Contacts of the helix formed by residues 241 - 253 (chain A) in PDB entry 1XAI
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 GLY 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A ASN 3.1 2.2 + - - -
240A LEU* 1.3 77.4 - - - +
242A HIS* 1.3 60.0 + - - +
243A THR* 3.5 3.3 - - - -
244A PHE 4.6 1.6 - - - -
245A GLY* 3.4 9.1 + - - -
260A VAL* 3.8 7.6 - - - +
263A GLY* 3.2 45.2 - - - -
264A ILE* 3.9 6.7 - - - -
267A GLN* 4.5 5.6 - - - +
323A MET* 6.2 1.8 - - - +
324A VAL* 4.4 5.9 + - - +
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Residues in contact with HIS 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A GLU* 4.2 0.9 - - - -
181A LYS* 3.6 12.8 - - + -
238A LEU 3.4 17.0 - - - -
239A ASN* 3.0 31.2 + - - +
240A LEU 2.9 25.7 + - - -
241A GLY* 1.3 76.9 - - - +
243A THR* 1.3 61.3 + - - +
244A PHE 3.3 2.2 - - - -
245A GLY* 3.5 3.6 - - - +
246A HIS* 2.7 51.1 + + + +
256A HIS* 3.8 8.1 - + - -
260A VAL* 3.7 15.2 - - + +
313A ASP* 4.6 0.8 - - - +
500A CRB 3.1 21.3 + - + -
600A ZN 2.2 36.4 - - - -
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Residues in contact with THR 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ASN 4.2 2.0 + - - -
241A GLY* 3.5 0.6 - - - -
242A HIS* 1.3 80.1 - - - +
244A PHE* 1.3 60.7 + - - +
246A HIS* 4.6 1.4 - - - +
247A ALA* 4.0 6.8 + - - +
309A TYR* 5.5 1.4 - - - -
310A MET* 3.4 38.0 - - + +
313A ASP* 3.5 22.1 - - + +
315A LYS* 2.8 26.9 + - - +
321A VAL* 4.4 7.2 - - + -
322A GLN 3.4 11.5 + - - +
323A MET* 3.6 32.5 - - + +
324A VAL 4.5 1.6 + - - -
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Residues in contact with PHE 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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241A GLY 4.5 1.6 + - - -
243A THR* 1.3 77.8 - - - +
245A GLY* 1.3 66.9 + - - +
247A ALA* 3.1 6.0 + - + +
248A VAL* 3.1 35.9 + - + +
262A VAL* 4.1 10.8 - - + -
263A GLY* 4.4 7.4 - - - +
266A TYR* 3.4 64.8 - + + -
301A LEU* 4.0 18.6 - - + -
303A PHE* 5.7 2.9 - + - -
306A LEU* 3.5 34.1 - - + -
310A MET* 3.9 21.3 - - + -
323A MET* 5.6 1.3 - - + +
346A CYS* 4.0 12.3 - - + -
349A LEU* 3.7 15.5 - - + -
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Residues in contact with GLY 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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241A GLY 3.4 21.7 + - - -
242A HIS* 3.8 1.6 - - - -
243A THR 3.4 0.2 - - - -
244A PHE* 1.3 80.5 - - - +
246A HIS* 1.3 56.8 + - - +
248A VAL* 3.1 3.6 + - - -
249A GLU* 2.9 26.5 + - - +
256A HIS* 6.0 0.7 - - - -
259A ALA* 3.4 32.1 - - - +
260A VAL* 4.6 2.5 - - - -
263A GLY* 4.0 1.9 - - - -
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Residues in contact with HIS 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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145A LYS* 3.7 20.7 + - + +
146A ASN* 4.4 1.3 - - - -
239A ASN* 4.8 1.2 + - - -
242A HIS* 2.7 36.8 + + + +
243A THR 4.6 2.0 - - - +
245A GLY* 1.3 72.3 - - - +
247A ALA* 1.3 56.1 + - - +
249A GLU* 3.2 23.6 - - - +
250A TYR* 3.0 31.0 + - - +
256A HIS* 3.5 22.1 - + - -
309A TYR* 3.5 19.5 + - + +
313A ASP* 5.4 6.1 + - - +
314A LYS* 5.2 2.4 + - - -
500A CRB 3.1 47.6 + - + -
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Residues in contact with ALA 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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243A THR 4.0 3.4 + - - +
244A PHE* 3.1 12.2 + - + +
245A GLY 3.1 0.2 - - - -
246A HIS* 1.3 80.2 - - - +
248A VAL* 1.3 57.3 + - + +
250A TYR* 4.4 0.3 - - - +
251A TYR* 3.1 32.6 + - - +
306A LEU* 3.2 25.9 - - + +
309A TYR* 3.9 17.3 - - + -
310A MET* 3.8 28.9 - - + -
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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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244A PHE* 3.1 35.6 + - + +
245A GLY* 3.1 6.5 + - - +
247A ALA* 1.3 75.1 - - - +
249A GLU* 1.3 62.0 + - - +
252A HIS* 2.8 51.1 + - + +
253A LYS 3.6 0.2 + - - -
254A ILE* 3.8 24.3 - - + +
259A ALA* 4.4 6.3 - - + +
262A VAL* 4.9 9.2 - - + -
297A MET* 4.7 3.8 - - + -
301A LEU* 4.0 24.9 - - + -
306A LEU* 4.3 9.6 - - + -
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Residues in contact with GLU 249 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A GLU* 4.7 7.2 - - + +
145A LYS* 3.0 39.7 + - + +
245A GLY 2.9 14.5 + - - +
246A HIS* 3.2 12.6 - - - +
248A VAL* 1.3 77.5 - - - +
250A TYR* 1.3 59.6 + - - +
253A LYS* 2.8 31.4 + - - +
254A ILE 3.8 18.8 - - - +
256A HIS* 3.0 40.2 + - - +
259A ALA* 3.8 13.6 - - + +
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Residues in contact with TYR 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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140A ASN* 4.9 9.9 - - + -
141A SER 2.9 26.9 + - - -
142A LYS* 3.3 24.8 + - - -
143A GLN 4.3 0.9 - - - -
144A GLY 4.1 8.1 - - - -
145A LYS* 4.2 15.5 - - + +
246A HIS 3.0 12.5 + - - +
249A GLU* 1.3 79.1 - - - +
251A TYR* 1.3 55.5 + - + +
253A LYS* 2.7 58.9 + - - +
309A TYR* 3.2 42.4 - + + +
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Residues in contact with TYR 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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247A ALA 3.1 18.4 + - - +
250A TYR* 1.3 83.4 - - + +
252A HIS* 1.3 92.3 + + - +
253A LYS* 3.4 7.9 - - - +
300A ASP 5.3 0.9 - - - -
302A ASP* 4.4 13.8 + - + +
305A THR* 3.8 38.4 + - + +
306A LEU* 3.7 16.4 - - + -
309A TYR* 5.6 4.3 - - + -
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Residues in contact with HIS 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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248A VAL* 2.8 25.4 + - + +
251A TYR* 1.3 107.9 + + - +
253A LYS* 1.3 75.4 + - - +
254A ILE* 3.3 17.9 + - + +
297A MET* 3.7 29.8 - - + -
300A ASP* 3.2 29.0 + - + +
301A LEU* 3.4 26.9 - - + +
302A ASP 4.6 1.1 - - - -
306A LEU* 4.7 4.7 - - + +
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Residues in contact with LYS 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 GLU 2.8 18.9 + - - +
250A TYR* 2.7 56.7 + - + +
251A TYR* 4.3 7.8 - - - +
252A HIS* 1.3 82.6 - - - +
254A ILE* 1.3 59.5 + - - +
255A PRO* 4.9 0.3 - - - +
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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