Contacts of the helix formed by residues 251 - 262 (chain E) 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 ASN 251 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195E ARG* 4.1 9.2 + - - +
226E MET* 4.6 11.3 - - - +
229E ALA* 3.5 33.9 - - + +
232E SER* 5.2 2.0 + - - +
235E LEU* 4.7 3.7 - - - +
250E GLY* 1.3 70.9 - - - -
252E GLU* 1.3 80.3 + - - +
253E ARG 3.3 0.4 - - - -
254E PHE* 3.3 35.9 + - + -
255E ARG* 3.6 35.3 + - - +
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Residues in contact with GLU 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188E LEU* 5.1 3.0 - - + +
191E ILE* 3.1 32.8 - - + +
192E LEU* 3.0 48.0 + - + +
194E GLU* 4.6 4.8 - - - +
195E ARG* 2.9 44.1 + - - +
249E ILE* 4.3 10.6 - - + +
250E GLY 4.6 2.7 - - - +
251E ASN* 1.3 86.1 + - - +
253E ARG* 1.3 63.9 + - - +
255E ARG* 3.3 25.2 + - - +
256E CYS* 3.7 7.8 + - - +
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Residues in contact with ARG 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188E LEU* 5.5 3.6 - - - -
215E LEU* 3.8 23.1 + - - +
216E CYS* 3.6 23.2 - - - +
217E TYR* 3.4 29.9 - - + -
234E SER 4.2 3.8 + - - -
235E LEU* 3.1 22.0 + - - +
237E LYS* 3.0 65.2 - - - +
249E ILE* 3.5 37.7 - - + +
250E GLY 3.2 12.8 + - - +
252E GLU* 1.3 80.7 - - - +
254E PHE* 1.3 72.4 + - + +
256E CYS* 3.6 1.7 + - - +
257E PRO* 3.0 22.9 - - - +
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Residues in contact with PHE 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217E TYR* 3.5 34.2 - - + +
218E VAL* 5.0 0.2 - - - -
219E ALA* 3.7 24.5 + - + +
222E PHE* 3.9 35.9 - + - -
225E GLU* 3.8 17.0 - - + -
226E MET* 3.5 30.3 - - + -
235E LEU* 4.2 21.1 - - + -
250E GLY 4.5 1.6 - - - -
251E ASN* 3.3 42.4 - - + -
253E ARG* 1.3 81.1 - - + +
255E ARG* 1.3 63.2 + - + +
256E CYS 3.3 0.2 - - - -
257E PRO* 3.0 18.0 - - - +
258E GLU* 3.4 9.4 + - - +
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Residues in contact with ARG 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E TYR* 4.1 21.4 + - + +
191E ILE* 3.8 14.8 - - + +
194E GLU* 2.6 36.2 + - - -
222E PHE* 3.4 27.5 - - + -
226E MET* 5.0 12.3 - - - -
251E ASN* 3.6 32.2 + - - +
252E GLU* 3.3 24.9 - - - +
254E PHE* 1.3 80.9 - - + +
256E CYS* 1.3 67.2 + - - +
258E GLU* 3.0 20.3 + - - +
259E ALA* 3.2 5.4 + - - +
265E PHE* 4.7 4.0 - - + -
112F LYS* 5.1 5.9 - - - +
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Residues in contact with CYS 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184E LEU* 3.2 55.8 - - - +
187E TYR* 3.8 14.5 - - + -
188E LEU* 3.3 40.2 - - + -
191E ILE* 5.5 0.4 - - + -
212E LYS* 5.0 5.8 - - - -
216E CYS* 4.7 3.1 - - - -
252E GLU 3.7 6.3 + - - +
253E ARG 3.6 7.3 + - - +
255E ARG* 1.3 80.6 - - - +
257E PRO* 1.4 68.2 - - + +
259E ALA* 3.2 8.3 + - - +
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Residues in contact with PRO 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184E LEU* 4.6 11.9 - - + -
212E LYS* 6.3 0.4 - - + -
216E CYS* 4.5 6.1 - - + -
217E TYR 3.1 25.8 - - - +
218E VAL* 3.7 22.0 - - + -
253E ARG 3.0 20.6 - - - +
254E PHE 3.0 16.6 - - - +
256E CYS* 1.4 88.5 - - + +
258E GLU* 1.3 61.1 + - - +
260E LEU* 3.2 25.0 + - - +
261E PHE* 3.7 7.8 - - - -
305E TYR* 4.0 19.1 - - + -
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Residues in contact with GLU 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E VAL* 4.8 3.9 - - - +
219E ALA* 4.9 3.8 + - - +
222E PHE* 3.2 35.1 - - + +
254E PHE 3.4 13.1 + - - +
255E ARG* 3.0 19.0 + - - +
257E PRO* 1.3 78.1 - - - +
259E ALA* 1.3 54.1 + - - +
261E PHE* 2.7 34.6 + - - +
262E GLN* 2.8 26.2 + - + +
265E PHE* 4.1 11.9 - - + -
311E ARG* 2.8 47.0 + - - -
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Residues in contact with ALA 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E LEU* 4.6 0.9 - - - +
184E LEU* 4.2 8.3 - - + -
187E TYR* 4.7 11.0 - - + -
255E ARG 3.2 7.2 + - - +
256E CYS 3.2 13.2 + - - +
258E GLU* 1.3 78.8 - - - +
260E LEU* 1.3 61.6 + - - +
261E PHE 3.2 0.2 - - - -
262E GLN 3.0 31.6 - - - +
263E PRO* 3.2 7.8 - - - +
265E PHE* 4.3 13.0 - - + -
266E LEU* 4.2 23.9 - - + +
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Residues in contact with LEU 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154E SER* 5.9 2.2 - - - +
159E THR* 5.0 3.4 - - - +
179E LEU* 3.5 38.3 - - + +
180E ALA 4.6 6.1 - - - +
184E LEU* 3.8 38.1 - - + +
218E VAL* 6.1 0.4 - - + -
257E PRO* 3.2 17.0 + - + +
258E GLU 3.0 0.8 + - - -
259E ALA* 1.3 79.4 - - - +
261E PHE* 1.3 62.0 + - + +
262E GLN 3.7 0.2 + - - -
263E PRO* 4.1 0.2 - - - +
272E GLY* 3.3 7.8 - - - -
273E ILE* 3.1 47.2 + - + -
302E THR* 3.9 19.3 - - + +
305E TYR* 4.8 6.7 - - + -
308E ILE* 5.6 5.2 - - + -
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Residues in contact with PHE 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E VAL* 3.7 24.2 - - + -
257E PRO 3.7 16.6 - - - -
258E GLU* 2.7 27.2 + - - +
260E LEU* 1.3 82.9 - - + +
262E GLN* 1.3 64.4 + - + +
263E PRO* 3.5 8.1 - - - +
272E GLY* 3.8 4.0 + - - -
273E ILE* 3.7 20.4 - - + +
274E HIS* 3.6 26.8 - - + -
275E GLU* 4.3 1.4 - - - +
308E ILE* 4.4 7.2 - - + -
311E ARG* 3.4 34.8 - - + +
312E MET* 3.4 27.4 - - + -
315E GLU* 3.0 29.2 - - - -
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Residues in contact with GLN 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222E PHE* 6.2 1.1 - - + -
223E GLU* 5.9 0.8 + - - -
258E GLU* 2.8 31.5 + - + +
259E ALA* 3.0 15.8 - - - +
261E PHE* 1.3 86.4 + - - +
263E PRO* 1.3 60.9 - - - +
264E SER* 3.0 22.9 + - - +
265E PHE* 3.1 37.1 + - + +
274E HIS* 5.2 5.3 + - - -
275E GLU* 5.7 1.6 + - - -
311E ARG* 5.3 3.8 - - - +
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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