Contacts of the helix formed by residues 307 - 324 (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 ASN 307 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A GLY* 3.0 30.5 + - - +
272A ASP* 3.7 12.3 + - + +
273A PRO* 3.8 2.0 - - + +
306A PHE* 1.3 75.7 - - - +
308A LEU* 1.3 59.8 + - - +
309A ALA* 3.5 8.0 + - - +
310A ASN* 3.2 41.1 + - + +
311A THR* 2.8 33.7 + - - -
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Residues in contact with LEU 308 (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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33A LYS 5.7 0.2 - - - +
34A ILE* 4.6 11.9 - - + -
35A PRO* 3.5 28.9 - - + +
36A LYS* 5.6 0.4 - - + -
37A ARG* 3.6 36.7 - - + +
40A MET* 3.6 30.7 - - + +
305A GLY 4.3 7.0 - - - +
306A PHE* 3.9 8.0 + - - +
307A ASN* 1.3 72.5 + - - +
309A ALA* 1.3 58.1 + - - +
311A THR* 3.4 5.8 + - - -
312A ALA* 2.9 28.2 + - - +
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Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A MET* 3.8 16.2 - - + +
307A ASN* 3.3 6.8 + - - +
308A LEU* 1.3 78.8 - - - +
310A ASN* 1.3 53.1 + - - +
312A ALA* 3.2 4.7 + - - +
313A ARG* 2.7 53.4 + - - +
339A ALA* 3.5 25.4 - - + +
340A TYR* 3.6 12.4 - - + -
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Residues in contact with ASN 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ALA* 5.5 0.9 - - - -
269A ILE* 4.6 8.6 - - + +
270A ALA 3.1 25.5 + - - -
271A GLY* 4.1 3.4 - - - -
307A ASN* 3.2 35.5 + - + +
309A ALA* 1.3 73.1 - - - +
311A THR* 1.3 55.7 + - - +
313A ARG* 2.8 41.1 + - - +
314A CYS* 2.7 35.3 + - - +
348A ILE* 3.5 24.0 - - + +
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Residues in contact with THR 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ARG* 4.0 19.3 - - + +
41A VAL* 4.5 0.9 - - + -
266A ALA* 3.9 16.3 + - + +
305A GLY* 3.2 25.6 - - - -
306A PHE 3.9 0.2 + - - -
307A ASN 2.8 21.7 + - - -
308A LEU 3.6 5.8 - - - -
310A ASN* 1.3 73.5 - - - +
312A ALA* 1.3 65.1 + - - +
314A CYS* 3.8 0.2 - - - +
315A TRP* 3.1 66.7 + - + +
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Residues in contact with ALA 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A MET* 3.9 25.1 - - + +
41A VAL* 4.0 14.5 - - + +
44A LEU* 3.6 4.7 - - + -
308A LEU 2.9 14.2 + - - +
309A ALA* 3.2 6.7 + - - +
311A THR* 1.3 74.1 - - - +
313A ARG* 1.3 62.9 + - - +
315A TRP 4.0 0.2 - - - -
316A THR* 2.7 32.6 + - - -
340A TYR* 3.3 25.1 - - + +
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Residues in contact with ARG 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 3.8 7.2 - - - +
281A PRO* 4.7 1.8 - - + -
309A ALA* 2.7 39.6 + - - +
310A ASN* 2.8 41.7 + - - +
312A ALA* 1.3 73.3 - - - +
314A CYS* 1.3 62.6 + - - +
317A TYR* 3.0 25.3 + - - +
339A ALA 4.9 0.2 + - - -
340A TYR* 2.8 54.6 + - + +
341A GLY 4.8 2.2 + - - -
344A TYR 4.6 0.6 - - - +
345A VAL* 2.8 27.7 + - - +
346A LEU* 3.4 36.2 - - + +
347A GLU 4.4 2.1 + - - -
348A ILE* 3.7 15.3 - - + -
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Residues in contact with CYS 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU 5.5 0.9 - - - -
266A ALA* 4.3 11.4 - - + -
269A ILE* 3.9 24.2 - - + -
281A PRO* 3.6 31.3 - - + +
284A ILE* 4.8 6.1 - - - -
310A ASN 2.7 18.4 + - - +
311A THR 3.8 4.5 - - - +
312A ALA 3.3 0.2 - - - -
313A ARG* 1.3 74.1 - - - +
315A TRP* 1.3 65.2 + - + +
317A TYR* 3.2 4.7 + - - +
318A LEU* 2.8 49.7 + - - +
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Residues in contact with TRP 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ARG* 3.4 34.1 - - - -
41A VAL* 3.8 22.9 - - + -
45A ILE* 4.8 1.3 - - - -
137A TRP* 3.2 67.7 - + + +
264A LEU 2.9 21.8 + - - -
266A ALA* 3.8 7.2 - - + +
302A GLY* 3.5 3.4 - - - -
303A GLY 3.5 25.6 - - - -
304A GLY 3.6 13.9 - - - -
311A THR* 3.1 33.0 + - + +
314A CYS* 1.3 78.2 - - + +
316A THR* 1.3 55.4 + - - +
318A LEU* 3.9 15.5 - - + -
319A THR* 2.6 36.6 + - - -
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Residues in contact with THR 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL* 3.9 2.3 + - - +
44A LEU* 3.3 31.0 - - + +
45A ILE* 3.5 24.8 - - + +
48A TYR* 3.6 34.3 - - + -
50A LEU* 3.7 10.4 - - + +
312A ALA 2.7 23.3 + - - -
313A ARG 3.9 2.0 - - - -
315A TRP* 1.3 75.2 - - - +
317A TYR* 1.3 65.8 + - - +
319A THR* 3.4 3.7 + - - -
320A GLY* 3.1 17.2 + - - -
327A LEU* 4.3 3.5 - - + +
346A LEU* 4.8 2.7 - - + -
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Residues in contact with TYR 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A PRO* 3.3 44.0 - - + -
282A VAL* 3.8 30.2 + - + +
285A GLY* 4.4 3.9 - - - -
289A LYS* 5.1 7.6 + - - -
313A ARG 3.0 17.5 + - - +
314A CYS 3.4 3.8 - - - +
316A THR* 1.3 76.1 - - - +
318A LEU* 1.3 61.0 + - + +
320A GLY* 3.0 4.3 + - - -
321A VAL* 3.0 48.1 + - + +
327A LEU* 4.2 14.9 - - + +
346A LEU* 4.5 23.0 - - + +
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Residues in contact with LEU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A TRP* 3.8 14.4 - - + -
264A LEU* 3.7 25.8 - - + +
281A PRO 3.9 8.7 - - - +
284A ILE* 3.9 12.8 - - + -
285A GLY* 3.6 35.2 - - - +
288A LEU* 3.7 13.3 - - + +
314A CYS* 2.8 37.0 + - - +
315A TRP* 3.9 13.9 - - + +
316A THR 3.3 0.2 - - - -
317A TYR* 1.3 75.3 - - + +
319A THR* 1.3 64.3 + - - +
321A VAL* 3.2 5.9 + - + +
322A ILE* 3.0 28.9 + - - +
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Residues in contact with THR 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE* 3.6 9.3 - - + +
50A LEU* 4.2 16.8 - - + -
54A MET* 3.8 37.2 - - + -
135A ILE* 4.4 6.5 - - + -
137A TRP* 2.8 23.8 + - - +
315A TRP 2.6 23.1 + - - -
316A THR* 3.5 7.6 - - - -
317A TYR 3.2 0.4 - - - -
318A LEU* 1.3 76.7 - - - +
320A GLY* 1.3 61.9 + - - +
322A ILE* 3.4 9.4 + - - +
323A LEU* 3.1 24.1 + - + +
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Residues in contact with GLY 320 (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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50A LEU* 4.0 8.7 - - - +
316A THR 3.1 7.4 + - - -
317A TYR 3.0 9.1 + - - -
319A THR* 1.3 75.4 - - - +
321A VAL* 1.3 57.9 + - - +
323A LEU* 3.3 5.3 + - - -
324A GLY 3.0 7.1 + - - -
325A LYS* 2.8 37.3 + - - +
327A LEU* 3.7 21.3 - - - -
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Residues in contact with VAL 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A GLY* 4.2 11.0 - - - +
288A LEU* 4.3 12.3 - - + -
289A LYS* 3.7 43.1 - - + +
292A LEU* 4.7 6.9 - - + +
317A TYR* 3.0 48.1 + - + +
318A LEU* 3.2 11.8 + - - +
320A GLY* 1.3 76.3 - - - +
322A ILE* 1.3 58.1 + - - +
324A GLY* 3.0 19.7 + - - +
325A LYS 4.8 1.1 - - - -
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Residues in contact with ILE 322 (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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16A PRO* 3.9 22.3 - - + +
133A VAL* 3.9 25.6 - - + -
135A ILE* 3.7 25.8 - - + -
137A TRP* 4.8 2.0 - - + -
288A LEU* 3.8 17.5 - - + -
292A LEU* 4.0 17.7 - - + +
300A ILE* 3.9 29.6 - - + -
318A LEU 3.0 16.9 + - - +
319A THR* 3.6 9.4 - - - +
321A VAL* 1.3 76.1 - - - +
323A LEU* 1.3 61.5 + - + +
324A GLY 3.2 0.9 + - - -
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Residues in contact with LEU 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PRO* 3.7 30.5 - - + -
50A LEU* 3.7 47.6 - - + +
53A GLN* 3.7 32.1 - - + +
54A MET* 3.7 10.5 - - + -
319A THR* 3.1 19.5 + - + +
320A GLY 3.3 4.5 + - - +
321A VAL 3.2 0.2 - - - -
322A ILE* 1.3 77.0 - - + +
324A GLY* 1.3 61.6 + - - +
325A LYS* 3.4 10.2 + - + +
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Residues in contact with GLY 324 (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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320A GLY 3.0 3.4 + - - -
321A VAL* 3.0 14.6 + - - -
322A ILE 3.2 1.0 + - - -
323A LEU* 1.3 78.4 - - - +
325A LYS* 1.3 59.2 + - - +
326A THR* 4.2 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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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