7 + - - +
161H PRO* 3.4 26.9 + - - +
237H TYR 4.2 0.3 - - - +
238H ARG* 3.5 1.0 - - - +
239H CYS* 2.9 32.7 + - - +
249H CYS* 1.3 75.8 - - - +
251H ASN* 1.3 75.6 + - - +
252H PHE* 4.3 1.2 + - - -
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Residues in contact with ASN 251 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160H ARG* 5.6 4.0 + - - +
161H PRO 5.3 1.4 - - - +
163H ASP* 4.6 0.7 - - - +
236H SER* 5.3 7.2 - - - +
237H TYR 3.8 3.8 - - - +
238H ARG* 3.2 37.8 + - - +
249H CYS* 5.4 2.7 - - - -
250H SER* 1.3 88.3 + - - +
252H PHE* 1.3 63.9 + - - +
253H ASN* 6.1 0.2 - - - +
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Residues in contact with PHE 252 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161H PRO* 3.5 29.2 - - + +
162H GLN 4.3 15.5 - - - +
163H ASP* 3.2 14.4 - - - +
174H PHE* 3.6 33.0 - + - -
191H TRP* 3.5 40.2 - + - -
224H LEU* 4.2 3.6 - - + -
236H SER* 3.8 0.9 + - - -
237H TYR* 2.8 74.0 + + + +
239H CYS* 4.0 7.6 - - + -
250H SER 4.6 2.9 - - - -
251H ASN* 1.3 76.8 - - - +
253H ASN* 1.3 72.4 + - - +
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Residues in contact with ASN 253 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163H ASP* 2.8 22.5 + - - +
164H GLY 3.6 23.4 + - - +
174H PHE* 4.8 0.5 - - - -
235H GLY 3.6 8.3 - - - +
236H SER* 3.3 24.0 + - - -
252H PHE* 1.3 87.9 + - - +
254H LEU* 1.3 61.5 + - - +
255H THR* 5.0 5.5 + - - +
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Residues in contact with LEU 254 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164H GLY 3.7 8.1 - - - +
166H VAL* 3.8 26.9 - - + -
172H ILE* 4.0 8.7 - - + -
174H PHE* 3.7 26.2 - - + -
226H ILE* 3.5 32.5 - - + -
229H ALA* 5.6 0.2 - - + -
233H PHE* 3.9 17.0 - - + +
234H THR* 3.4 4.0 - - - +
235H GLY 3.0 34.0 + - - +
237H TYR* 3.5 32.7 - - + +
252H PHE* 4.4 0.6 + - - -
253H ASN* 1.3 74.2 - - - +
255H THR* 1.3 69.0 + - - +
256H VAL* 4.7 1.3 - - + -
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Residues in contact with THR 255 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164H GLY 3.5 10.8 + - - -
165H GLU* 3.6 10.7 - - - +
166H VAL* 3.0 27.0 + - - +
234H THR* 4.1 11.9 - - + +
253H ASN* 4.1 5.9 + - - +
254H LEU* 1.3 78.6 + - - +
256H VAL* 1.3 68.6 + - - +
257H HIS* 3.5 32.3 + - + +
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Residues in contact with VAL 256 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166H VAL* 3.3 28.3 - - + +
167H THR 4.6 0.9 - - - -
168H VAL* 4.0 15.9 - - + -
229H ALA* 3.7 21.5 - - + +
230H GLN 3.4 16.6 - - - +
231H PRO* 3.7 20.5 - - + +
233H PHE* 4.3 7.6 - - + -
234H THR* 3.0 32.0 + - - +
254H LEU* 4.7 3.4 - - + -
255H THR* 1.3 78.4 - - - +
257H HIS* 1.3 64.3 + - - +
258H GLU* 4.1 1.9 + - - +
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Residues in contact with HIS 257 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165H GLU* 3.8 33.9 + - + -
166H VAL 3.2 11.4 + - - +
167H THR* 4.1 9.2 - - + -
168H VAL* 3.5 19.8 + - - +
255H THR* 3.5 31.9 - - + +
256H VAL* 1.3 73.0 + - - +
258H GLU* 1.3 72.8 + - - +
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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