Contacts of the helix formed by residues 238 - 251 (chain B) in PDB entry 6G1V
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 VAL 238 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A SER* 6.0 3.4 - - - +
157B ALA* 4.9 1.3 - - - +
159B HIS* 3.8 43.3 + - + +
237B SER* 1.3 74.4 - - - +
239B ALA* 1.3 62.3 + - + +
241B GLY* 3.8 0.3 - - - -
242B ARG* 2.9 31.5 + - - +
295B VAL* 3.6 17.2 - - + +
296B ILE 3.3 22.7 + - - +
297B ASP* 3.9 8.3 - - + -
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Residues in contact with ALA 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B SER* 3.2 8.0 + - - +
238B VAL* 1.3 86.8 - - + +
240B GLU* 1.3 56.6 + - - +
242B ARG* 3.3 6.8 + - - +
243B ARG* 2.9 28.3 + - - +
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Residues in contact with GLU 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B VAL* 4.0 13.7 - - + -
237B SER* 3.0 20.7 + - - +
239B ALA* 1.3 73.4 - - - +
241B GLY* 1.3 62.1 + - - +
243B ARG* 2.8 39.9 + - - -
244B ARG* 2.7 71.6 + - - +
283B PRO* 3.6 8.1 - - - +
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Residues in contact with GLY 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ALA* 3.3 26.4 + - - +
236B VAL* 3.9 14.9 - - - +
237B SER 2.8 20.6 + - - -
238B VAL 3.8 1.1 - - - -
240B GLU* 1.3 74.0 - - - +
242B ARG* 1.3 60.6 + - - +
244B ARG* 3.3 7.1 + - - +
245B ALA* 3.0 19.9 + - - +
292B PHE* 5.4 1.8 - - - -
295B VAL* 5.2 0.2 - - - -
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Residues in contact with ARG 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B ALA 3.4 12.7 + - - +
158B LEU* 3.5 25.7 - - + +
159B HIS* 2.9 31.2 + - - +
238B VAL 2.9 17.8 + - - +
239B ALA* 3.6 7.2 - - - +
241B GLY* 1.3 74.7 - - - +
243B ARG* 1.3 63.3 + - - +
245B ALA* 3.2 2.4 + - - +
246B VAL* 2.9 35.0 + - + +
259B ASP* 2.7 42.4 + - - -
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Residues in contact with ARG 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B ALA 2.9 16.3 + - - +
240B GLU* 2.8 43.2 + - - +
242B ARG* 1.3 77.8 - - - +
244B ARG* 1.3 62.9 + - - +
246B VAL* 3.4 6.2 + - - +
247B GLU* 2.9 44.0 + - + +
281B VAL 3.1 26.6 + - - -
282B LEU 5.2 0.6 + - - -
283B PRO* 3.5 23.5 - - - +
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Residues in contact with ARG 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B VAL* 3.8 28.3 - - - +
240B GLU* 2.7 48.0 + - - +
241B GLY* 3.8 6.3 - - - +
243B ARG* 1.3 78.6 - - - +
245B ALA* 1.3 57.1 + - - +
247B GLU* 3.4 1.7 + - - -
248B LEU* 2.9 27.4 + - - +
281B VAL* 3.6 40.6 - - + +
282B LEU* 3.8 6.4 - - - +
283B PRO* 3.5 23.5 - - - +
289B ARG* 5.9 5.1 - - - +
290B PHE 2.9 19.8 + - - -
291B SER* 2.9 30.4 + - - +
292B PHE* 4.0 11.2 - - + -
293B VAL* 4.8 0.2 - - - +
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Residues in contact with ALA 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B LEU* 3.5 31.6 - - + -
157B ALA 4.0 4.0 - - - +
158B LEU* 3.7 26.5 - - + -
241B GLY 3.0 16.7 + - - +
242B ARG 3.2 4.2 + - - +
244B ARG* 1.3 73.9 - - - +
246B VAL* 1.3 65.2 + - - +
248B LEU* 3.1 13.7 + - - +
249B GLY 3.1 9.2 + - - -
262B LEU* 4.0 8.7 - - + +
266B LEU* 4.5 2.3 - - - +
292B PHE* 4.3 1.5 - - + -
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Residues in contact with VAL 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B LEU* 4.5 3.8 - - + -
242B ARG* 2.9 36.2 + - + +
243B ARG* 3.8 5.6 - - - +
245B ALA* 1.3 75.7 - - - +
247B GLU* 1.3 58.3 + - - +
249B GLY* 3.1 3.8 + - - -
250B ARG* 2.9 51.0 + - - +
256B LEU* 3.8 19.4 - - + +
259B ASP* 5.9 0.2 - - - +
262B LEU* 3.9 19.3 - - + -
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Residues in contact with GLU 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B ARG* 2.9 32.6 + - + +
244B ARG* 3.8 5.8 - - - +
246B VAL* 1.3 73.5 - - - +
248B LEU* 1.3 61.3 + - - +
250B ARG* 2.5 46.6 + - - +
251B ASN* 2.8 52.4 + - - +
280B ASN 4.6 3.5 - - - +
281B VAL* 4.0 21.1 - - + -
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Residues in contact with LEU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B PHE* 5.8 0.4 - - + -
152B ALA* 4.0 18.4 - - + -
156B LEU* 4.1 11.2 - - + -
244B ARG 2.9 14.9 + - - +
245B ALA 3.1 9.1 + - - +
247B GLU* 1.3 78.1 - - - +
249B GLY* 1.3 60.5 + - - +
251B ASN* 3.4 4.4 + - - +
252B LEU* 3.4 33.8 + - + +
266B LEU* 4.3 16.4 - - + -
274B LEU* 4.2 17.7 - - + +
277B VAL* 3.7 29.8 - - + +
278B GLU* 4.3 0.9 - - - -
281B VAL* 3.7 12.5 - - + +
292B PHE* 3.8 31.6 - - + -
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Residues in contact with GLY 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B ALA 3.1 6.9 + - - -
246B VAL 3.1 7.8 + - - -
248B LEU* 1.3 74.8 - - - +
250B ARG* 1.3 62.5 + - - +
252B LEU 3.0 7.1 + - - -
254B CYS* 2.9 49.5 + - - +
256B LEU* 3.8 2.7 - - - -
262B LEU* 3.7 14.3 - - - +
266B LEU* 4.2 3.3 - - - +
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Residues in contact with ARG 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B VAL* 2.9 23.2 + - - +
247B GLU* 2.5 54.5 + - - +
249B GLY* 1.3 76.0 - - - +
251B ASN* 1.3 61.2 + - - +
252B LEU 3.1 1.2 + - - -
253B ASN* 3.3 14.8 + - - +
254B CYS 4.9 1.6 - - - +
256B LEU* 3.6 31.8 - - + +
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Residues in contact with ASN 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B GLU* 2.8 50.3 + - - +
248B LEU* 3.7 7.9 - - - +
250B ARG* 1.3 76.6 - - - +
252B LEU* 1.3 64.5 + - - +
253B ASN* 3.6 2.6 + - - +
277B VAL* 4.0 22.7 - - + +
280B ASN* 2.8 43.0 + - - +
281B VAL* 4.6 1.8 - - - +
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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