Contacts of the helix formed by residues 280 - 293 (chain A) in PDB entry 4QA7
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 THR 280 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237A ASP* 2.2 39.3 + - - +
269A ILE* 3.7 7.1 - - - +
278A ASN 4.9 0.4 - - - +
279A MET* 1.3 79.0 - - - +
281A PRO* 1.3 75.3 - - - +
282A VAL* 3.0 19.6 + - - +
283A GLY 3.1 10.7 + - - -
284A ILE* 3.6 7.6 + - - +
348A ILE* 3.4 26.5 - - + +
349A THR 4.8 0.2 - - - -
350A PRO* 3.8 26.2 - - + -
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Residues in contact with PRO 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ILE* 3.8 4.5 - - + -
280A THR* 1.3 86.3 - - - +
282A VAL* 1.3 57.8 + - + +
284A ILE* 3.5 3.9 + - + +
285A GLY 2.9 23.9 + - - -
313A ARG* 4.7 2.2 - - + -
314A CYS* 3.6 46.7 - - + +
317A TYR* 3.3 31.2 - - + -
318A LEU* 3.9 1.4 - - - +
346A LEU 5.4 2.5 - - - +
347A GLU* 6.4 0.2 - - - -
348A ILE* 3.9 33.2 - - + +
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Residues in contact with VAL 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ASP* 4.4 3.1 - - + +
280A THR* 3.0 13.4 + - - +
281A PRO* 1.3 79.2 - - + +
283A GLY* 1.3 65.0 + - - +
285A GLY* 3.1 2.9 + - - -
286A LYS* 3.1 32.5 + - + +
317A TYR* 3.8 29.6 + - + +
347A GLU* 6.2 4.0 - - + -
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Residues in contact with GLY 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ASP* 3.4 35.4 + - - -
240A TYR* 5.1 0.3 - - - -
241A TYR* 4.7 3.1 - - - +
279A MET* 4.2 8.1 - - - -
280A THR 3.1 4.9 + - - -
282A VAL* 1.3 79.2 - - - +
284A ILE* 1.3 61.1 + - - +
286A LYS* 3.4 19.0 + - - +
287A CYS* 3.4 17.2 + - - -
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Residues in contact with ILE 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LEU* 4.7 10.5 - - + +
240A TYR* 4.2 19.1 - - + +
264A LEU* 3.8 31.0 - - + +
268A THR* 4.1 14.8 - - - +
269A ILE* 4.1 16.6 - - + -
279A MET* 3.8 18.6 - - + -
280A THR 3.6 12.0 + - - +
281A PRO* 3.5 7.5 + - + +
282A VAL 3.3 0.2 - - - -
283A GLY* 1.3 73.8 - - - +
285A GLY* 1.3 58.3 + - - +
287A CYS* 3.1 7.6 + - - +
288A LEU* 2.9 25.3 + - - +
314A CYS* 4.8 2.9 - - - -
318A LEU* 3.9 20.2 - - + -
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Residues in contact with GLY 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A PRO 2.9 16.1 + - - -
282A VAL 3.1 4.9 + - - -
284A ILE* 1.3 77.6 - - - +
286A LYS* 1.3 55.8 + - - +
288A LEU* 3.2 5.6 + - - +
289A LYS* 2.8 38.8 + - - +
317A TYR* 4.4 8.5 - - - -
318A LEU* 3.6 15.7 - - - +
321A VAL* 4.2 5.3 - - - +
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Residues in contact with LYS 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ASP* 4.9 5.4 + - - -
238A GLU* 5.1 9.7 + - - +
241A TYR* 3.2 61.9 + - + +
282A VAL* 3.1 22.9 + - + +
283A GLY* 3.7 11.2 - - - +
284A ILE 3.2 0.4 - - - -
285A GLY* 1.3 73.6 - - - +
287A CYS* 1.3 64.8 + - - +
289A LYS* 3.4 16.8 + - + +
290A TYR 3.1 17.8 + - - -
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Residues in contact with CYS 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LEU* 3.8 19.7 - - + -
240A TYR* 3.9 23.8 - - - -
241A TYR* 4.0 14.6 - - - -
244A CYS* 3.7 32.1 - - - -
248A LEU* 4.9 1.2 - - + +
283A GLY 3.4 15.9 - - - -
284A ILE* 3.1 9.7 + - - +
286A LYS* 1.3 73.3 - - - +
288A LEU* 1.3 65.9 + - - +
290A TYR* 3.4 4.5 + - - +
291A ILE* 3.2 29.0 + - + +
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Residues in contact with LEU 288 (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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177A LEU* 5.6 0.4 - - - +
262A LEU* 3.8 30.1 - - + -
264A LEU* 4.2 11.0 - - + +
284A ILE 2.9 11.9 + - - +
285A GLY 3.3 10.1 - - - +
287A CYS* 1.3 76.5 - - - +
289A LYS* 1.3 56.8 + - - +
291A ILE* 3.1 3.6 + - + +
292A LEU* 2.8 56.2 + - + +
300A ILE* 4.1 10.1 - - + -
318A LEU* 3.7 45.1 - - + +
321A VAL* 4.3 9.0 - - + -
322A ILE* 3.8 13.2 - - + -
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Residues in contact with LYS 289 (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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285A GLY 2.8 20.8 + - - +
286A LYS* 3.7 16.4 - - + +
287A CYS 3.3 0.2 - - - -
288A LEU* 1.3 76.0 - - - +
290A TYR* 1.3 63.3 + - - +
292A LEU* 3.3 10.4 + - + +
293A GLN* 3.1 26.8 + - - +
317A TYR* 5.1 7.4 + - - -
321A VAL* 3.7 33.4 - - + +
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Residues in contact with TYR 290 (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 TYR* 3.6 24.0 + + + +
245A GLU* 3.6 31.0 - - + -
248A LEU* 4.0 24.7 - - + -
249A LYS* 3.3 37.3 - - + +
286A LYS 3.1 17.2 + - - +
287A CYS* 3.6 5.4 - - - +
289A LYS* 1.3 75.5 - - - +
291A ILE* 1.3 60.1 + - - +
293A GLN* 2.8 45.1 + - + +
294A TRP* 3.7 33.7 + + - -
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Residues in contact with ILE 291 (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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175A VAL* 4.2 14.6 - - + -
177A LEU* 5.6 2.2 - - + -
248A LEU* 3.8 26.2 - - + -
260A VAL* 4.0 20.4 - - + +
262A LEU* 3.7 37.5 - - + -
287A CYS* 3.3 13.7 - - + +
288A LEU* 3.1 7.9 + - - +
290A TYR* 1.3 77.4 - - - +
292A LEU* 1.3 64.3 + - + +
294A TRP* 3.1 44.0 + - + +
295A GLN 4.4 0.2 + - - -
296A LEU* 5.3 0.9 + - - +
298A THR* 4.6 17.6 + - + +
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Residues in contact with LEU 292 (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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133A VAL* 4.1 27.4 - - + -
288A LEU* 2.8 43.7 + - + +
289A LYS* 3.3 7.4 + - + +
291A ILE* 1.3 78.5 - - + +
293A GLN* 1.3 56.0 + - - +
294A TRP 3.0 0.2 - - - -
295A GLN* 3.0 26.3 + - - +
296A LEU 4.8 0.5 + - - -
298A THR* 4.6 17.5 - - + +
300A ILE* 5.1 0.4 - - + -
321A VAL* 4.7 9.9 - - + +
322A ILE* 4.0 33.0 - - + +
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Residues in contact with GLN 293 (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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289A LYS 3.1 14.6 + - - +
290A TYR* 2.8 48.1 + - + +
292A LEU* 1.3 72.0 - - - +
294A TRP* 1.3 76.7 + - - +
295A GLN* 3.1 19.3 + - - +
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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