Contacts of the helix formed by residues 240 - 250 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A PRO 4.0 0.9 + - - +
239A GLY* 1.3 69.3 - - - -
241A LYS* 1.3 66.4 + - - +
242A GLN* 3.5 13.5 + - - +
243A GLN* 2.7 55.1 + - + +
244A PHE* 3.1 21.8 + - - +
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Residues in contact with LYS 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A GLY 3.1 4.0 + - - -
240A ASP* 1.3 73.7 + - - +
242A GLN* 1.3 64.6 + - - +
244A PHE* 3.2 3.1 + - - +
245A VAL* 3.0 35.9 + - + +
255A TYR* 5.5 3.5 + - - -
259A LEU* 3.6 37.7 - - - +
262A TYR* 3.5 43.9 + - + +
263A GLU* 5.1 3.0 + - - +
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Residues in contact with GLN 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A ASP* 3.4 13.2 + - - +
241A LYS* 1.3 81.0 - - - +
243A GLN* 1.3 65.1 + - + +
245A VAL* 3.3 5.3 + - - +
246A GLU* 3.0 53.0 + - + +
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Residues in contact with GLN 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A ASP* 2.7 41.7 + - + +
241A LYS 3.4 0.2 - - - -
242A GLN* 1.3 72.0 - - + +
244A PHE* 1.3 57.1 + - - +
246A GLU* 3.8 12.2 - - - +
247A ARG* 2.9 56.8 + - - +
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Residues in contact with PHE 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A PRO* 3.8 24.9 - - + +
240A ASP 3.1 14.1 + - - +
241A LYS 3.4 8.5 - - - +
243A GLN* 1.3 78.8 - - - +
245A VAL* 1.3 66.8 + - - +
247A ARG* 3.5 19.1 + - - +
248A LEU* 3.0 43.0 + - + +
258A ALA 3.9 3.1 - - - -
261A GLN* 3.6 18.2 - - + -
262A TYR* 3.4 42.6 - + + -
265A GLU* 3.2 40.4 - - + -
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Residues in contact with VAL 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A LYS* 3.0 30.9 + - + +
242A GLN* 3.8 5.2 - - - +
244A PHE* 1.3 80.2 - - + +
246A GLU* 1.3 66.0 + - + +
248A LEU* 3.2 2.4 + - - +
249A ILE* 2.9 41.6 + - + +
255A TYR* 3.8 27.1 - - + +
258A ALA* 3.6 32.3 - - + +
259A LEU* 4.7 12.3 - - + -
262A TYR* 4.7 2.2 - - + -
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Residues in contact with GLU 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A GLN* 3.0 44.3 + - + +
243A GLN* 3.8 12.4 - - - +
245A VAL* 1.3 75.7 - - + +
247A ARG* 1.3 66.0 + - - +
249A ILE* 3.0 12.6 + - + +
250A ALA* 2.9 24.1 + - - +
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Residues in contact with ARG 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A PRO 5.4 2.4 + - - -
243A GLN* 2.9 55.3 + - - +
244A PHE* 3.5 29.2 + - - +
246A GLU* 1.3 77.5 - - - +
248A LEU* 1.3 65.3 + - + +
250A ALA* 3.5 12.0 + - - +
251A ARG* 3.4 29.9 - - - +
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Residues in contact with LEU 248 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A LEU* 4.4 9.4 - - + -
244A PHE* 3.0 37.6 + - + +
245A VAL 3.6 3.4 - - - +
247A ARG* 1.3 79.2 - - + +
249A ILE* 1.3 59.5 + - - +
250A ALA 3.1 0.2 - - - -
251A ARG* 2.7 53.3 + - - +
252A GLY 3.5 3.6 + - - -
253A LEU* 3.5 37.6 + - + +
258A ALA* 3.9 12.8 - - + -
261A GLN* 3.5 37.0 - - + -
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Residues in contact with ILE 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A VAL* 2.9 38.7 + - + +
246A GLU* 3.5 12.1 - - + +
248A LEU* 1.3 76.2 - - - +
250A ALA* 1.3 59.5 + - - +
251A ARG 3.0 4.5 + - - -
252A GLY* 3.1 12.1 + - - -
253A LEU 3.3 17.6 - - - +
254A THR* 3.9 17.9 - - - +
255A TYR* 4.1 21.8 - - + +
258A ALA* 4.2 0.7 - - + -
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Residues in contact with ALA 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ARG* 4.6 9.0 + - - -
246A GLU 2.9 12.0 + - - +
247A ARG* 3.6 13.5 - - + +
248A LEU 3.1 0.2 - - - -
249A ILE* 1.3 75.9 - - - +
251A ARG* 1.3 61.6 + - + +
252A 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