Contacts of the helix formed by residues 246 - 254 (chain B) in PDB entry 1A7A
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 PRO 246 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392A GLU* 3.5 28.0 - - + +
395A ALA* 3.8 3.4 - - + -
396A GLU* 3.5 35.7 - - + +
399A LEU* 4.0 9.1 - - + +
406A LEU* 3.7 15.0 - - + -
425A PHE* 3.8 16.8 - - + -
244B ILE 3.8 6.0 - - - +
245B ASP* 1.3 91.1 - - - +
247B ILE* 1.3 51.5 + - - +
249B ALA* 3.1 7.4 + - + +
250B LEU* 2.6 37.6 + - - +
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Residues in contact with ILE 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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184A VAL* 3.5 27.4 - - + -
185A THR* 4.1 2.2 - - + -
189A PHE* 3.7 16.6 - - + -
388A LYS* 5.4 0.4 - - - +
391A ASP* 4.3 6.5 - - + +
392A GLU* 4.0 31.0 - - + +
395A ALA* 3.8 20.2 - - + -
432A TYR* 3.5 48.0 - - + +
245B ASP* 2.9 8.4 + - - +
246B PRO* 1.3 74.2 - - - +
248B ASN* 1.3 63.4 + - - +
250B LEU* 2.9 5.0 + - - +
251B GLN* 2.8 27.8 + - - +
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Residues in contact with ASN 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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426A LYS* 3.0 19.8 - - - +
430A TYR* 4.0 10.9 + - - -
432A TYR* 4.1 5.8 - - - -
221B TYR* 3.1 31.2 - - - +
226B LYS* 3.5 2.6 + - - -
243B GLU* 3.4 24.0 - - + +
245B ASP* 2.9 32.9 + - - +
247B ILE* 1.3 76.7 - - - +
249B ALA* 1.3 63.5 + - - +
251B GLN* 3.2 19.1 + - - +
252B ALA* 3.0 19.1 + - - +
434B NAD 3.5 12.2 + - - -
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Residues in contact with ALA 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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399A LEU* 4.4 7.9 - - + -
404A VAL* 4.5 4.4 - - + +
406A LEU* 3.7 22.2 - - + -
243B GLU* 4.0 13.6 - - + +
245B ASP 2.9 19.6 + - - +
246B PRO* 3.2 5.8 - - + +
248B ASN* 1.3 76.7 - - - +
250B LEU* 1.3 62.7 + - - +
252B ALA* 3.1 8.9 + - - +
253B ALA* 3.1 19.3 + - - +
259B VAL* 3.7 17.3 - - + +
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Residues in contact with LEU 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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189A PHE* 3.7 19.5 - - + -
360A ASN* 3.6 31.0 - - - +
395A ALA* 4.1 19.3 - - + +
398A HIS* 4.5 9.9 - - + +
399A LEU* 4.1 19.9 - - + +
402A LEU* 3.8 27.8 - - + -
404A VAL* 5.8 0.4 - - + -
246B PRO 2.6 19.8 + - - +
247B ILE 3.5 4.3 - - - +
249B ALA* 1.3 72.4 - - - +
251B GLN* 1.3 64.5 - - - +
253B ALA* 3.2 5.6 + - + +
254B MSE 2.8 41.9 + - + +
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Residues in contact with GLN 251 (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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188A LYS* 5.0 11.6 - - - +
189A PHE* 3.6 24.7 - - + -
193A TYR* 4.1 14.5 + - + +
432A TYR* 3.1 32.8 + - - +
221B TYR* 3.9 10.3 - - + -
226B LYS* 2.9 29.5 - - - +
247B ILE* 2.8 17.4 + - - +
248B ASN* 3.2 28.9 + - - +
250B LEU* 1.3 75.9 - - - +
252B ALA* 1.3 65.9 + - - +
254B MSE 2.9 5.4 + - - +
255B GLU* 2.9 25.0 + - - +
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Residues in contact with ALA 252 (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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221B TYR* 3.6 22.8 - - + -
241B ILE* 4.1 22.2 - - + -
248B ASN 3.0 12.2 + - - +
249B ALA* 3.3 9.2 - - - +
251B GLN* 1.3 74.2 - - - +
253B ALA* 1.3 55.0 + - - +
255B GLU* 2.7 24.9 + - - +
256B GLY 3.1 8.0 + - - -
257B TYR* 3.3 12.0 + - + -
259B VAL* 3.4 17.3 - - + -
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Residues in contact with ALA 253 (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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402A LEU* 4.3 18.4 - - + -
404A VAL* 3.9 28.5 - - + -
249B ALA 3.1 7.0 + - - +
250B LEU* 3.6 8.7 - - - +
252B ALA* 1.3 78.9 - - - +
254B MSE 1.3 58.6 + - - +
256B GLY* 3.0 18.7 + - - -
257B TYR 3.5 15.1 + - - +
259B VAL* 3.9 1.1 - - + +
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Residues in contact with MSE 254 (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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189A PHE* 4.2 6.3 - - + -
193A TYR* 3.2 45.8 - - + -
196A ARG* 3.1 22.5 + - - -
356A PHE* 3.2 40.8 - - + -
357A VAL* 5.0 14.1 - - + -
360A ASN* 5.1 2.5 - - - +
402A LEU* 5.0 4.3 - - - -
250B LEU* 2.8 45.6 + - + +
251B GLN 2.9 4.7 + - - +
253B ALA* 1.3 72.1 - - - +
255B GLU* 1.3 59.8 + - - +
256B GLY 3.2 0.9 + - - -
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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