Contacts of the helix formed by residues 242 - 248 (chain B) in PDB entry 2IAG
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 SER 242 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238B TRP 3.3 17.0 + - - -
239B LYS* 3.1 20.2 + - - -
240B LEU 3.5 0.6 - - - -
241B LEU* 1.3 80.1 - - - +
243B PRO* 1.4 74.8 - - - +
244B ALA* 4.1 8.4 + - - +
245B ARG* 3.1 20.3 + - - +
246B LEU* 3.0 19.5 + - - +
270B GLU 5.5 0.2 - - - -
274B ALA* 4.0 4.3 - - - -
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Residues in contact with PRO 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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241B LEU 3.7 2.2 - - - +
242B SER* 1.4 84.2 - - - +
244B ALA* 1.3 56.8 + - - +
246B LEU* 3.2 9.9 + - + +
247B ALA* 2.9 32.7 + - - +
252B ARG* 4.2 3.0 + - - +
260B LEU* 4.6 7.9 - - + -
270B GLU* 3.5 45.1 - - + +
273B GLN* 3.8 35.0 - - + +
274B ALA 4.1 5.6 - - - +
277B LEU* 4.3 7.2 - - + -
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Residues in contact with ALA 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B SER* 3.2 7.4 - - - +
243B PRO* 1.3 79.8 - - - +
245B ARG* 1.3 61.5 + - - +
247B ALA* 3.4 17.9 - - - +
248B ARG* 3.6 25.1 + - - +
270B GLU* 4.2 11.1 + - - +
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Residues in contact with ARG 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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199B HIS* 5.6 10.6 + - + -
239B LYS* 3.7 21.2 + - - +
240B LEU* 3.4 40.5 - - - +
242B SER* 3.1 22.8 + - - +
244B ALA* 1.3 79.2 - - - +
246B LEU* 1.3 60.1 + - + +
248B ARG* 3.4 42.5 - - - +
249B ARG* 3.7 11.7 + - - +
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Residues in contact with LEU 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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177B TYR* 4.3 8.5 - - - +
181B TYR* 3.9 37.0 - - + +
240B LEU 4.6 2.0 - - - +
241B LEU* 3.6 19.5 - - + +
242B SER 3.0 16.6 + - - +
243B PRO* 3.8 3.4 - - + +
245B ARG* 1.3 75.8 - - + +
247B ALA* 1.3 64.2 + - - +
248B ARG 3.3 0.2 - - - -
249B ARG* 3.1 35.9 + - - +
252B ARG* 3.0 30.7 + - - +
256B LEU* 4.2 12.8 - - + -
260B LEU* 5.3 1.3 - - + -
277B LEU* 3.6 31.0 - - + -
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Residues in contact with ALA 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 PRO 2.9 16.4 + - - +
244B ALA* 3.4 12.3 - - - +
245B ARG 3.3 1.0 - - - -
246B LEU* 1.3 76.5 - - - +
248B ARG* 1.3 59.6 + - - +
249B ARG 3.3 5.2 + - - +
252B ARG* 3.4 17.0 + - - +
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Residues in contact with ARG 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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184B GLU 4.5 8.0 - - - +
244B ALA* 3.6 21.6 + - - +
245B ARG* 3.4 48.2 + - - +
247B ALA* 1.3 76.8 - - - +
249B ARG* 1.3 63.2 + - + +
250B ALA* 3.8 1.4 + - - +
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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