Contacts of the helix formed by residues 240 - 250 (chain B) in PDB entry 2GH1
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 ASP 240 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238B PRO 4.0 0.9 + - - +
239B GLY* 1.3 69.8 - - - -
241B LYS* 1.3 66.4 + - - +
242B GLN* 3.5 13.9 + - - +
243B GLN* 2.7 55.4 + - + +
244B PHE* 3.1 21.7 + - - +
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Residues in contact with LYS 241 (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 GLY 3.1 4.0 + - - -
240B ASP* 1.3 73.3 + - - +
242B GLN* 1.3 64.2 + - - +
244B PHE* 3.2 3.1 + - - +
245B VAL* 3.0 36.1 + - + +
255B TYR* 5.5 3.5 + - - -
259B LEU* 3.6 37.7 - - - +
262B TYR* 3.5 43.9 + - + +
263B GLU* 5.1 3.0 + - - +
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Residues in contact with GLN 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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240B ASP* 3.4 13.2 + - - +
241B LYS* 1.3 81.2 - - - +
243B GLN* 1.3 64.9 + - + +
245B VAL* 3.3 5.3 + - - +
246B GLU* 3.0 52.8 + - + +
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Residues in contact with GLN 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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240B ASP* 2.7 42.3 + - + +
241B LYS 3.4 0.2 - - - -
242B GLN* 1.3 72.2 - - + +
244B PHE* 1.3 57.3 + - - +
246B GLU* 3.8 12.2 - - - +
247B ARG* 2.9 56.6 + - - +
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Residues in contact with PHE 244 (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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238B PRO* 3.8 25.6 - - + +
240B ASP 3.1 14.1 + - - +
241B LYS 3.4 8.5 - - - +
243B GLN* 1.3 78.4 - - - +
245B VAL* 1.3 66.8 + - - +
247B ARG* 3.5 18.9 + - - +
248B LEU* 3.0 42.0 + - + +
258B ALA 3.9 3.4 - - - -
261B GLN* 3.6 18.4 - - + -
262B TYR* 3.4 43.5 - + + -
265B GLU* 3.2 40.2 - - + -
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Residues in contact with VAL 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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241B LYS* 3.0 30.9 + - + +
242B GLN* 3.8 5.2 - - - +
244B PHE* 1.3 80.7 - - + +
246B GLU* 1.3 65.6 + - + +
248B LEU* 3.2 2.4 + - - +
249B ILE* 2.9 41.8 + - + +
255B TYR* 3.8 26.9 - - + +
258B ALA* 3.6 31.8 - - + +
259B LEU* 4.7 12.3 - - + -
262B TYR* 4.7 2.2 - - + -
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Residues in contact with GLU 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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242B GLN* 3.0 44.5 + - + +
243B GLN* 3.8 11.9 - - - +
245B VAL* 1.3 75.9 - - + +
247B ARG* 1.3 66.1 + - - +
249B ILE* 3.0 12.6 + - + +
250B ALA* 2.9 23.8 + - - +
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Residues in contact with ARG 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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238B PRO 5.4 2.4 + - - -
243B GLN* 2.9 55.3 + - - +
244B PHE* 3.5 29.6 + - - +
246B GLU* 1.3 77.7 - - - +
248B LEU* 1.3 65.5 + - + +
250B ALA* 3.5 11.7 + - - +
251B ARG* 3.4 29.5 - - - +
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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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172B LEU* 4.4 9.6 - - + -
244B PHE* 3.0 37.8 + - + +
245B VAL 3.6 3.4 - - - +
247B ARG* 1.3 78.6 - - + +
249B ILE* 1.3 59.9 + - - +
250B ALA 3.1 0.2 - - - -
251B ARG* 2.7 52.9 + - - +
252B GLY 3.5 3.6 + - - -
253B LEU* 3.5 37.4 + - + +
258B ALA* 3.9 12.8 - - + -
261B GLN* 3.5 37.2 - - + -
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Residues in contact with ILE 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 VAL* 2.9 38.9 + - + +
246B GLU* 3.5 12.1 - - + +
248B LEU* 1.3 76.0 - - - +
250B ALA* 1.3 59.5 + - - +
251B ARG 3.0 4.5 + - - -
252B GLY* 3.1 12.1 + - - -
253B LEU 3.3 17.9 - - - +
254B THR* 3.9 17.9 - - - +
255B TYR* 4.1 21.8 - - + +
258B ALA* 4.2 0.7 - - + -
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Residues in contact with ALA 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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179B ARG* 4.6 9.2 + - - -
246B GLU 2.9 11.9 + - - +
247B ARG* 3.6 13.5 - - + +
248B LEU 3.1 0.2 - - - -
249B ILE* 1.3 75.9 - - - +
251B ARG* 1.3 61.6 + - + +
252B GLY 3.4 0.4 + - - -
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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