Contacts of the helix formed by residues 268 - 280 (chain A) in PDB entry 4IQJ
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 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A LEU* 3.9 17.8 - - + +
258A ARG* 2.8 26.7 + - - +
263A GLU* 4.6 10.3 - - - +
267A GLY* 1.3 73.0 - - - -
269A GLU* 1.3 58.9 + - - +
270A PRO* 3.5 1.1 - - - -
271A PHE* 3.2 5.1 + - - +
272A ASP* 2.8 48.2 + - - +
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Residues in contact with GLU 269 (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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206A GLY* 3.7 10.2 - - - -
207A MET* 3.4 39.4 + - + +
266A TRP 5.1 3.8 - - - +
267A GLY 3.4 0.4 - - - -
268A ASP* 1.3 77.6 - - - +
270A PRO* 1.3 70.3 - - + +
272A ASP* 4.7 3.8 - - - -
273A ASN* 3.0 44.4 + - - +
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Residues in contact with PRO 270 (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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181A ILE* 5.1 4.3 - - + -
207A MET* 3.4 35.4 - - + +
208A VAL* 4.1 2.3 - - - -
209A ALA* 3.2 31.6 + - + +
261A LEU* 4.9 5.6 - - + -
266A TRP* 4.3 21.5 - - + +
267A GLY 3.7 12.6 - - - +
268A ASP 3.6 2.2 - - - -
269A GLU* 1.3 96.5 - - + +
271A PHE* 1.3 64.1 + - + +
273A ASN 4.3 0.2 - - - -
274A THR* 2.8 24.8 + - - -
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Residues in contact with PHE 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 4.6 15.0 - - + -
6A LYS 3.9 14.4 - - - +
7A PHE* 3.8 22.7 - + + -
209A ALA* 4.8 2.5 - - + -
254A PRO* 4.1 8.5 - - + -
257A MET* 3.7 28.9 - - + -
258A ARG* 3.3 60.8 - - + +
261A LEU* 4.3 24.2 - - + -
266A TRP* 5.8 0.4 - - + -
267A GLY 4.2 3.8 - - - -
268A ASP* 3.2 6.0 + - - +
269A GLU 3.1 0.6 - - - -
270A PRO* 1.3 85.3 - - + +
272A ASP* 1.3 70.6 + - - +
274A THR* 3.4 18.3 + - - -
275A VAL* 3.5 13.3 + - - +
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Residues in contact with ASP 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 3.7 23.9 - - - +
6A LYS 5.7 0.2 - - - +
268A ASP* 2.8 31.3 + - - +
269A GLU* 4.4 3.4 - - - +
271A PHE* 1.3 74.7 - - - +
273A ASN* 1.3 67.5 + - - +
274A THR 3.4 0.2 + - - -
275A VAL* 3.4 7.6 + - - +
276A GLU* 3.1 22.0 + - - +
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Residues in contact with ASN 273 (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 PHE* 4.3 13.1 - - - -
206A GLY* 4.3 2.3 - - - -
207A MET 3.3 30.2 + - - +
208A VAL* 4.3 9.4 - - + -
269A GLU* 3.0 36.5 + - - +
270A PRO 4.5 0.4 - - - +
272A ASP* 1.3 78.1 - - - +
274A THR* 1.3 60.8 + - - +
276A GLU* 4.3 7.6 - - - +
277A ILE* 2.8 39.9 + - + +
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Residues in contact with THR 274 (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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7A PHE* 4.0 9.5 - - + -
8A ALA* 2.7 48.7 - - - +
10A LEU* 4.4 14.4 - - + +
208A VAL* 3.8 3.7 - - - +
209A ALA 3.4 20.2 + - - +
270A PRO 2.8 18.6 + - - -
271A PHE* 3.4 13.0 + - - -
272A ASP 3.2 0.2 - - - -
273A ASN* 1.3 78.6 - - - +
275A VAL* 1.3 62.1 + - - +
277A ILE* 4.2 1.6 - - - +
278A ALA* 3.2 22.9 + - - +
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Residues in contact with VAL 275 (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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6A LYS* 3.6 60.1 - - + +
7A PHE* 4.6 6.7 - - - +
8A ALA* 4.9 3.8 - - + -
39A ASP* 6.1 1.3 - - + +
271A PHE 3.6 8.3 - - - +
272A ASP* 3.4 8.2 + - - +
273A ASN 3.3 0.2 - - - -
274A THR* 1.3 76.0 - - + +
276A GLU* 1.3 58.7 + - - +
278A ALA* 3.4 6.2 + - + +
279A ARG* 3.0 28.5 + - + +
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Residues in contact with GLU 276 (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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272A ASP 3.1 16.6 + - - +
273A ASN* 3.2 10.5 + - - +
275A VAL* 1.3 75.1 - - - +
277A ILE* 1.3 64.9 + - + +
279A ARG* 3.4 33.5 + - - +
280A MET* 3.1 48.2 + - + +
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Residues in contact with ILE 277 (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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10A LEU* 4.3 22.0 - - + -
99A LEU* 4.5 6.5 - - + -
140A ILE* 4.0 23.6 - - + -
142A LEU* 4.9 1.3 - - + -
178A PHE* 3.4 43.1 - - + -
208A VAL* 3.5 25.6 - - + -
273A ASN* 2.8 24.7 + - + +
274A THR 4.2 2.7 - - - +
276A GLU* 1.3 73.7 - - + +
278A ALA* 1.3 62.4 + - - +
280A MET* 3.2 25.0 + - - +
281A CYS* 3.5 17.1 + - - -
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Residues in contact with ALA 278 (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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8A ALA* 4.3 8.5 - - + -
10A LEU* 4.4 3.3 - - + +
41A ALA* 3.7 27.1 - - + -
66A LYS* 2.7 35.2 + - - +
68A ILE* 3.7 20.8 - - + +
274A THR 3.2 17.1 + - - +
275A VAL* 3.7 5.8 - - + +
276A GLU 3.4 0.2 - - - -
277A ILE* 1.3 78.3 - - - +
279A ARG* 1.3 50.5 + - - +
280A MET 3.6 0.2 + - - -
281A CYS* 3.8 4.9 + - - +
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Residues in contact with ARG 279 (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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66A LYS* 2.8 18.3 + - - +
275A VAL* 3.0 15.3 + - + +
276A GLU* 3.5 36.2 + - - +
277A ILE 3.2 0.4 - - - -
278A ALA* 1.3 78.5 - - - +
280A MET* 1.3 57.4 + - - +
281A CYS 3.3 0.6 + - - -
282A ASP* 4.9 1.9 + - - +
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Residues in contact with MET 280 (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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101A LYS* 3.2 46.3 + - - +
140A ILE* 4.8 8.1 - - + -
178A PHE* 6.4 0.9 - - - -
276A GLU* 3.1 43.3 - - + +
277A ILE* 3.2 20.4 + - + +
279A ARG* 1.3 78.5 - - + +
281A CYS* 1.3 57.1 + - - +
282A ASP* 3.6 4.0 + - - -
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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