Contacts of the helix formed by residues 242 - 249 (chain A) in PDB entry 2EIT
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 GLU 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A LYS* 4.2 14.5 + - - -
72A GLY* 6.4 1.3 - - - -
73A LYS* 5.7 4.4 - - - +
239A VAL* 3.0 38.2 + - + +
240A GLY 3.1 0.2 - - - -
241A GLU* 1.3 97.1 - - + +
243A VAL* 1.3 61.6 + - - +
244A GLY 3.2 0.2 - - - -
245A ALA* 3.5 0.9 + - - +
246A TYR* 3.0 29.5 + - - +
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Residues in contact with VAL 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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71A ALA* 3.8 16.4 - - + +
72A GLY* 4.0 13.4 - - - +
73A LYS* 5.6 0.9 - - - +
76A ALA* 3.6 28.9 - - + -
207A LYS* 3.8 20.2 - - + -
236A LEU* 4.1 19.7 - - + +
238A GLY* 4.0 20.2 - - - -
239A VAL 3.0 14.3 + - - +
242A GLU* 1.3 78.1 - - - +
244A GLY* 1.3 65.6 + - - +
246A TYR* 3.4 5.5 + - - +
247A LEU* 3.1 27.5 + - + +
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Residues in contact with GLY 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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178A VAL* 5.8 0.4 - - - -
180A ILE* 4.1 9.9 - - - +
207A LYS* 4.6 8.7 - - - -
239A VAL 3.6 0.4 + - - -
240A GLY* 3.0 16.9 + - - -
243A VAL* 1.3 84.2 - - - +
245A ALA* 1.3 60.8 + - - +
247A LEU* 3.2 6.1 + - - +
248A VAL* 3.0 26.7 + - - +
1518A NAD 3.6 13.5 - - - -
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Residues in contact with ALA 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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240A GLY 3.0 7.1 + - - -
241A GLU* 3.5 25.8 - - + +
242A GLU 3.5 1.5 + - - +
243A VAL 3.5 0.2 - - - -
244A GLY* 1.3 75.1 - - - +
246A TYR* 1.3 63.3 + - - +
248A VAL* 3.4 0.4 + - - -
249A GLU* 3.0 45.6 + - - +
1518A NAD 3.6 3.0 - - - +
1519A ACT 3.7 26.2 - - - +
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Residues in contact with TYR 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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73A LYS* 3.7 60.9 - - + +
76A ALA* 3.8 22.7 - - + -
77A GLU* 2.5 36.0 + - - +
242A GLU 3.0 18.3 + - - +
243A VAL* 3.5 8.3 - - - +
244A GLY 3.2 0.2 - - - -
245A ALA* 1.3 77.4 - - - +
247A LEU* 1.3 61.8 + - + +
249A GLU* 3.7 5.9 + - - +
250A HIS* 3.3 37.6 + + - +
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Residues in contact with LEU 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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76A ALA* 4.0 29.6 - - + +
80A LEU* 4.6 8.5 - - + -
178A VAL* 3.7 28.9 - - + -
205A ILE* 3.7 33.0 - - + -
207A LYS* 5.7 4.0 - - + -
236A LEU* 4.4 0.9 - - + -
243A VAL* 3.1 29.9 + - + +
244A GLY* 3.8 3.6 - - - +
246A TYR* 1.3 80.5 - - + +
248A VAL* 1.3 65.6 + - - +
250A HIS* 3.0 11.7 + - + -
253A ILE* 3.2 42.2 - - + +
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Residues in contact with VAL 248 (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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178A VAL* 4.5 0.6 - - + +
180A ILE* 3.6 23.6 - - + -
244A GLY 3.0 21.8 + - - +
245A ALA 3.8 3.6 - - - +
247A LEU* 1.3 74.9 - - - +
249A GLU* 1.3 58.2 + - - +
256A ILE* 3.8 35.4 - - + +
268A ILE* 4.1 19.1 - - + +
271A ALA* 3.8 27.4 - - + +
272A ALA 4.8 0.4 - - - +
283A LYS* 2.8 22.7 + - - +
1519A ACT 3.9 21.1 - - + +
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Residues in contact with GLU 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 ALA* 3.0 27.8 + - - +
246A TYR* 4.2 4.9 - - - +
248A VAL* 1.3 77.5 - - - +
250A HIS* 1.3 62.2 - - - +
251A PRO* 4.0 1.2 - - - +
271A ALA* 4.4 4.0 - - + -
274A ARG* 4.1 21.3 + - - +
276A ALA* 3.4 19.6 - - - +
283A LYS* 3.5 3.7 + - - +
1519A ACT 3.4 27.9 - - + +
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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