Contacts of the helix formed by residues 244 - 255 (chain A) in PDB entry 7KAC
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 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A GLU* 2.6 35.7 + - - -
243A TRP* 1.3 72.1 - - - +
245A ALA* 1.3 62.4 + - - +
246A ALA* 3.4 16.3 + - - +
247A PHE* 3.3 4.0 + - - +
248A HIS* 3.1 25.5 + - - -
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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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244A SER* 1.3 71.4 - - - +
246A ALA* 1.4 59.4 + - - +
248A HIS* 3.6 10.3 + - - +
249A ASN* 3.0 29.3 + - - +
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Residues in contact with ALA 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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244A SER* 3.2 10.4 + - - +
245A ALA* 1.4 76.7 - - - +
247A PHE* 1.4 57.6 + - - +
249A ASN* 3.3 4.3 + - - -
250A PHE* 2.9 24.4 + - - +
271A HIS* 3.4 12.5 - - - -
272A GLN* 3.5 28.8 + - + +
273A LEU* 4.0 24.7 - - + +
276A GLN* 6.5 0.4 - - - -
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Residues in contact with PHE 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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111A GLU* 3.7 27.8 - - + +
114A ILE* 3.9 20.6 - - + -
205A ALA* 3.9 28.3 - - + -
209A ALA* 4.3 3.1 - - + -
237A LEU* 3.7 19.7 - - + -
243A TRP* 3.5 48.5 - + + -
244A SER* 3.3 9.4 + - - +
246A ALA* 1.4 75.2 - - - +
248A HIS* 1.3 63.7 + - - +
250A PHE* 3.2 2.5 + + + -
251A ILE* 3.1 44.0 + - + +
273A LEU* 3.7 24.2 - - + +
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Residues in contact with HIS 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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236A ARG* 6.0 1.2 - - - +
237A LEU* 3.7 35.6 + - + +
239A GLU 3.9 5.6 - - - -
240A LYS* 2.8 44.4 + - + +
243A TRP* 3.5 12.6 + - + +
244A SER 3.1 26.2 + - - -
245A ALA* 3.9 9.6 - - - +
246A ALA 3.4 0.2 - - - -
247A PHE* 1.3 75.9 - - - +
249A ASN* 1.3 56.4 + - - +
251A ILE* 3.5 4.2 + - - +
252A LYS* 3.0 27.2 + - - +
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Residues in contact with ASN 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 19.3 + - - +
246A ALA* 3.8 5.4 - - - +
247A PHE 3.3 0.2 - - - -
248A HIS* 1.3 74.6 - - - +
250A PHE* 1.3 59.5 + - - +
252A LYS* 3.5 35.0 - - - +
253A VAL* 2.9 37.2 + - - +
271A HIS* 2.8 25.1 + - + +
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Residues in contact with PHE 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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118A CYS* 3.8 33.0 - - + -
122A LEU* 4.1 6.3 - - + -
201A LEU* 4.0 16.8 - - + -
202A GLY* 4.9 1.3 - - - -
205A ALA* 4.5 7.2 - - + -
246A ALA 2.9 17.4 + - - +
247A PHE* 3.2 5.6 + + - +
249A ASN* 1.3 75.0 - - - +
251A ILE* 1.3 69.3 + - + +
253A VAL* 3.9 0.9 - - - +
254A THR* 2.9 55.6 + - + +
268A MET* 3.5 27.4 - - + -
271A HIS* 3.5 20.4 + + + -
273A LEU* 3.6 24.7 - - + -
274A VAL* 4.1 18.4 - - + -
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Residues in contact with ILE 251 (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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202A GLY* 3.8 11.4 - - - +
205A ALA* 3.6 20.6 - - + -
206A ILE* 3.9 17.7 - - + -
235A PRO 4.1 8.5 - - - +
236A ARG* 4.5 8.3 - - + -
237A LEU* 4.0 17.3 - - + +
247A PHE* 3.1 40.4 + - + +
248A HIS* 3.7 7.6 - - - +
250A PHE* 1.3 79.1 - - + +
252A LYS* 1.3 62.3 + - - +
254A THR* 3.2 4.4 + - - -
255A LEU* 2.9 50.4 + - + +
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Residues in contact with LYS 252 (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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235A PRO 6.0 0.7 - - - -
248A HIS 3.0 17.8 + - - +
249A ASN* 3.5 29.6 - - - +
251A ILE* 1.3 79.4 - - - +
253A VAL* 1.3 73.6 + - - +
255A LEU* 3.6 17.5 - - - +
256A THR* 3.6 5.2 + - - -
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Residues in contact with VAL 253 (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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249A ASN* 2.9 34.8 + - - +
250A PHE* 4.1 3.4 - - - +
252A LYS* 1.3 94.2 - - - +
254A THR* 1.3 61.5 + - - +
256A THR* 2.7 23.9 + - - +
263A PRO* 3.3 36.6 - - + +
268A MET* 3.6 14.4 - - + -
271A HIS* 4.8 5.8 - - + +
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Residues in contact with THR 254 (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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198A ILE* 3.6 29.8 - - + +
199A TRP* 3.5 9.7 + - - -
201A LEU* 5.1 2.9 - - + -
202A GLY* 3.3 20.1 - - - +
250A PHE* 2.9 40.4 + - + +
251A ILE* 3.2 6.4 + - - -
253A VAL* 1.3 75.1 - - - +
255A LEU* 1.4 60.3 + - - +
256A THR 3.3 4.3 + - - -
262A ARG* 3.4 21.8 - - - -
268A MET* 3.7 28.5 - - + -
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Residues in contact with LEU 255 (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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199A TRP* 3.3 55.7 - - + +
202A GLY* 4.0 4.7 - - - -
203A ILE* 3.7 13.5 - - + +
206A ILE* 4.0 14.6 - - + -
234A PRO* 3.2 28.4 - - + +
235A PRO* 3.5 33.0 - - + +
251A ILE* 2.9 32.1 + - + +
252A LYS* 3.6 8.0 - - - +
254A THR* 1.4 77.6 - - - +
256A THR* 1.3 62.6 + - - +
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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