Contacts of the strand formed by residues 247 - 257 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231B SER* 6.2 5.6 - - - -
233B SER* 6.4 1.1 - - - -
156I LEU* 4.4 0.2 - - - -
240I GLU* 4.2 17.9 - - - -
241I VAL 4.4 2.2 - - - -
242I SER* 4.6 17.9 - - - -
243I THR 4.7 8.5 - - - -
244I LYS 5.8 1.8 - - - -
245I ASP 5.5 1.6 - - - -
246I LYS* 1.3 83.3 - - - +
248I ASP* 1.3 64.2 + - - +
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Residues in contact with ASP 248 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155I GLY* 3.1 13.3 - - - -
156I LEU* 2.9 43.6 + - + +
157I PHE* 4.2 14.3 + - + +
240I GLU* 3.5 7.7 + - - +
241I VAL 3.1 32.2 + - - +
247I PHE* 1.3 76.9 - - - +
249I CYS* 1.3 90.6 + - - +
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Residues in contact with CYS 249 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157I PHE* 3.9 6.0 - - - -
160I ARG* 5.4 3.3 + - - -
238I ARG* 3.3 44.2 - - - +
239I CYS 3.1 12.6 - - - +
240I GLU* 4.2 9.4 - - + -
248I ASP* 1.3 92.8 + - - +
250I SER* 1.3 63.2 + - - +
251I ASN* 5.3 3.8 - - - -
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Residues in contact with SER 250 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157I PHE* 3.3 26.0 - - - -
160I ARG* 3.6 27.1 + - - +
161I PRO* 3.6 24.9 + - - +
237I TYR 4.1 0.2 - - - +
238I ARG* 3.5 0.9 - - - +
239I CYS* 2.9 31.3 + - - +
249I CYS* 1.3 73.7 - - - +
251I ASN* 1.3 75.4 + - - +
252I PHE* 4.5 1.4 - - - -
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Residues in contact with ASN 251 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160I ARG* 5.1 4.5 + - - +
161I PRO 5.2 1.4 - - - +
163I ASP* 4.8 0.5 - - - +
236I SER* 5.1 8.7 - - - +
237I TYR 3.7 3.4 - - - +
238I ARG* 3.3 29.4 + - - +
249I CYS* 5.3 3.7 - - - -
250I SER* 1.3 89.5 + - - +
252I PHE* 1.3 62.1 + - - +
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Residues in contact with PHE 252 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161I PRO* 3.5 35.2 - - + +
162I GLN 4.3 10.3 - - - -
163I ASP* 3.4 12.8 - - - +
174I PHE* 3.7 28.5 - + - -
191I TRP* 3.5 38.1 - + - -
224I LEU* 4.2 3.1 - - + -
236I SER* 4.0 0.5 + - - -
237I TYR* 2.8 77.6 + + + +
238I ARG 4.4 0.2 - - - -
239I CYS* 4.0 9.2 - - + -
250I SER 4.5 3.4 - - - -
251I ASN* 1.3 77.8 - - - +
253I ASN* 1.3 73.2 + - - +
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Residues in contact with ASN 253 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163I ASP* 2.8 24.6 + - - +
164I GLY 3.6 22.3 + - - +
174I PHE* 4.7 0.2 - - - -
235I GLY 3.6 7.6 - - - +
236I SER* 3.3 24.9 + - - -
251I ASN 5.5 0.2 - - - -
252I PHE* 1.3 87.8 + - - +
254I LEU* 1.3 61.3 + - - +
255I THR* 4.0 7.1 + - - +
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Residues in contact with LEU 254 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164I GLY 3.7 10.8 - - - +
166I VAL* 4.2 9.6 - - + -
172I ILE* 3.9 17.9 - - + -
174I PHE* 3.6 24.2 - - + -
226I ILE* 3.5 32.3 - - + -
229I ALA* 5.9 0.4 - - + -
233I PHE* 3.9 15.9 - - + +
234I THR* 3.3 5.5 - - - +
235I GLY 3.0 31.3 + - - +
237I TYR* 3.5 34.9 - - + +
252I PHE* 4.3 0.8 + - - -
253I ASN* 1.3 72.1 - - - +
255I THR* 1.3 65.8 + - - +
256I VAL* 4.6 7.9 - - + -
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Residues in contact with THR 255 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164I GLY 3.4 7.7 + - - +
165I GLU* 3.6 18.5 - - + +
166I VAL* 3.2 24.3 + - - +
234I THR* 4.1 13.3 - - + +
253I ASN* 4.0 7.0 + - - +
254I LEU* 1.3 76.5 + - - +
256I VAL* 1.3 69.3 + - - +
257I HIS* 3.4 34.5 + - + +
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Residues in contact with VAL 256 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166I VAL* 3.1 31.2 - - + +
167I THR 5.2 2.7 - - - -
168I VAL* 5.2 4.0 - - + -
229I ALA* 4.0 17.3 - - + -
230I GLN 3.3 24.9 - - - +
231I PRO* 3.6 15.0 - - + +
233I PHE* 4.8 3.1 - - + -
234I THR* 3.0 29.8 + - - +
254I LEU* 4.6 13.0 - - + -
255I THR* 1.3 80.3 - - - +
257I HIS* 1.3 67.4 + - - +
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Residues in contact with HIS 257 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165I GLU* 4.8 21.0 + - + -
166I VAL 3.4 9.6 + - - +
167I THR* 4.1 10.5 - - + -
168I VAL* 3.2 24.9 + - - +
255I THR* 3.4 33.7 - - + +
256I VAL* 1.3 74.4 + - - +
258I GLU* 1.3 75.3 + - + +
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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