Contacts of the helix formed by residues 299 - 315 (chain A) in PDB entry 4A69
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 299 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A CYS 2.7 26.5 + - - +
264A ASP* 3.4 7.4 + - - -
265A ARG* 3.2 13.2 + - - +
298A TYR* 1.3 74.9 + - - +
300A VAL* 1.3 56.9 + - - +
301A ARG* 3.6 40.8 - - + +
302A ASN* 2.8 47.6 + - - +
303A VAL* 3.0 13.0 + - - +
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Residues in contact with VAL 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS* 3.7 38.1 - - + -
27A HIS 5.2 0.4 - - - -
28A ARG* 4.1 26.0 - - + +
31A LEU* 3.9 24.2 - - + -
297A GLY 5.5 0.2 - - - +
298A TYR* 3.6 7.7 + - - +
299A THR* 1.3 71.1 - - - +
301A ARG* 1.3 63.3 + - - +
303A VAL* 3.2 9.1 + - - +
304A ALA* 3.2 23.4 + - - +
331A TYR* 5.0 3.4 - - + -
471C TYR* 6.0 3.4 - - + -
501C I0P 3.7 32.0 + - - +
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Residues in contact with ARG 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 5.0 2.0 - - - -
263A CYS* 5.6 4.0 + - - +
299A THR* 3.6 24.2 - - + +
300A VAL* 1.3 80.5 - - - +
302A ASN* 1.3 78.3 + - - +
305A ARG* 3.1 37.1 + - - +
331A TYR* 3.4 30.9 - - + +
332A PHE* 3.5 19.5 - - + +
333A ALA 4.8 2.5 - - - -
54B SER* 4.4 6.1 + - - -
56B HIS* 3.3 54.2 + - - +
57B ASP* 5.4 2.2 + - - -
501C I0P 3.4 28.5 + - - -
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Residues in contact with ASN 302 (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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261A LEU* 4.0 18.3 - - + +
262A GLY 4.4 7.4 + - - +
263A CYS* 4.6 7.1 - - - +
273A ILE* 4.2 3.8 - - + +
299A THR* 2.8 33.9 + - + +
301A ARG* 1.3 84.1 + - - +
303A VAL* 1.3 59.6 + - + +
305A ARG* 3.0 30.1 + - - +
306A CYS* 3.0 29.5 + - - +
340A PRO* 4.0 5.0 - - - +
342A VAL* 3.4 29.2 - - + +
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Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG* 4.0 17.0 - - + +
258A ALA* 4.1 14.8 - - + +
261A LEU* 5.7 0.4 - - + -
264A ASP* 5.0 1.1 - - - +
297A GLY* 3.4 35.9 - - - +
298A TYR 3.7 1.1 - - - +
299A THR 3.0 17.0 + - - +
300A VAL* 3.2 8.9 + - - +
302A ASN* 1.3 75.9 - - + +
304A ALA* 1.3 67.0 + - - +
306A CYS* 3.2 2.8 + - - +
307A TRP* 3.1 64.2 + - + -
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Residues in contact with ALA 304 (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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28A ARG* 4.2 2.6 + - - +
31A LEU* 3.7 30.7 - - + +
32A THR* 3.3 26.7 + - - +
35A LEU* 4.3 2.5 - - + -
300A VAL 3.2 11.3 + - - +
301A ARG 4.3 4.3 - - - +
303A VAL* 1.3 79.3 - - - +
305A ARG* 1.3 53.3 + - - +
308A THR* 2.7 37.5 + - - -
332A PHE* 4.4 9.6 - - + -
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Residues in contact with ARG 305 (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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35A LEU* 4.0 9.4 - - + -
273A ILE* 4.3 5.7 - - + +
301A ARG* 3.1 35.6 + - - +
302A ASN* 3.0 30.1 + - - +
303A VAL 3.2 0.4 - - - -
304A ALA* 1.3 75.2 - - - +
306A CYS* 1.3 59.9 + - - +
308A THR* 3.7 5.8 - - - -
309A TYR* 2.9 31.4 + - - +
323A LEU* 4.1 8.1 - - + -
332A PHE* 3.6 38.0 + - + +
335A ASP* 2.9 26.5 + - - -
337A THR 2.8 37.2 + - - +
338A LEU* 3.6 22.6 - - + +
340A PRO* 3.4 15.8 - - - +
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Residues in contact with CYS 306 (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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258A ALA* 4.2 9.2 - - + -
261A LEU* 3.9 24.0 - - + -
273A ILE* 4.0 17.4 - - + +
276A HIS* 3.5 39.5 - - - -
302A ASN 3.0 18.3 + - - +
303A VAL 3.5 5.6 - - - +
305A ARG* 1.3 77.5 - - - +
307A TRP* 1.3 57.3 - - + +
309A TYR* 3.2 2.8 + - - +
310A GLU* 2.9 42.3 + - - +
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Residues in contact with TRP 307 (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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28A ARG* 3.4 30.1 - - + -
29A LEU* 3.9 14.1 - - + -
32A THR* 3.9 22.4 - - + -
129A TRP* 3.3 58.8 - + + -
256A CYS 3.0 20.9 + - - -
258A ALA* 4.0 6.4 - - + +
294A GLY* 3.5 17.5 - - - -
295A GLY 3.6 10.5 - - - -
296A GLY 3.6 17.9 - - - -
303A VAL* 3.1 30.0 + - + +
306A CYS* 1.3 77.2 - - - +
308A THR* 1.3 56.5 + - - +
310A GLU* 3.4 18.6 - - - +
311A THR* 2.6 37.5 + - - -
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Residues in contact with THR 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A THR* 3.6 10.4 + - - +
35A LEU* 3.4 25.2 - - + +
36A VAL* 4.0 18.3 - - + +
39A TYR* 3.7 33.9 - - + -
41A LEU* 3.9 4.8 - - + +
304A ALA 2.7 23.5 + - - -
305A ARG* 3.7 7.0 - - - -
306A CYS 3.3 0.2 - - - -
307A TRP* 1.3 75.9 - - - +
309A TYR* 1.3 62.4 + - - +
311A THR* 3.1 6.2 + - - -
312A SER* 3.1 18.9 + - - -
319A ILE* 4.2 5.6 - - + -
338A LEU* 4.4 3.1 - - + -
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Residues in contact with TYR 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ILE* 3.6 36.3 - - + -
274A ARG* 3.6 24.3 + - + +
277A GLY* 4.1 4.0 - - - -
305A ARG 2.9 17.4 + - - +
306A CYS 3.5 2.2 - - - +
308A THR* 1.3 76.3 - - - +
310A GLU* 1.3 68.6 + - + +
312A SER* 2.8 27.7 + - - -
313A LEU* 3.1 45.4 + - + +
319A ILE* 5.5 0.7 - - + -
338A LEU* 4.3 18.8 - - + +
339A HIS* 3.5 31.6 - + + -
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Residues in contact with GLU 310 (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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129A TRP* 4.0 17.0 - - + -
256A CYS* 4.3 1.9 - - - +
276A HIS* 2.5 51.3 + - - +
277A GLY* 3.2 14.4 + - - -
280A VAL* 3.6 25.4 - - + +
306A CYS* 2.9 20.1 + - - +
307A TRP* 3.4 25.4 - - - +
309A TYR* 1.3 76.5 - - + +
311A THR* 1.3 66.3 + - - +
313A LEU* 3.2 7.8 + - + +
314A LEU* 2.9 30.7 + - - +
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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
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7A TYR* 4.1 12.3 - - + -
36A VAL* 3.8 9.1 - - + +
41A LEU* 3.9 17.0 - - + -
45A MET* 3.9 30.3 - - + -
127A ILE* 4.5 3.5 - - + +
129A TRP* 3.0 19.5 + - - -
307A TRP 2.6 22.4 + - - -
308A THR 3.1 8.9 + - - -
310A GLU* 1.3 75.7 - - - +
312A SER* 1.3 61.8 + - - +
314A LEU* 3.1 12.9 + - - +
315A VAL* 3.0 23.4 + - + +
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Residues in contact with SER 312 (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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41A LEU* 3.9 20.6 - - - +
308A THR 3.1 5.8 + - - -
309A TYR* 2.8 30.1 + - - -
311A THR* 1.3 75.4 - - - +
313A LEU* 1.3 57.1 + - - +
315A VAL* 3.4 1.4 + - - -
316A GLU 2.9 8.3 + - - -
317A GLU 2.8 47.4 + - - -
318A ALA* 5.4 0.2 - - - -
319A ILE* 3.8 29.0 + - - +
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Residues in contact with LEU 313 (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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277A GLY* 3.4 30.3 - - - +
280A VAL* 5.3 1.8 - - + -
281A GLU* 3.7 39.8 - - + +
284A LYS* 3.8 13.6 - - - +
309A TYR* 3.1 56.5 + - + +
310A GLU* 3.5 9.9 - - + +
312A SER* 1.3 77.0 + - - +
314A LEU* 1.3 66.3 + - + +
316A GLU* 3.1 15.3 + - - +
317A GLU 5.0 1.1 - - - +
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Residues in contact with LEU 314 (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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3A LYS* 5.8 0.9 - - - +
5A VAL* 4.0 7.1 - - + +
125A ILE* 3.9 19.5 - - + +
127A ILE* 4.1 25.1 - - + -
129A TRP* 4.5 4.3 - - + -
280A VAL* 3.7 25.6 - - + -
281A GLU* 6.0 0.2 - - - -
284A LYS* 3.3 34.4 - - + -
290A LEU* 4.2 23.8 - - + -
292A VAL* 4.0 29.8 - - + -
310A GLU 2.9 25.6 + - - +
311A THR* 3.1 6.2 + - - +
313A LEU* 1.3 76.6 - - + +
315A VAL* 1.3 59.5 + - - +
316A GLU* 3.3 0.8 - - - +
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Residues in contact with VAL 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL* 4.2 14.6 - - + -
41A LEU* 3.9 16.6 - - + +
44A LYS* 2.9 50.4 + - + +
45A MET* 3.4 35.9 - - + -
127A ILE* 6.1 0.2 - - + -
311A THR 3.0 11.9 + - - +
312A SER 3.8 3.4 - - - +
314A LEU* 1.3 77.4 - - - +
316A GLU* 1.3 58.5 + - - +
317A GLU* 3.6 23.6 - - + -
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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
------------------------------------------------------------
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